Iodine in PDB 5dn4: Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Protein crystallography data
The structure of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj, PDB code: 5dn4
was solved by
P.Zaloba,
B.A.Bailey-Elkin,
B.L.Mark,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.99 /
1.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
38.790,
43.630,
107.930,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.2 /
21.2
|
Other elements in 5dn4:
The structure of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj also contains other interesting chemical elements:
Iodine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Iodine atom in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
(pdb code 5dn4). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 11 binding sites of Iodine where determined in the
Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj, PDB code: 5dn4:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iodine binding site 1 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 1 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I401
b:22.5
occ:0.63
|
HE
|
A:ARG13
|
2.8
|
31.0
|
1.0
|
HA
|
A:LEU10
|
3.3
|
25.6
|
1.0
|
O
|
A:HOH640
|
3.4
|
16.6
|
1.0
|
HD13
|
A:LEU10
|
3.4
|
27.0
|
1.0
|
HB2
|
A:LEU10
|
3.5
|
25.7
|
1.0
|
NE
|
A:ARG13
|
3.6
|
25.8
|
1.0
|
HH21
|
A:ARG13
|
3.7
|
38.9
|
1.0
|
HD2
|
A:ARG13
|
3.8
|
29.9
|
1.0
|
HD12
|
A:LEU10
|
3.9
|
27.0
|
1.0
|
CA
|
A:LEU10
|
4.0
|
21.4
|
1.0
|
CD1
|
A:LEU10
|
4.1
|
22.5
|
1.0
|
CB
|
A:LEU10
|
4.2
|
21.4
|
1.0
|
CD
|
A:ARG13
|
4.3
|
24.9
|
1.0
|
N
|
A:LEU10
|
4.3
|
17.2
|
1.0
|
OG
|
A:SER9
|
4.3
|
37.6
|
1.0
|
NH2
|
A:ARG13
|
4.3
|
32.4
|
1.0
|
HB3
|
A:SER9
|
4.4
|
32.6
|
1.0
|
CZ
|
A:ARG13
|
4.4
|
32.9
|
1.0
|
HB2
|
A:ARG13
|
4.5
|
25.6
|
1.0
|
O
|
A:HOH508
|
4.5
|
34.2
|
1.0
|
H
|
A:LEU10
|
4.6
|
20.6
|
1.0
|
HB3
|
A:ARG13
|
4.6
|
25.6
|
1.0
|
C
|
A:SER9
|
4.6
|
20.2
|
1.0
|
CG
|
A:LEU10
|
4.8
|
21.3
|
1.0
|
O
|
A:SER9
|
4.8
|
19.5
|
1.0
|
CB
|
A:SER9
|
4.9
|
27.2
|
1.0
|
HD11
|
A:LEU10
|
4.9
|
27.0
|
1.0
|
HD3
|
A:ARG13
|
4.9
|
29.9
|
1.0
|
HE2
|
A:HIS23
|
4.9
|
38.1
|
1.0
|
CB
|
A:ARG13
|
4.9
|
21.3
|
1.0
|
HB3
|
A:LEU10
|
5.0
|
25.7
|
1.0
|
|
Iodine binding site 2 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 2 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I402
b:26.2
occ:0.41
|
O
|
A:HOH589
|
3.0
|
37.3
|
1.0
|
HD21
|
A:LEU5
|
3.2
|
37.2
|
1.0
|
O
|
A:HOH578
|
3.5
|
38.1
|
1.0
|
HD11
|
A:LEU5
|
3.5
|
30.6
|
1.0
|
HG
|
A:LEU5
|
3.5
|
36.0
|
1.0
|
HG11
|
A:VAL153
|
3.5
|
38.1
|
1.0
|
HA
|
A:SER150
|
3.6
|
33.5
|
1.0
|
HG21
|
A:VAL153
|
3.6
|
32.0
|
1.0
|
O
|
A:HOH508
|
3.7
|
34.2
|
1.0
|
OG
|
A:SER9
|
3.7
|
37.6
|
1.0
|
HB2
|
A:SER9
|
3.8
|
32.6
|
1.0
|
HB
|
A:VAL153
|
3.8
|
33.8
|
1.0
|
HG
|
A:SER9
|
3.8
|
45.1
|
1.0
|
HB3
|
A:SER150
|
3.9
|
34.9
|
1.0
|
CD2
|
A:LEU5
|
4.0
|
31.0
|
1.0
|
HB2
|
A:SER150
|
4.0
|
34.9
|
1.0
|
CG
|
A:LEU5
|
4.0
|
30.0
|
1.0
|
CB
|
A:SER9
|
4.2
|
27.2
|
1.0
|
CD1
|
A:LEU5
|
4.2
|
25.5
|
1.0
|
HD23
|
A:LEU5
|
4.3
|
37.2
|
1.0
|
CB
|
A:SER150
|
4.3
|
29.1
|
1.0
|
CG1
|
A:VAL153
|
4.3
|
31.7
|
1.0
|
HB3
|
A:SER9
|
4.3
|
32.6
|
1.0
|
CB
|
A:VAL153
|
4.3
|
28.2
|
1.0
|
CA
|
A:SER150
|
4.4
|
27.9
|
1.0
|
CG2
|
A:VAL153
|
4.4
|
26.7
|
1.0
|
HD12
|
A:LEU5
|
4.5
|
30.6
|
1.0
|
HG12
|
A:VAL153
|
4.6
|
38.1
|
1.0
|
HG23
|
A:VAL153
|
4.7
|
32.0
|
1.0
|
HH
|
A:TYR157
|
4.8
|
30.8
|
1.0
|
HD22
|
A:LEU5
|
4.8
|
37.2
|
1.0
|
HD13
|
A:LEU5
|
5.0
|
30.6
|
1.0
|
|
Iodine binding site 3 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 3 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I403
b:23.4
occ:0.31
|
OH
|
A:TYR91
|
2.4
|
41.2
|
1.0
|
HH
|
A:TYR91
|
2.9
|
49.5
|
1.0
|
HE22
|
A:GLN40
|
2.9
|
53.9
|
1.0
|
I
|
A:IOD408
|
2.9
|
31.4
|
0.3
|
HE3
|
A:MET-1
|
2.9
|
53.3
|
1.0
|
HE1
|
A:TYR91
|
3.0
|
42.8
|
1.0
|
CZ
|
A:TYR91
|
3.1
|
36.7
|
1.0
|
HE1
|
A:PHE4
|
3.2
|
30.3
|
1.0
|
HE1
|
A:MET-1
|
3.2
|
53.3
|
1.0
|
CE1
|
A:TYR91
|
3.4
|
35.7
|
1.0
|
HD21
|
A:LEU8
|
3.4
|
40.5
|
1.0
|
HA2
|
A:GLY37
|
3.5
|
29.6
|
1.0
|
CE
|
A:MET-1
|
3.5
|
44.4
|
1.0
|
HA3
|
A:GLY37
|
3.5
|
29.6
|
1.0
|
NE2
|
A:GLN40
|
3.6
|
44.9
|
1.0
|
HD1
|
A:PHE4
|
3.7
|
24.9
|
1.0
|
HG23
|
A:VAL52
|
3.8
|
36.8
|
1.0
|
HH11
|
A:ARG7
|
3.8
|
58.8
|
1.0
|
HE21
|
A:GLN40
|
3.8
|
53.9
|
1.0
|
CE1
|
A:PHE4
|
3.8
|
25.3
|
1.0
|
HE2
|
A:MET-1
|
3.9
|
53.3
|
1.0
|
CA
|
A:GLY37
|
4.0
|
24.6
|
1.0
|
CD1
|
A:PHE4
|
4.1
|
20.8
|
1.0
|
HB
|
A:VAL52
|
4.2
|
29.9
|
1.0
|
CD2
|
A:LEU8
|
4.3
|
33.7
|
1.0
|
CE2
|
A:TYR91
|
4.3
|
40.0
|
1.0
|
HG21
|
A:VAL52
|
4.4
|
36.8
|
1.0
|
CG2
|
A:VAL52
|
4.5
|
30.6
|
1.0
|
NH1
|
A:ARG7
|
4.5
|
49.0
|
1.0
|
HD23
|
A:LEU8
|
4.5
|
40.5
|
1.0
|
HD2
|
A:ARG7
|
4.5
|
56.8
|
1.0
|
HH12
|
A:ARG7
|
4.5
|
58.8
|
1.0
|
HE2
|
A:TYR91
|
4.6
|
48.1
|
1.0
|
CD1
|
A:TYR91
|
4.6
|
30.6
|
1.0
|
HD11
|
A:LEU8
|
4.6
|
44.5
|
1.0
|
CD
|
A:GLN40
|
4.7
|
53.9
|
1.0
|
HD22
|
A:LEU8
|
4.8
|
40.5
|
1.0
|
CB
|
A:VAL52
|
4.9
|
24.9
|
1.0
|
O
|
A:GLY37
|
4.9
|
29.4
|
1.0
|
HG
|
A:LEU8
|
4.9
|
33.3
|
1.0
|
N
|
A:GLY37
|
4.9
|
20.0
|
1.0
|
OE1
|
A:GLN40
|
4.9
|
51.5
|
1.0
|
HA
|
A:VAL52
|
5.0
|
25.3
|
1.0
|
CZ
|
A:PHE4
|
5.0
|
22.1
|
1.0
|
C
|
A:GLY37
|
5.0
|
28.2
|
1.0
|
SD
|
A:MET-1
|
5.0
|
41.8
|
1.0
|
HD3
|
A:ARG7
|
5.0
|
56.8
|
1.0
|
|
Iodine binding site 4 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 4 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I404
b:28.8
occ:0.50
|
H
|
A:ILE41
|
2.7
|
31.4
|
1.0
|
H
|
A:TYR50
|
3.1
|
23.6
|
1.0
|
OE1
|
A:GLN40
|
3.2
|
51.5
|
1.0
|
HG
|
A:SER49
|
3.3
|
26.3
|
1.0
|
HA
|
A:GLN40
|
3.3
|
43.5
|
1.0
|
H
|
A:SER49
|
3.4
|
24.9
|
1.0
|
N
|
A:ILE41
|
3.4
|
26.1
|
1.0
|
O
|
A:ILE41
|
3.5
|
26.3
|
1.0
|
HB3
|
A:PRO48
|
3.6
|
30.8
|
1.0
|
HB3
|
A:GLN40
|
3.7
|
51.0
|
1.0
|
I
|
A:IOD408
|
3.7
|
31.4
|
0.3
|
HA
|
A:TYR50
|
3.7
|
26.1
|
1.0
|
N
|
A:TYR50
|
3.8
|
19.7
|
1.0
|
HD23
|
A:LEU42
|
3.8
|
31.6
|
1.0
|
CD
|
A:GLN40
|
3.8
|
53.9
|
1.0
|
H
|
A:ASN51
|
3.8
|
24.2
|
1.0
|
HA
|
A:PRO48
|
3.9
|
26.6
|
1.0
|
OG
|
A:SER49
|
4.0
|
21.9
|
1.0
|
CA
|
A:GLN40
|
4.0
|
36.3
|
1.0
|
C
|
A:ILE41
|
4.1
|
25.4
|
1.0
|
N
|
A:SER49
|
4.1
|
20.7
|
1.0
|
HB
|
A:ILE41
|
4.2
|
29.9
|
1.0
|
CA
|
A:TYR50
|
4.2
|
21.7
|
1.0
|
CB
|
A:GLN40
|
4.2
|
42.5
|
1.0
|
C
|
A:GLN40
|
4.2
|
38.2
|
1.0
|
N
|
A:ASN51
|
4.3
|
20.1
|
1.0
|
CA
|
A:ILE41
|
4.3
|
23.3
|
1.0
|
CB
|
A:PRO48
|
4.3
|
25.7
|
1.0
|
HE22
|
A:GLN40
|
4.4
|
53.9
|
1.0
|
NE2
|
A:GLN40
|
4.4
|
44.9
|
1.0
|
CA
|
A:PRO48
|
4.5
|
22.2
|
1.0
|
HB2
|
A:PRO48
|
4.5
|
30.8
|
1.0
|
C
|
A:TYR50
|
4.6
|
21.3
|
1.0
|
CG
|
A:GLN40
|
4.6
|
43.4
|
1.0
|
CD2
|
A:LEU42
|
4.6
|
26.4
|
1.0
|
HD21
|
A:LEU42
|
4.6
|
31.6
|
1.0
|
C
|
A:SER49
|
4.8
|
23.8
|
1.0
|
C
|
A:PRO48
|
4.8
|
18.5
|
1.0
|
CB
|
A:ILE41
|
4.8
|
24.9
|
1.0
|
CA
|
A:SER49
|
4.8
|
19.5
|
1.0
|
HA
|
A:LEU42
|
4.8
|
25.9
|
1.0
|
HE1
|
A:TYR91
|
4.9
|
42.8
|
1.0
|
CB
|
A:SER49
|
5.0
|
23.3
|
1.0
|
O
|
A:ARG39
|
5.0
|
43.4
|
1.0
|
|
Iodine binding site 5 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 5 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I405
b:23.6
occ:0.59
|
O
|
A:HOH649
|
3.2
|
48.1
|
1.0
|
O
|
A:HOH575
|
3.3
|
32.5
|
1.0
|
HA
|
A:ALA100
|
3.3
|
28.4
|
1.0
|
HB3
|
A:SER19
|
3.3
|
30.1
|
1.0
|
HA
|
A:SER19
|
3.3
|
27.7
|
1.0
|
HG23
|
A:VAL99
|
3.7
|
27.1
|
1.0
|
HG21
|
A:THR103
|
3.7
|
45.6
|
1.0
|
HB2
|
A:SER19
|
3.8
|
30.1
|
1.0
|
OG1
|
A:THR103
|
3.8
|
31.0
|
1.0
|
CB
|
A:SER19
|
3.9
|
25.1
|
1.0
|
O
|
A:HOH604
|
3.9
|
49.8
|
1.0
|
HB2
|
A:ALA100
|
3.9
|
31.4
|
1.0
|
HB
|
A:THR103
|
4.0
|
40.6
|
1.0
|
CA
|
A:SER19
|
4.0
|
23.1
|
1.0
|
HG1
|
A:THR103
|
4.0
|
37.2
|
1.0
|
CA
|
A:ALA100
|
4.1
|
23.7
|
1.0
|
O
|
A:HOH545
|
4.2
|
32.2
|
1.0
|
HB3
|
A:GLN18
|
4.2
|
31.1
|
1.0
|
O
|
A:GLN18
|
4.2
|
28.8
|
1.0
|
N
|
A:ALA100
|
4.3
|
20.1
|
1.0
|
CB
|
A:THR103
|
4.3
|
33.9
|
1.0
|
CB
|
A:ALA100
|
4.4
|
26.2
|
1.0
|
C
|
A:GLN18
|
4.5
|
29.4
|
1.0
|
CG2
|
A:THR103
|
4.5
|
38.0
|
1.0
|
O
|
A:VAL99
|
4.5
|
24.5
|
1.0
|
N
|
A:SER19
|
4.5
|
23.2
|
1.0
|
C
|
A:VAL99
|
4.5
|
21.2
|
1.0
|
CG2
|
A:VAL99
|
4.6
|
22.6
|
1.0
|
H
|
A:ALA100
|
4.6
|
24.1
|
1.0
|
HB1
|
A:ALA100
|
4.7
|
31.4
|
1.0
|
HG21
|
A:VAL99
|
4.7
|
27.1
|
1.0
|
HB2
|
A:GLN18
|
4.7
|
31.1
|
1.0
|
HB
|
A:VAL99
|
4.8
|
28.1
|
1.0
|
CB
|
A:GLN18
|
4.9
|
25.9
|
1.0
|
|
Iodine binding site 6 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 6 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I406
b:40.7
occ:0.41
|
H
|
A:VAL65
|
2.9
|
31.1
|
1.0
|
HA
|
A:PRO64
|
3.2
|
29.6
|
1.0
|
HB3
|
A:PRO64
|
3.5
|
30.0
|
1.0
|
N
|
A:VAL65
|
3.7
|
26.0
|
1.0
|
O
|
A:VAL65
|
3.8
|
27.0
|
1.0
|
HG22
|
A:VAL65
|
3.8
|
37.3
|
1.0
|
HH21
|
A:ARG43
|
3.9
|
38.7
|
1.0
|
CA
|
A:PRO64
|
3.9
|
24.6
|
1.0
|
CB
|
A:PRO64
|
4.0
|
25.0
|
1.0
|
HB2
|
A:PRO64
|
4.0
|
30.0
|
1.0
|
HH22
|
A:ARG43
|
4.2
|
38.7
|
1.0
|
O
|
A:HOH579
|
4.3
|
37.1
|
1.0
|
O
|
A:HOH623
|
4.3
|
49.7
|
1.0
|
NH2
|
A:ARG43
|
4.4
|
32.2
|
1.0
|
C
|
A:PRO64
|
4.4
|
23.7
|
1.0
|
C
|
A:VAL65
|
4.7
|
24.7
|
1.0
|
CG2
|
A:VAL65
|
4.7
|
31.1
|
1.0
|
CA
|
A:VAL65
|
4.7
|
23.8
|
1.0
|
O
|
A:HOH527
|
4.7
|
26.1
|
1.0
|
HG23
|
A:VAL65
|
4.7
|
37.3
|
1.0
|
|
Iodine binding site 7 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 7 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I407
b:30.5
occ:0.32
|
HD3
|
A:LYS2
|
2.3
|
52.2
|
1.0
|
HE3
|
A:LYS2
|
2.6
|
54.5
|
1.0
|
HG2
|
A:LYS2
|
2.9
|
41.9
|
1.0
|
CD
|
A:LYS2
|
3.0
|
43.5
|
1.0
|
O
|
A:HOH635
|
3.2
|
38.4
|
1.0
|
CE
|
A:LYS2
|
3.2
|
45.4
|
1.0
|
HG23
|
A:VAL153
|
3.2
|
32.0
|
1.0
|
HB3
|
A:MET149
|
3.3
|
26.2
|
1.0
|
CG
|
A:LYS2
|
3.4
|
35.0
|
1.0
|
HE2
|
A:MET149
|
3.4
|
32.2
|
1.0
|
HE3
|
A:MET149
|
3.5
|
32.2
|
1.0
|
HE2
|
A:LYS2
|
3.6
|
54.5
|
1.0
|
HG22
|
A:VAL153
|
3.6
|
32.0
|
1.0
|
HG2
|
A:MET149
|
3.7
|
28.9
|
1.0
|
HD23
|
A:LEU5
|
3.7
|
37.2
|
1.0
|
HA
|
A:LYS2
|
3.8
|
29.9
|
1.0
|
CG2
|
A:VAL153
|
3.8
|
26.7
|
1.0
|
HD2
|
A:LYS2
|
3.9
|
52.2
|
1.0
|
O
|
A:HOH551
|
3.9
|
25.3
|
1.0
|
HA
|
A:MET149
|
3.9
|
29.2
|
1.0
|
CE
|
A:MET149
|
3.9
|
26.9
|
1.0
|
O
|
A:MET149
|
3.9
|
25.2
|
1.0
|
HB3
|
A:LYS2
|
4.0
|
32.4
|
1.0
|
CB
|
A:MET149
|
4.0
|
21.8
|
1.0
|
HG21
|
A:VAL153
|
4.1
|
32.0
|
1.0
|
HB3
|
A:LYS152
|
4.1
|
39.7
|
1.0
|
CB
|
A:LYS2
|
4.2
|
27.0
|
1.0
|
HG3
|
A:LYS2
|
4.2
|
41.9
|
1.0
|
CG
|
A:MET149
|
4.3
|
24.1
|
1.0
|
CD
|
A:LYS152
|
4.3
|
45.2
|
1.0
|
CA
|
A:MET149
|
4.4
|
24.3
|
1.0
|
NZ
|
A:LYS2
|
4.5
|
46.6
|
1.0
|
CA
|
A:LYS2
|
4.5
|
24.9
|
1.0
|
HZ1
|
A:LYS2
|
4.5
|
55.9
|
1.0
|
C
|
A:MET149
|
4.5
|
23.7
|
1.0
|
CD2
|
A:LEU5
|
4.5
|
31.0
|
1.0
|
O
|
A:HOH546
|
4.6
|
30.9
|
1.0
|
HD22
|
A:LEU5
|
4.6
|
37.2
|
1.0
|
HE1
|
A:MET149
|
4.6
|
32.2
|
1.0
|
H
|
A:VAL153
|
4.8
|
36.3
|
1.0
|
HG2
|
A:LYS152
|
4.8
|
46.7
|
1.0
|
HZ3
|
A:LYS2
|
4.8
|
55.9
|
1.0
|
HB2
|
A:MET149
|
4.9
|
26.2
|
1.0
|
HD21
|
A:LEU5
|
4.9
|
37.2
|
1.0
|
CB
|
A:LYS152
|
4.9
|
33.1
|
1.0
|
CG
|
A:LYS152
|
5.0
|
39.0
|
1.0
|
|
Iodine binding site 8 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 8 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I408
b:31.4
occ:0.27
|
I
|
A:IOD403
|
2.9
|
23.4
|
0.3
|
HG23
|
A:VAL52
|
3.0
|
36.8
|
1.0
|
HA
|
A:VAL52
|
3.0
|
25.3
|
1.0
|
O
|
A:ARG39
|
3.0
|
43.4
|
1.0
|
HA2
|
A:GLY37
|
3.2
|
29.6
|
1.0
|
HE22
|
A:GLN40
|
3.2
|
53.9
|
1.0
|
NE2
|
A:GLN40
|
3.4
|
44.9
|
1.0
|
HA
|
A:GLN40
|
3.5
|
43.5
|
1.0
|
HE21
|
A:GLN40
|
3.5
|
53.9
|
1.0
|
I
|
A:IOD404
|
3.7
|
28.8
|
0.5
|
HB2
|
A:SER34
|
3.8
|
28.8
|
1.0
|
HB
|
A:VAL52
|
3.9
|
29.9
|
1.0
|
CG2
|
A:VAL52
|
3.9
|
30.6
|
1.0
|
CA
|
A:VAL52
|
3.9
|
21.1
|
1.0
|
HE1
|
A:TYR91
|
3.9
|
42.8
|
1.0
|
O
|
A:HOH507
|
4.0
|
40.6
|
1.0
|
CD
|
A:GLN40
|
4.0
|
53.9
|
1.0
|
CA
|
A:GLY37
|
4.1
|
24.6
|
1.0
|
CB
|
A:VAL52
|
4.1
|
24.9
|
1.0
|
C
|
A:ARG39
|
4.2
|
40.0
|
1.0
|
HA3
|
A:GLY37
|
4.3
|
29.6
|
1.0
|
O
|
A:GLY37
|
4.3
|
29.4
|
1.0
|
HE1
|
A:PHE4
|
4.3
|
30.3
|
1.0
|
OE1
|
A:GLN40
|
4.4
|
51.5
|
1.0
|
CA
|
A:GLN40
|
4.4
|
36.3
|
1.0
|
HG22
|
A:VAL52
|
4.4
|
36.8
|
1.0
|
OH
|
A:TYR91
|
4.4
|
41.2
|
1.0
|
HG21
|
A:VAL52
|
4.4
|
36.8
|
1.0
|
CB
|
A:SER34
|
4.5
|
24.0
|
1.0
|
C
|
A:GLY37
|
4.5
|
28.2
|
1.0
|
HB3
|
A:SER34
|
4.6
|
28.8
|
1.0
|
N
|
A:VAL52
|
4.6
|
20.2
|
1.0
|
H
|
A:ILE41
|
4.6
|
31.4
|
1.0
|
HG2
|
A:GLN40
|
4.7
|
52.1
|
1.0
|
CE1
|
A:TYR91
|
4.7
|
35.7
|
1.0
|
O
|
A:VAL52
|
4.8
|
26.1
|
1.0
|
N
|
A:GLN40
|
4.8
|
36.1
|
1.0
|
CG
|
A:GLN40
|
4.8
|
43.4
|
1.0
|
O
|
A:ASN51
|
4.9
|
23.8
|
1.0
|
C
|
A:VAL52
|
4.9
|
23.7
|
1.0
|
OG
|
A:SER34
|
4.9
|
21.0
|
1.0
|
C
|
A:ASN51
|
5.0
|
24.3
|
1.0
|
H
|
A:GLY37
|
5.0
|
24.0
|
1.0
|
|
Iodine binding site 9 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 9 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 9 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I409
b:65.4
occ:0.38
|
HG1
|
A:THR58
|
2.5
|
56.7
|
1.0
|
HB3
|
A:SER60
|
3.0
|
39.5
|
1.0
|
OG1
|
A:THR58
|
3.1
|
47.3
|
1.0
|
HG
|
A:SER60
|
3.1
|
47.5
|
1.0
|
OG
|
A:SER60
|
3.5
|
39.5
|
1.0
|
H
|
A:SER60
|
3.6
|
31.0
|
1.0
|
HB
|
A:THR58
|
3.6
|
49.6
|
1.0
|
CB
|
A:SER60
|
3.7
|
32.9
|
1.0
|
CB
|
A:THR58
|
3.9
|
41.3
|
1.0
|
HG21
|
A:THR58
|
4.1
|
54.5
|
1.0
|
N
|
A:SER60
|
4.2
|
25.8
|
1.0
|
H
|
A:ALA59
|
4.3
|
41.3
|
1.0
|
HB2
|
A:SER60
|
4.4
|
39.5
|
1.0
|
CG2
|
A:THR58
|
4.6
|
45.4
|
1.0
|
CA
|
A:SER60
|
4.6
|
27.8
|
1.0
|
N
|
A:ALA59
|
4.8
|
34.4
|
1.0
|
HB3
|
A:ALA59
|
4.9
|
41.1
|
1.0
|
|
Iodine binding site 10 out
of 11 in 5dn4
Go back to
Iodine Binding Sites List in 5dn4
Iodine binding site 10 out
of 11 in the Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 10 of Structure of the Glycoside Hydrolase Domain From Salmonella Typhimurium Flgj within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I410
b:18.8
occ:0.88
|
HA
|
A:GLN125
|
2.9
|
26.3
|
1.0
|
H
|
A:ALA130
|
3.0
|
32.2
|
1.0
|
HB3
|
A:TYR129
|
3.1
|
33.2
|
1.0
|
HD2
|
A:TYR135
|
3.2
|
24.8
|
1.0
|
HB2
|
A:ALA136
|
3.3
|
25.6
|
1.0
|
O
|
A:HOH583
|
3.4
|
20.9
|
1.0
|
HB3
|
A:ALA130
|
3.5
|
36.7
|
1.0
|
O
|
A:HOH559
|
3.5
|
23.4
|
1.0
|
HG3
|
A:GLN125
|
3.5
|
32.4
|
1.0
|
O
|
A:HOH534
|
3.6
|
40.5
|
1.0
|
CA
|
A:GLN125
|
3.7
|
21.9
|
1.0
|
N
|
A:ALA130
|
3.8
|
26.9
|
1.0
|
HB2
|
A:GLN125
|
3.8
|
27.4
|
1.0
|
HD2
|
A:TYR129
|
3.9
|
32.1
|
1.0
|
HB3
|
A:LEU124
|
3.9
|
29.8
|
1.0
|
CD2
|
A:TYR135
|
4.0
|
20.6
|
1.0
|
H
|
A:TYR129
|
4.1
|
31.2
|
1.0
|
CB
|
A:TYR129
|
4.1
|
27.7
|
1.0
|
O
|
A:ALA130
|
4.1
|
37.5
|
1.0
|
N
|
A:GLN125
|
4.1
|
20.3
|
1.0
|
HB3
|
A:TYR135
|
4.1
|
28.1
|
1.0
|
CB
|
A:GLN125
|
4.1
|
22.9
|
1.0
|
O
|
A:LEU124
|
4.2
|
23.8
|
1.0
|
HA
|
A:ALA136
|
4.2
|
25.8
|
1.0
|
CB
|
A:ALA136
|
4.2
|
21.3
|
1.0
|
C
|
A:LEU124
|
4.3
|
20.0
|
1.0
|
CG
|
A:GLN125
|
4.3
|
27.0
|
1.0
|
CB
|
A:ALA130
|
4.3
|
30.6
|
1.0
|
H
|
A:ALA136
|
4.4
|
22.6
|
1.0
|
HE2
|
A:TYR135
|
4.4
|
28.0
|
1.0
|
N
|
A:TYR129
|
4.4
|
26.0
|
1.0
|
CA
|
A:ALA130
|
4.5
|
31.9
|
1.0
|
N
|
A:ALA136
|
4.5
|
18.9
|
1.0
|
H
|
A:GLN125
|
4.5
|
24.3
|
1.0
|
HB2
|
A:TYR129
|
4.5
|
33.2
|
1.0
|
HB2
|
A:ALA130
|
4.5
|
36.7
|
1.0
|
CA
|
A:ALA136
|
4.6
|
21.5
|
1.0
|
HB2
|
A:LEU124
|
4.6
|
29.8
|
1.0
|
CA
|
A:TYR129
|
4.6
|
26.1
|
1.0
|
CE2
|
A:TYR135
|
4.6
|
23.3
|
1.0
|
CB
|
A:LEU124
|
4.6
|
24.8
|
1.0
|
CD2
|
A:TYR129
|
4.6
|
26.7
|
1.0
|
C
|
A:TYR129
|
4.6
|
26.1
|
1.0
|
HB1
|
A:ALA136
|
4.7
|
25.6
|
1.0
|
C
|
A:ALA130
|
4.8
|
34.2
|
1.0
|
HG2
|
A:GLN125
|
4.8
|
32.4
|
1.0
|
O
|
A:HOH556
|
4.8
|
36.4
|
1.0
|
HB3
|
A:ALA136
|
4.9
|
25.6
|
1.0
|
CG
|
A:TYR129
|
4.9
|
30.0
|
1.0
|
CG
|
A:TYR135
|
4.9
|
23.0
|
1.0
|
CB
|
A:TYR135
|
4.9
|
23.4
|
1.0
|
C
|
A:GLN125
|
4.9
|
23.2
|
1.0
|
|
Reference:
P.Zaloba,
B.A.Bailey-Elkin,
M.Derksen,
B.L.Mark.
Structural and Biochemical Insights Into the Peptidoglycan Hydrolase Domain of Flgj From Salmonella Typhimurium. Plos One V. 11 49204 2016.
ISSN: ESSN 1932-6203
PubMed: 26871950
DOI: 10.1371/JOURNAL.PONE.0149204
Page generated: Sun Aug 11 20:49:15 2024
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