Iodine in PDB 5ksr: Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
Enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
All present enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).:
3.1.3.5;
Protein crystallography data
The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger)., PDB code: 5ksr
was solved by
A.T.P.Machado,
E.M.B.Fonseca,
M.A.Dos Reis,
A.M.Saraiva,
C.A.Dos Santos,
M.A.De Toledo,
I.Polikarpov,
A.P.De Souza,
R.De Aparicio,
J.Iulek,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.25 /
1.96
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
172.336,
84.170,
87.310,
90.00,
96.62,
90.00
|
R / Rfree (%)
|
19.6 /
23.8
|
Other elements in 5ksr:
The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
(pdb code 5ksr). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the
Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger)., PDB code: 5ksr:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
Iodine binding site 1 out
of 6 in 5ksr
Go back to
Iodine Binding Sites List in 5ksr
Iodine binding site 1 out
of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I502
b:20.2
occ:1.00
|
O
|
A:HOH689
|
3.5
|
23.7
|
1.0
|
O
|
B:HOH660
|
3.6
|
22.7
|
1.0
|
N
|
A:ASN44
|
3.8
|
14.2
|
1.0
|
N
|
B:ASN44
|
3.8
|
13.7
|
1.0
|
ND2
|
A:ASN44
|
4.0
|
22.4
|
1.0
|
CG
|
A:ASN44
|
4.1
|
21.3
|
1.0
|
ND2
|
B:ASN44
|
4.2
|
20.0
|
1.0
|
CD1
|
A:TYR103
|
4.2
|
17.0
|
1.0
|
CD1
|
B:TYR103
|
4.2
|
17.4
|
1.0
|
CB
|
A:ASN44
|
4.3
|
16.0
|
1.0
|
CG
|
B:ASN44
|
4.3
|
19.4
|
1.0
|
CA
|
B:SER43
|
4.4
|
23.5
|
1.0
|
CB
|
B:ASN44
|
4.4
|
11.7
|
1.0
|
CB
|
A:TYR103
|
4.4
|
19.2
|
1.0
|
CA
|
A:SER43
|
4.4
|
20.9
|
1.0
|
CB
|
B:TYR103
|
4.5
|
28.0
|
1.0
|
CG
|
A:TYR103
|
4.6
|
17.1
|
1.0
|
C
|
A:SER43
|
4.6
|
19.0
|
1.0
|
C
|
B:SER43
|
4.6
|
20.7
|
1.0
|
CG
|
B:TYR103
|
4.6
|
18.8
|
1.0
|
CA
|
A:ASN44
|
4.6
|
14.5
|
1.0
|
CA
|
B:ASN44
|
4.7
|
13.2
|
1.0
|
OD1
|
A:ASN44
|
4.7
|
20.1
|
1.0
|
OD1
|
B:ASN44
|
4.8
|
21.4
|
1.0
|
OG
|
B:SER43
|
4.8
|
19.6
|
1.0
|
O
|
A:TYR103
|
4.8
|
13.9
|
1.0
|
CA
|
A:TYR103
|
5.0
|
15.3
|
1.0
|
O
|
B:TYR103
|
5.0
|
14.4
|
1.0
|
|
Iodine binding site 2 out
of 6 in 5ksr
Go back to
Iodine Binding Sites List in 5ksr
Iodine binding site 2 out
of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I503
b:39.2
occ:0.69
|
NE2
|
A:GLN242
|
3.8
|
44.3
|
1.0
|
N
|
A:TYR241
|
3.8
|
32.2
|
1.0
|
NE2
|
B:HIS235
|
3.9
|
27.3
|
1.0
|
N
|
A:GLN242
|
4.0
|
38.5
|
1.0
|
CE1
|
B:HIS235
|
4.1
|
27.0
|
1.0
|
CB
|
A:TYR241
|
4.1
|
36.1
|
1.0
|
NE2
|
B:GLN242
|
4.2
|
40.7
|
1.0
|
O
|
A:HOH635
|
4.4
|
24.7
|
1.0
|
CA
|
A:TYR241
|
4.4
|
35.6
|
1.0
|
CG
|
A:GLN242
|
4.4
|
45.9
|
1.0
|
O
|
B:HOH693
|
4.5
|
34.5
|
1.0
|
C
|
A:ARG240
|
4.5
|
30.4
|
1.0
|
O
|
A:THR239
|
4.5
|
24.6
|
1.0
|
CD2
|
A:TYR241
|
4.6
|
34.0
|
1.0
|
CD
|
A:GLN242
|
4.6
|
48.1
|
1.0
|
CB
|
A:GLN242
|
4.6
|
44.2
|
1.0
|
I
|
B:IOD502
|
4.7
|
40.1
|
0.8
|
CA
|
A:ARG240
|
4.7
|
27.6
|
1.0
|
C
|
A:TYR241
|
4.7
|
37.9
|
1.0
|
CE1
|
A:HIS235
|
4.9
|
29.3
|
1.0
|
CG
|
A:TYR241
|
4.9
|
35.9
|
1.0
|
CA
|
A:GLN242
|
5.0
|
41.8
|
1.0
|
|
Iodine binding site 3 out
of 6 in 5ksr
Go back to
Iodine Binding Sites List in 5ksr
Iodine binding site 3 out
of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I502
b:40.1
occ:0.76
|
O
|
A:HOH734
|
3.4
|
50.8
|
1.0
|
N
|
B:TYR241
|
3.7
|
31.1
|
1.0
|
NE2
|
A:HIS235
|
3.7
|
27.3
|
1.0
|
NE2
|
B:GLN242
|
3.9
|
40.7
|
1.0
|
N
|
B:GLN242
|
3.9
|
35.1
|
1.0
|
CE1
|
A:HIS235
|
4.0
|
29.3
|
1.0
|
CB
|
B:TYR241
|
4.1
|
29.8
|
1.0
|
CG
|
B:GLN242
|
4.2
|
42.5
|
1.0
|
CA
|
B:TYR241
|
4.3
|
33.3
|
1.0
|
O
|
B:HOH635
|
4.4
|
22.7
|
1.0
|
NE2
|
A:GLN242
|
4.4
|
44.3
|
1.0
|
C
|
B:ARG240
|
4.4
|
29.6
|
1.0
|
CD
|
B:GLN242
|
4.4
|
46.1
|
1.0
|
O
|
B:THR239
|
4.6
|
24.3
|
1.0
|
CB
|
B:GLN242
|
4.6
|
39.2
|
1.0
|
C
|
B:TYR241
|
4.6
|
35.7
|
1.0
|
CA
|
B:ARG240
|
4.6
|
26.6
|
1.0
|
CD2
|
B:TYR241
|
4.6
|
27.1
|
1.0
|
O
|
A:HOH722
|
4.6
|
39.5
|
1.0
|
I
|
A:IOD503
|
4.7
|
39.2
|
0.7
|
CG
|
B:TYR241
|
4.9
|
29.8
|
1.0
|
CA
|
B:GLN242
|
4.9
|
35.6
|
1.0
|
CE1
|
B:HIS235
|
4.9
|
27.0
|
1.0
|
CD2
|
A:HIS235
|
5.0
|
25.6
|
1.0
|
|
Iodine binding site 4 out
of 6 in 5ksr
Go back to
Iodine Binding Sites List in 5ksr
Iodine binding site 4 out
of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:I502
b:25.9
occ:0.82
|
O
|
D:HOH656
|
3.7
|
29.7
|
1.0
|
N
|
C:ASN44
|
3.9
|
23.8
|
1.0
|
N
|
D:ASN44
|
3.9
|
20.7
|
1.0
|
ND2
|
C:ASN44
|
3.9
|
26.1
|
1.0
|
O
|
C:HOH647
|
3.9
|
40.7
|
1.0
|
ND2
|
D:ASN44
|
4.1
|
26.8
|
1.0
|
CG
|
C:ASN44
|
4.1
|
27.0
|
1.0
|
CD1
|
D:TYR103
|
4.2
|
29.6
|
1.0
|
CD1
|
C:TYR103
|
4.2
|
26.1
|
1.0
|
CG
|
D:ASN44
|
4.3
|
31.8
|
1.0
|
CB
|
C:ASN44
|
4.3
|
22.4
|
1.0
|
CA
|
D:SER43
|
4.4
|
29.7
|
1.0
|
CB
|
D:ASN44
|
4.4
|
17.4
|
1.0
|
CA
|
C:SER43
|
4.5
|
29.2
|
1.0
|
CB
|
C:TYR103
|
4.5
|
23.5
|
1.0
|
CB
|
D:TYR103
|
4.6
|
25.3
|
1.0
|
CG
|
D:TYR103
|
4.6
|
28.5
|
1.0
|
CG
|
C:TYR103
|
4.6
|
24.2
|
1.0
|
C
|
D:SER43
|
4.6
|
25.5
|
1.0
|
C
|
C:SER43
|
4.7
|
26.8
|
1.0
|
CA
|
C:ASN44
|
4.7
|
21.5
|
1.0
|
OD1
|
C:ASN44
|
4.8
|
29.6
|
1.0
|
CA
|
D:ASN44
|
4.8
|
21.2
|
1.0
|
OD1
|
D:ASN44
|
4.8
|
36.0
|
1.0
|
O
|
C:TYR103
|
4.8
|
19.6
|
1.0
|
O
|
D:TYR103
|
4.9
|
19.5
|
1.0
|
CE1
|
D:TYR103
|
4.9
|
30.8
|
1.0
|
OG
|
D:SER43
|
4.9
|
33.6
|
1.0
|
OG
|
C:SER43
|
4.9
|
27.3
|
1.0
|
O
|
C:ALA42
|
4.9
|
33.3
|
1.0
|
CE1
|
C:TYR103
|
5.0
|
25.0
|
1.0
|
CB
|
D:SER43
|
5.0
|
29.7
|
1.0
|
CA
|
C:TYR103
|
5.0
|
20.1
|
1.0
|
|
Iodine binding site 5 out
of 6 in 5ksr
Go back to
Iodine Binding Sites List in 5ksr
Iodine binding site 5 out
of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:I503
b:32.6
occ:0.67
|
NE2
|
C:GLN242
|
3.6
|
42.7
|
1.0
|
NE2
|
D:HIS235
|
3.8
|
28.3
|
1.0
|
N
|
C:TYR241
|
3.8
|
29.6
|
1.0
|
CE1
|
D:HIS235
|
4.0
|
27.1
|
1.0
|
N
|
C:GLN242
|
4.0
|
34.1
|
1.0
|
CG
|
C:GLN242
|
4.1
|
44.1
|
1.0
|
NE2
|
D:GLN242
|
4.1
|
38.7
|
1.0
|
CB
|
C:TYR241
|
4.2
|
34.0
|
1.0
|
O
|
D:HOH720
|
4.2
|
52.5
|
1.0
|
CD
|
C:GLN242
|
4.3
|
46.1
|
1.0
|
O
|
C:HOH650
|
4.4
|
23.6
|
1.0
|
CA
|
C:TYR241
|
4.4
|
32.3
|
1.0
|
CD2
|
C:TYR241
|
4.5
|
27.8
|
1.0
|
C
|
C:ARG240
|
4.6
|
28.6
|
1.0
|
CB
|
C:GLN242
|
4.6
|
41.6
|
1.0
|
O
|
C:THR239
|
4.6
|
26.6
|
1.0
|
CA
|
C:ARG240
|
4.7
|
28.8
|
1.0
|
C
|
C:TYR241
|
4.7
|
34.1
|
1.0
|
O
|
D:HOH700
|
4.8
|
46.3
|
1.0
|
I
|
D:IOD502
|
4.8
|
31.5
|
0.7
|
CG
|
C:TYR241
|
4.9
|
33.0
|
1.0
|
CA
|
C:GLN242
|
5.0
|
37.4
|
1.0
|
|
Iodine binding site 6 out
of 6 in 5ksr
Go back to
Iodine Binding Sites List in 5ksr
Iodine binding site 6 out
of 6 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger).
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Tb (Tetramer Bigger). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I502
b:31.5
occ:0.72
|
NE2
|
D:GLN242
|
3.7
|
38.7
|
1.0
|
N
|
D:TYR241
|
3.8
|
25.6
|
1.0
|
N
|
D:GLN242
|
3.9
|
34.2
|
1.0
|
CE1
|
C:HIS235
|
3.9
|
26.7
|
1.0
|
CG
|
D:GLN242
|
4.0
|
39.2
|
1.0
|
NE2
|
C:HIS235
|
4.0
|
28.6
|
1.0
|
O
|
C:HOH731
|
4.2
|
49.6
|
1.0
|
CB
|
D:TYR241
|
4.2
|
31.5
|
1.0
|
NE2
|
C:GLN242
|
4.2
|
42.7
|
1.0
|
CD
|
D:GLN242
|
4.3
|
42.0
|
1.0
|
CA
|
D:TYR241
|
4.4
|
28.8
|
1.0
|
CB
|
D:GLN242
|
4.5
|
37.1
|
1.0
|
CD2
|
D:TYR241
|
4.5
|
28.4
|
1.0
|
C
|
D:ARG240
|
4.5
|
25.8
|
1.0
|
O
|
D:HOH628
|
4.6
|
21.9
|
1.0
|
O
|
D:THR239
|
4.6
|
24.8
|
1.0
|
C
|
D:TYR241
|
4.7
|
31.8
|
1.0
|
CA
|
D:ARG240
|
4.7
|
26.4
|
1.0
|
O
|
C:HOH671
|
4.7
|
41.9
|
1.0
|
CA
|
D:GLN242
|
4.8
|
34.8
|
1.0
|
I
|
C:IOD503
|
4.8
|
32.6
|
0.7
|
CG
|
D:TYR241
|
4.9
|
29.6
|
1.0
|
|
Reference:
A.T.P.Machado,
E.M.B.Fonseca,
M.A.D.Reis,
A.M.Saraiva,
C.A.D.Santos,
M.A.S.De Toledo,
I.Polikarpov,
A.P.De Souza,
R.Aparicio,
J.Iulek.
Conformational Variability of the Stationary Phase Survival Protein E From Xylella Fastidiosa Revealed By X-Ray Crystallography, Small-Angle X-Ray Scattering Studies, and Normal Mode Analysis. Proteins V. 85 1931 2017.
ISSN: ESSN 1097-0134
PubMed: 28677327
DOI: 10.1002/PROT.25347
Page generated: Sun Aug 11 21:20:33 2024
|