Iodine in PDB 5ceg: X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Protein crystallography data
The structure of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum, PDB code: 5ceg
was solved by
C.D.Aakre,
J.Herrou,
S.Crosson,
M.T.Laub,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.71 /
1.59
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.180,
118.840,
211.420,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.9 /
19.5
|
Other elements in 5ceg:
The structure of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
(pdb code 5ceg). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the
X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum, PDB code: 5ceg:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iodine binding site 1 out
of 8 in 5ceg
Go back to
Iodine Binding Sites List in 5ceg
Iodine binding site 1 out
of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I102
b:16.8
occ:0.57
|
O
|
A:HOH242
|
3.2
|
24.4
|
1.0
|
NH1
|
A:ARG57
|
3.5
|
14.0
|
1.0
|
CG
|
A:ARG54
|
4.1
|
13.6
|
1.0
|
CD
|
A:ARG57
|
4.3
|
11.2
|
1.0
|
CD
|
A:ARG54
|
4.3
|
14.3
|
1.0
|
CB
|
A:ARG54
|
4.6
|
11.3
|
1.0
|
CZ
|
A:ARG57
|
4.6
|
13.4
|
1.0
|
CA
|
A:ARG54
|
4.9
|
10.3
|
1.0
|
NE
|
A:ARG57
|
4.9
|
11.6
|
1.0
|
NE
|
A:ARG54
|
5.0
|
19.9
|
1.0
|
|
Iodine binding site 2 out
of 8 in 5ceg
Go back to
Iodine Binding Sites List in 5ceg
Iodine binding site 2 out
of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I103
b:20.6
occ:0.46
|
O
|
A:HOH222
|
3.4
|
16.3
|
1.0
|
O
|
D:HOH364
|
3.4
|
28.1
|
1.0
|
NE1
|
A:TRP60
|
3.4
|
11.3
|
1.0
|
CD1
|
A:TRP60
|
4.3
|
10.6
|
1.0
|
CG
|
A:LYS64
|
4.3
|
16.4
|
1.0
|
CG
|
D:ARG58
|
4.5
|
12.9
|
1.0
|
CE2
|
A:TRP60
|
4.5
|
11.6
|
1.0
|
CB
|
D:ARG58
|
4.5
|
14.3
|
1.0
|
CE
|
A:LYS64
|
4.5
|
31.7
|
1.0
|
O
|
D:HOH328
|
4.7
|
38.5
|
1.0
|
CD
|
D:ARG58
|
4.7
|
14.0
|
1.0
|
CB
|
A:LYS64
|
4.8
|
15.7
|
1.0
|
CZ2
|
A:TRP60
|
4.8
|
13.2
|
1.0
|
CD
|
A:LYS64
|
4.9
|
22.7
|
1.0
|
|
Iodine binding site 3 out
of 8 in 5ceg
Go back to
Iodine Binding Sites List in 5ceg
Iodine binding site 3 out
of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I204
b:40.5
occ:0.48
|
O
|
C:HOH208
|
3.0
|
40.0
|
1.0
|
O
|
C:HOH257
|
3.2
|
36.7
|
1.0
|
NH1
|
B:ARG54
|
3.7
|
26.9
|
1.0
|
NH2
|
B:ARG54
|
3.8
|
20.5
|
1.0
|
CD1
|
C:LEU56
|
4.0
|
11.9
|
1.0
|
CD1
|
C:ILE53
|
4.1
|
12.2
|
0.4
|
CZ
|
B:ARG54
|
4.2
|
23.7
|
1.0
|
CD1
|
B:LEU102
|
4.5
|
22.8
|
1.0
|
CB
|
C:ASP52
|
4.6
|
9.6
|
1.0
|
O
|
C:HOH302
|
4.7
|
35.9
|
1.0
|
CG
|
B:LEU102
|
4.8
|
24.7
|
1.0
|
CE
|
B:MET63
|
4.8
|
23.6
|
1.0
|
OD2
|
C:ASP52
|
5.0
|
13.7
|
1.0
|
|
Iodine binding site 4 out
of 8 in 5ceg
Go back to
Iodine Binding Sites List in 5ceg
Iodine binding site 4 out
of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:I102
b:21.0
occ:0.38
|
NH2
|
C:ARG49
|
3.0
|
21.5
|
0.5
|
NE
|
C:ARG49
|
3.1
|
22.4
|
0.5
|
O
|
B:HOH347
|
3.2
|
26.6
|
1.0
|
O
|
C:HOH302
|
3.2
|
35.9
|
1.0
|
NE
|
B:ARG101
|
3.3
|
20.4
|
1.0
|
CZ
|
C:ARG49
|
3.4
|
20.1
|
0.5
|
CE
|
C:LYS45
|
3.6
|
17.2
|
1.0
|
CG
|
B:ARG101
|
3.9
|
18.9
|
1.0
|
CD
|
C:ARG49
|
4.0
|
15.4
|
0.5
|
CD
|
B:ARG101
|
4.0
|
19.9
|
1.0
|
CB
|
C:ARG49
|
4.2
|
13.9
|
0.5
|
CD
|
C:ARG49
|
4.2
|
19.2
|
0.5
|
CB
|
C:ARG49
|
4.2
|
13.7
|
0.5
|
CZ
|
B:ARG101
|
4.2
|
22.9
|
1.0
|
NH2
|
B:ARG101
|
4.3
|
21.9
|
1.0
|
CG
|
C:ARG49
|
4.3
|
15.0
|
0.5
|
CB
|
B:ARG101
|
4.3
|
18.5
|
1.0
|
CG
|
C:ARG49
|
4.3
|
17.8
|
0.5
|
NZ
|
C:LYS45
|
4.4
|
13.4
|
1.0
|
CD
|
C:LYS45
|
4.4
|
19.7
|
1.0
|
O
|
B:HOH417
|
4.4
|
31.7
|
1.0
|
CG
|
C:LYS45
|
4.5
|
16.1
|
1.0
|
NH1
|
C:ARG49
|
4.7
|
17.2
|
0.5
|
O
|
B:HOH317
|
4.8
|
19.8
|
1.0
|
NE
|
C:ARG49
|
4.9
|
19.6
|
0.5
|
O
|
C:HOH293
|
4.9
|
18.1
|
1.0
|
|
Iodine binding site 5 out
of 8 in 5ceg
Go back to
Iodine Binding Sites List in 5ceg
Iodine binding site 5 out
of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I204
b:0.6
occ:0.72
|
O
|
C:HOH293
|
3.1
|
18.1
|
1.0
|
O
|
D:HOH427
|
3.1
|
46.5
|
1.0
|
O
|
D:HOH397
|
3.6
|
21.0
|
1.0
|
CD2
|
D:LEU102
|
3.7
|
37.4
|
1.0
|
CG
|
D:LEU102
|
4.0
|
25.8
|
1.0
|
O
|
D:PRO68
|
4.1
|
17.3
|
1.0
|
CA
|
D:GLY95
|
4.1
|
13.4
|
1.0
|
C
|
D:GLY95
|
4.1
|
16.3
|
1.0
|
CD1
|
D:LEU102
|
4.1
|
35.7
|
1.0
|
O
|
D:HOH376
|
4.2
|
31.1
|
1.0
|
N
|
D:ARG96
|
4.3
|
11.4
|
1.0
|
O
|
B:HOH347
|
4.4
|
26.6
|
1.0
|
O
|
D:GLY95
|
4.5
|
15.5
|
1.0
|
CA
|
D:PRO68
|
4.6
|
18.8
|
1.0
|
CG
|
D:ARG96
|
4.7
|
13.0
|
1.0
|
O
|
D:HOH303
|
4.7
|
7.9
|
1.0
|
C
|
D:PRO68
|
4.7
|
17.0
|
1.0
|
CB
|
D:PRO68
|
4.8
|
18.0
|
1.0
|
N
|
D:GLY95
|
4.8
|
14.4
|
1.0
|
CA
|
D:ARG96
|
5.0
|
11.1
|
1.0
|
|
Iodine binding site 6 out
of 8 in 5ceg
Go back to
Iodine Binding Sites List in 5ceg
Iodine binding site 6 out
of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I205
b:25.9
occ:0.50
|
O
|
D:MET63
|
3.7
|
18.6
|
1.0
|
N
|
D:VAL65
|
3.7
|
12.8
|
1.0
|
CZ
|
D:PHE103
|
3.8
|
23.5
|
0.6
|
CG1
|
D:VAL65
|
3.9
|
19.1
|
0.3
|
CG2
|
D:VAL52
|
4.0
|
19.0
|
0.7
|
CE1
|
D:PHE103
|
4.0
|
23.1
|
0.6
|
O
|
B:HOH426
|
4.0
|
38.7
|
1.0
|
CG2
|
D:VAL65
|
4.1
|
19.7
|
0.7
|
CZ
|
D:PHE103
|
4.1
|
24.1
|
0.4
|
CA
|
D:LEU64
|
4.1
|
12.4
|
1.0
|
CE2
|
D:PHE103
|
4.1
|
22.6
|
0.4
|
CB
|
D:VAL65
|
4.4
|
19.1
|
0.3
|
CB
|
D:VAL65
|
4.4
|
19.1
|
0.7
|
CD1
|
D:LEU64
|
4.4
|
18.2
|
1.0
|
C
|
D:LEU64
|
4.4
|
13.7
|
1.0
|
C
|
D:MET63
|
4.5
|
16.0
|
1.0
|
CG1
|
D:VAL52
|
4.5
|
18.0
|
0.3
|
CG2
|
B:VAL65
|
4.5
|
18.4
|
1.0
|
N
|
D:VAL52
|
4.6
|
14.2
|
1.0
|
CA
|
D:VAL65
|
4.7
|
16.1
|
0.3
|
CA
|
D:VAL65
|
4.7
|
16.1
|
0.7
|
CB
|
D:VAL52
|
4.7
|
20.1
|
0.7
|
N
|
D:LEU64
|
4.7
|
12.6
|
1.0
|
CB
|
D:VAL52
|
4.8
|
20.5
|
0.3
|
CB
|
B:VAL65
|
4.9
|
14.2
|
1.0
|
CA
|
D:GLY51
|
4.9
|
19.9
|
1.0
|
O
|
B:HOH318
|
4.9
|
28.4
|
1.0
|
|
Iodine binding site 7 out
of 8 in 5ceg
Go back to
Iodine Binding Sites List in 5ceg
Iodine binding site 7 out
of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I206
b:18.5
occ:0.77
|
O
|
D:HOH374
|
3.4
|
35.3
|
1.0
|
N
|
D:ARG49
|
3.6
|
14.6
|
1.0
|
O
|
B:HOH356
|
3.7
|
25.2
|
1.0
|
C
|
D:GLN47
|
3.7
|
16.3
|
1.0
|
CA
|
D:GLN47
|
3.8
|
17.7
|
1.0
|
CB
|
D:GLN47
|
3.9
|
18.6
|
1.0
|
CB
|
D:ARG49
|
4.0
|
15.4
|
1.0
|
N
|
D:PRO48
|
4.0
|
16.3
|
1.0
|
CG
|
B:GLN47
|
4.0
|
22.6
|
1.0
|
CE
|
B:MET50
|
4.0
|
19.9
|
1.0
|
CA
|
D:ARG49
|
4.1
|
15.8
|
1.0
|
O
|
D:GLN47
|
4.1
|
18.1
|
1.0
|
C
|
D:ARG49
|
4.2
|
15.7
|
1.0
|
CD
|
D:PRO48
|
4.2
|
16.4
|
1.0
|
CB
|
B:GLN47
|
4.3
|
17.3
|
1.0
|
N
|
D:MET50
|
4.3
|
16.8
|
1.0
|
SD
|
B:MET50
|
4.4
|
21.2
|
1.0
|
CG
|
D:GLN47
|
4.5
|
24.7
|
1.0
|
C
|
D:PRO48
|
4.7
|
19.4
|
1.0
|
O
|
D:ARG49
|
4.8
|
18.5
|
1.0
|
CG
|
D:ARG49
|
4.8
|
21.1
|
1.0
|
CB
|
B:MET50
|
4.8
|
21.5
|
1.0
|
CG
|
D:PRO48
|
4.8
|
22.2
|
1.0
|
CA
|
D:PRO48
|
4.9
|
17.4
|
1.0
|
CD
|
B:GLN47
|
5.0
|
30.8
|
1.0
|
CA
|
D:MET50
|
5.0
|
16.1
|
1.0
|
|
Iodine binding site 8 out
of 8 in 5ceg
Go back to
Iodine Binding Sites List in 5ceg
Iodine binding site 8 out
of 8 in the X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of X-Ray Structure of Toxin/Anti-Toxin Complex From Mesorhizobium Opportunistum within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:I207
b:45.7
occ:0.35
|
NE
|
D:ARG101
|
3.3
|
30.2
|
1.0
|
CG
|
D:ARG101
|
3.6
|
24.1
|
1.0
|
CD
|
D:ARG101
|
3.7
|
36.2
|
1.0
|
O
|
D:ASN100
|
3.8
|
12.5
|
1.0
|
NH1
|
B:ARG101
|
3.8
|
24.7
|
1.0
|
O
|
A:HOH263
|
3.9
|
19.0
|
1.0
|
O
|
D:HOH372
|
3.9
|
42.7
|
1.0
|
CB
|
D:ASN100
|
4.0
|
11.3
|
1.0
|
C
|
D:ASN100
|
4.2
|
12.4
|
1.0
|
NH2
|
B:ARG101
|
4.3
|
21.9
|
1.0
|
CZ
|
D:ARG101
|
4.4
|
24.0
|
1.0
|
CZ
|
B:ARG101
|
4.5
|
22.9
|
1.0
|
NH2
|
D:ARG101
|
4.5
|
35.6
|
1.0
|
CA
|
D:ASN100
|
4.6
|
11.9
|
1.0
|
O
|
B:HOH402
|
4.7
|
35.4
|
1.0
|
CB
|
D:ARG101
|
4.7
|
19.3
|
1.0
|
CD1
|
A:LEU48
|
4.8
|
17.6
|
1.0
|
N
|
D:ARG101
|
4.8
|
13.3
|
1.0
|
CG
|
D:ASN100
|
4.9
|
13.7
|
1.0
|
OD1
|
D:ASN100
|
5.0
|
17.4
|
1.0
|
|
Reference:
C.D.Aakre,
J.Herrou,
T.N.Phung,
B.S.Perchuk,
S.Crosson,
M.T.Laub.
Evolving New Protein-Protein Interaction Specificity Through Promiscuous Intermediates. Cell V. 163 594 2015.
ISSN: ISSN 1097-4172
PubMed: 26478181
DOI: 10.1016/J.CELL.2015.09.055
Page generated: Sun Aug 11 20:37:52 2024
|