Iodine in PDB 8e7f: Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.
Protein crystallography data
The structure of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens., PDB code: 8e7f
was solved by
L.Hor,
A.Pilapitiya,
S.Panjikar,
J.J.Paxman,
B.Heras,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.89 /
2.00
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.482,
55.356,
61.883,
91.52,
93.04,
102.76
|
R / Rfree (%)
|
16.3 /
20.2
|
Other elements in 8e7f:
The structure of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.
(pdb code 8e7f). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the
Crystal Structure of the Autotransporter Ssp From Serratia Marcescens., PDB code: 8e7f:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
Iodine binding site 1 out
of 6 in 8e7f
Go back to
Iodine Binding Sites List in 8e7f
Iodine binding site 1 out
of 6 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I705
b:58.0
occ:0.83
|
CD1
|
A:LEU184
|
4.5
|
49.1
|
1.0
|
CD2
|
A:TYR249
|
4.5
|
30.0
|
1.0
|
CE2
|
A:TYR249
|
4.5
|
30.0
|
1.0
|
ND2
|
A:ASN186
|
4.7
|
61.0
|
1.0
|
O
|
A:HOH823
|
4.7
|
35.5
|
1.0
|
|
Iodine binding site 2 out
of 6 in 8e7f
Go back to
Iodine Binding Sites List in 8e7f
Iodine binding site 2 out
of 6 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I706
b:72.2
occ:0.57
|
CD2
|
A:LEU595
|
3.1
|
69.1
|
1.0
|
N
|
A:ARG639
|
3.8
|
58.0
|
1.0
|
NH1
|
A:ARG639
|
3.9
|
76.6
|
1.0
|
CA
|
A:THR638
|
4.0
|
55.3
|
1.0
|
CA
|
A:GLY596
|
4.0
|
51.0
|
1.0
|
N
|
A:GLY596
|
4.0
|
52.2
|
1.0
|
O
|
A:ILE637
|
4.3
|
58.1
|
1.0
|
C
|
A:THR638
|
4.3
|
59.5
|
1.0
|
CD
|
A:ARG639
|
4.5
|
69.6
|
1.0
|
CG
|
A:LEU595
|
4.6
|
64.1
|
1.0
|
CB
|
A:THR638
|
4.6
|
58.2
|
1.0
|
CG
|
A:ARG639
|
4.6
|
66.4
|
1.0
|
CB
|
A:ARG639
|
4.6
|
60.5
|
1.0
|
C
|
A:LEU595
|
4.8
|
56.6
|
1.0
|
CA
|
A:ARG639
|
4.9
|
57.5
|
1.0
|
CZ
|
A:ARG639
|
4.9
|
68.9
|
1.0
|
|
Iodine binding site 3 out
of 6 in 8e7f
Go back to
Iodine Binding Sites List in 8e7f
Iodine binding site 3 out
of 6 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I707
b:65.0
occ:0.62
|
NZ
|
A:LYS196
|
2.6
|
61.2
|
0.5
|
CE
|
A:LYS196
|
2.9
|
56.3
|
0.5
|
CA
|
A:GLY289
|
3.7
|
29.9
|
1.0
|
C
|
A:GLY289
|
3.7
|
32.5
|
1.0
|
O
|
A:HOH801
|
3.7
|
44.9
|
1.0
|
N
|
A:GLN290
|
3.9
|
33.4
|
1.0
|
O
|
A:GLY289
|
4.2
|
35.8
|
1.0
|
CD
|
A:LYS196
|
4.4
|
54.9
|
0.5
|
CD
|
A:LYS196
|
4.4
|
49.6
|
0.5
|
CA
|
A:GLN290
|
4.5
|
32.4
|
1.0
|
CB
|
A:ASN384
|
4.6
|
36.8
|
1.0
|
CE1
|
A:TYR413
|
4.7
|
39.3
|
1.0
|
CG2
|
A:ILE251
|
4.8
|
33.4
|
1.0
|
O
|
A:HOH866
|
4.8
|
44.0
|
1.0
|
CG
|
A:LYS196
|
4.9
|
47.1
|
0.5
|
|
Iodine binding site 4 out
of 6 in 8e7f
Go back to
Iodine Binding Sites List in 8e7f
Iodine binding site 4 out
of 6 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I708
b:54.3
occ:0.67
|
OE1
|
A:GLN588
|
3.2
|
78.8
|
1.0
|
NE2
|
A:GLN592
|
3.3
|
86.9
|
1.0
|
N
|
A:PHE621
|
3.8
|
44.9
|
1.0
|
CB
|
A:TYR619
|
3.9
|
49.4
|
1.0
|
CD
|
A:PRO620
|
4.0
|
45.2
|
1.0
|
CD
|
A:GLN588
|
4.0
|
75.5
|
1.0
|
CB
|
A:PHE621
|
4.1
|
52.2
|
1.0
|
CG
|
A:GLN588
|
4.2
|
70.0
|
1.0
|
CD
|
A:GLN592
|
4.2
|
89.3
|
1.0
|
N
|
A:PRO620
|
4.3
|
48.5
|
1.0
|
CA
|
A:PHE621
|
4.4
|
48.5
|
1.0
|
N
|
A:VAL622
|
4.4
|
48.5
|
1.0
|
CG1
|
A:VAL622
|
4.4
|
60.1
|
1.0
|
CD2
|
A:PHE621
|
4.4
|
49.9
|
1.0
|
C
|
A:PHE621
|
4.6
|
50.5
|
1.0
|
CB
|
A:GLN588
|
4.6
|
64.9
|
1.0
|
CG
|
A:TYR619
|
4.8
|
49.5
|
1.0
|
C
|
A:TYR619
|
4.8
|
48.9
|
1.0
|
CG
|
A:PHE621
|
4.8
|
53.3
|
1.0
|
CB
|
A:PRO620
|
4.8
|
46.9
|
1.0
|
C
|
A:PRO620
|
4.8
|
42.1
|
1.0
|
CG
|
A:PRO620
|
4.8
|
47.0
|
1.0
|
OE1
|
A:GLN592
|
4.9
|
89.8
|
1.0
|
CA
|
A:PRO620
|
4.9
|
46.5
|
1.0
|
CA
|
A:TYR619
|
4.9
|
51.6
|
1.0
|
CG
|
A:GLN592
|
5.0
|
85.8
|
1.0
|
|
Iodine binding site 5 out
of 6 in 8e7f
Go back to
Iodine Binding Sites List in 8e7f
Iodine binding site 5 out
of 6 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I709
b:66.9
occ:0.47
|
O
|
A:HOH865
|
3.1
|
47.1
|
1.0
|
CA
|
A:GLY36
|
3.7
|
47.6
|
1.0
|
C
|
A:GLY36
|
3.9
|
50.5
|
1.0
|
O
|
A:GLY36
|
4.0
|
51.9
|
1.0
|
CB
|
A:ALA62
|
4.0
|
42.0
|
1.0
|
O
|
A:ALA62
|
4.2
|
46.8
|
1.0
|
CG
|
A:ARG63
|
4.3
|
45.7
|
1.0
|
N
|
A:GLY36
|
4.3
|
46.0
|
1.0
|
CG
|
A:PRO38
|
4.3
|
50.7
|
1.0
|
CD
|
A:PRO38
|
4.3
|
51.9
|
1.0
|
CD
|
A:ARG63
|
4.4
|
47.9
|
1.0
|
C
|
A:ALA62
|
4.5
|
44.4
|
1.0
|
O
|
A:HOH1031
|
4.6
|
39.4
|
1.0
|
N
|
A:ALA37
|
4.7
|
52.8
|
1.0
|
CA
|
A:ALA62
|
4.9
|
41.4
|
1.0
|
N
|
A:ARG63
|
4.9
|
43.0
|
1.0
|
|
Iodine binding site 6 out
of 6 in 8e7f
Go back to
Iodine Binding Sites List in 8e7f
Iodine binding site 6 out
of 6 in the Crystal Structure of the Autotransporter Ssp From Serratia Marcescens.
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Crystal Structure of the Autotransporter Ssp From Serratia Marcescens. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I710
b:65.2
occ:0.61
|
OG
|
A:SER242
|
3.2
|
34.0
|
1.0
|
OG
|
A:SER341
|
3.7
|
58.7
|
1.0
|
CB
|
A:SER242
|
4.0
|
32.0
|
1.0
|
C
|
A:TRP167
|
4.0
|
36.2
|
1.0
|
CA
|
A:GLY244
|
4.1
|
29.8
|
1.0
|
OG1
|
A:THR340
|
4.1
|
30.4
|
1.0
|
CA
|
A:TRP167
|
4.2
|
36.4
|
1.0
|
N
|
A:TRP167
|
4.3
|
35.2
|
1.0
|
N
|
A:GLY168
|
4.3
|
36.9
|
1.0
|
NZ
|
A:LYS256
|
4.3
|
53.7
|
1.0
|
O
|
A:TRP167
|
4.3
|
35.0
|
1.0
|
N
|
A:GLY244
|
4.4
|
28.6
|
1.0
|
C
|
A:SER166
|
4.5
|
39.4
|
1.0
|
ND2
|
A:ASN245
|
4.6
|
41.4
|
1.0
|
O
|
A:SER166
|
4.6
|
41.1
|
1.0
|
O
|
A:HOH947
|
4.6
|
51.2
|
1.0
|
OH
|
A:TYR246
|
4.7
|
44.9
|
1.0
|
O
|
A:HOH893
|
4.7
|
46.7
|
1.0
|
C
|
A:GLY244
|
4.9
|
27.1
|
1.0
|
N
|
A:ASN245
|
4.9
|
30.2
|
1.0
|
CA
|
A:GLY168
|
4.9
|
36.2
|
1.0
|
N
|
A:SER341
|
4.9
|
32.9
|
1.0
|
|
Reference:
L.Hor,
A.Pilapitiya,
J.A.Mckenna,
S.Panjikar,
M.A.Anderson,
M.Desvaux,
J.J.Paxman,
B.Heras.
Crystal Structure of A Subtilisin-Like Autotransporter Reveals Insights Into Its Cytotoxic Function Nat Commun 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-36719-2
Page generated: Mon Aug 12 02:44:14 2024
|