Zinc in PDB 7p0h: Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)
Protein crystallography data
The structure of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2), PDB code: 7p0h
was solved by
L.Celma,
H.Walbott,
P.Legrand,
S.Quevillon-Cheruel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.47 /
2.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.88,
87.98,
122.79,
80.23,
76.44,
76.39
|
R / Rfree (%)
|
22.1 /
24.5
|
Other elements in 7p0h:
The structure of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) also contains other interesting chemical elements:
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)
(pdb code 7p0h). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2), PDB code: 7p0h:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7p0h
Go back to
Zinc Binding Sites List in 7p0h
Zinc binding site 1 out
of 4 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)
![](/pictures/ZN/pdb/p0/7p0h-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/p0/7p0h-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn501
b:52.8
occ:1.00
|
SG
|
A:CYS254
|
2.2
|
55.9
|
1.0
|
SG
|
A:CYS242
|
2.3
|
53.0
|
1.0
|
SG
|
A:CYS239
|
2.3
|
49.3
|
1.0
|
SG
|
A:CYS251
|
2.4
|
48.2
|
1.0
|
CB
|
A:CYS254
|
3.2
|
54.7
|
1.0
|
CB
|
A:CYS242
|
3.3
|
48.5
|
1.0
|
CB
|
A:CYS239
|
3.3
|
51.1
|
1.0
|
CB
|
A:CYS251
|
3.5
|
48.6
|
1.0
|
N
|
A:CYS242
|
3.8
|
47.5
|
1.0
|
N
|
A:CYS251
|
3.9
|
49.2
|
1.0
|
OG1
|
A:THR241
|
4.0
|
51.3
|
1.0
|
CA
|
A:CYS242
|
4.1
|
47.8
|
1.0
|
CA
|
A:CYS251
|
4.3
|
49.4
|
1.0
|
N
|
A:CYS254
|
4.3
|
54.4
|
1.0
|
CA
|
A:CYS254
|
4.4
|
54.8
|
1.0
|
C
|
A:THR241
|
4.6
|
48.1
|
1.0
|
O1
|
A:GOL507
|
4.6
|
77.2
|
1.0
|
C1
|
A:GOL507
|
4.7
|
77.1
|
1.0
|
CA
|
A:CYS239
|
4.7
|
52.4
|
1.0
|
CE
|
A:LYS244
|
4.8
|
64.0
|
1.0
|
C
|
A:CYS242
|
4.8
|
48.1
|
1.0
|
O
|
A:CYS251
|
4.8
|
51.3
|
1.0
|
C3
|
A:GOL507
|
4.8
|
77.0
|
1.0
|
N
|
A:THR241
|
4.9
|
49.9
|
1.0
|
C
|
A:CYS251
|
4.9
|
51.1
|
1.0
|
CB
|
A:LYS244
|
4.9
|
49.4
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7p0h
Go back to
Zinc Binding Sites List in 7p0h
Zinc binding site 2 out
of 4 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)
![](/pictures/ZN/pdb/p0/7p0h-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/p0/7p0h-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn501
b:66.4
occ:1.00
|
SG
|
B:CYS254
|
2.3
|
71.2
|
1.0
|
SG
|
B:CYS242
|
2.3
|
66.9
|
1.0
|
SG
|
B:CYS239
|
2.3
|
65.4
|
1.0
|
SG
|
B:CYS251
|
2.4
|
69.7
|
1.0
|
CB
|
B:CYS254
|
3.2
|
70.8
|
1.0
|
CB
|
B:CYS239
|
3.3
|
65.8
|
1.0
|
CB
|
B:CYS242
|
3.3
|
63.5
|
1.0
|
CB
|
B:CYS251
|
3.5
|
66.9
|
1.0
|
N
|
B:CYS242
|
3.8
|
62.8
|
1.0
|
N
|
B:CYS251
|
3.9
|
65.5
|
1.0
|
OG1
|
B:THR241
|
4.0
|
68.3
|
1.0
|
CA
|
B:CYS242
|
4.1
|
63.0
|
1.0
|
CA
|
B:CYS251
|
4.3
|
66.4
|
1.0
|
N
|
B:CYS254
|
4.3
|
71.1
|
1.0
|
CA
|
B:CYS254
|
4.4
|
71.0
|
1.0
|
C
|
B:THR241
|
4.6
|
63.1
|
1.0
|
O1
|
B:GOL505
|
4.7
|
89.5
|
1.0
|
CA
|
B:CYS239
|
4.7
|
67.1
|
1.0
|
O
|
B:CYS251
|
4.8
|
67.7
|
1.0
|
CE
|
B:LYS244
|
4.8
|
78.9
|
1.0
|
C
|
B:CYS242
|
4.8
|
63.8
|
1.0
|
N
|
B:THR241
|
4.9
|
64.0
|
1.0
|
C
|
B:CYS251
|
4.9
|
67.8
|
1.0
|
CB
|
B:LYS244
|
4.9
|
67.2
|
1.0
|
C3
|
B:GOL505
|
4.9
|
89.1
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7p0h
Go back to
Zinc Binding Sites List in 7p0h
Zinc binding site 3 out
of 4 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)
![](/pictures/ZN/pdb/p0/7p0h-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/p0/7p0h-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn501
b:54.5
occ:1.00
|
SG
|
C:CYS254
|
2.2
|
59.4
|
1.0
|
SG
|
C:CYS242
|
2.3
|
54.7
|
1.0
|
SG
|
C:CYS239
|
2.3
|
53.3
|
1.0
|
SG
|
C:CYS251
|
2.4
|
54.3
|
1.0
|
CB
|
C:CYS254
|
3.2
|
59.8
|
1.0
|
CB
|
C:CYS239
|
3.3
|
53.5
|
1.0
|
CB
|
C:CYS242
|
3.3
|
52.0
|
1.0
|
CB
|
C:CYS251
|
3.6
|
53.6
|
1.0
|
N
|
C:CYS242
|
3.8
|
51.8
|
1.0
|
N
|
C:CYS251
|
4.0
|
52.8
|
1.0
|
OG1
|
C:THR241
|
4.0
|
58.0
|
1.0
|
CA
|
C:CYS242
|
4.1
|
51.7
|
1.0
|
CA
|
C:CYS251
|
4.3
|
53.8
|
1.0
|
N
|
C:CYS254
|
4.3
|
60.4
|
1.0
|
CA
|
C:CYS254
|
4.3
|
60.5
|
1.0
|
O1
|
A:GOL508
|
4.5
|
73.3
|
1.0
|
C
|
C:THR241
|
4.6
|
52.1
|
1.0
|
CA
|
C:CYS239
|
4.7
|
54.4
|
1.0
|
C
|
C:CYS242
|
4.8
|
52.4
|
1.0
|
CE
|
C:LYS244
|
4.8
|
73.8
|
1.0
|
O
|
C:CYS251
|
4.8
|
56.0
|
1.0
|
N
|
C:THR241
|
4.9
|
53.6
|
1.0
|
C3
|
A:GOL508
|
4.9
|
73.4
|
1.0
|
CB
|
C:LYS244
|
4.9
|
56.3
|
1.0
|
C
|
C:CYS251
|
4.9
|
55.9
|
1.0
|
C1
|
A:GOL508
|
5.0
|
73.4
|
1.0
|
N
|
C:LEU243
|
5.0
|
52.1
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7p0h
Go back to
Zinc Binding Sites List in 7p0h
Zinc binding site 4 out
of 4 in the Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2)
![](/pictures/ZN/pdb/p0/7p0h-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/p0/7p0h-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of Helicobacter Pylori Comf Fused to An Artificial Alpharep Crystallization Helper(Named B2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn501
b:59.3
occ:1.00
|
SG
|
D:CYS254
|
2.2
|
63.9
|
1.0
|
SG
|
D:CYS242
|
2.3
|
59.8
|
1.0
|
SG
|
D:CYS239
|
2.3
|
58.6
|
1.0
|
SG
|
D:CYS251
|
2.3
|
61.6
|
1.0
|
CB
|
D:CYS254
|
3.2
|
63.0
|
1.0
|
CB
|
D:CYS242
|
3.3
|
56.9
|
1.0
|
CB
|
D:CYS239
|
3.3
|
59.5
|
1.0
|
CB
|
D:CYS251
|
3.5
|
60.6
|
1.0
|
N
|
D:CYS242
|
3.8
|
56.4
|
1.0
|
N
|
D:CYS251
|
3.9
|
60.8
|
1.0
|
OG1
|
D:THR241
|
4.0
|
60.4
|
1.0
|
CA
|
D:CYS242
|
4.1
|
56.5
|
1.0
|
CA
|
D:CYS251
|
4.3
|
60.8
|
1.0
|
O3
|
D:GOL504
|
4.3
|
70.5
|
1.0
|
N
|
D:CYS254
|
4.3
|
63.5
|
1.0
|
CA
|
D:CYS254
|
4.3
|
63.4
|
1.0
|
C
|
D:THR241
|
4.6
|
56.7
|
1.0
|
CE
|
D:LYS244
|
4.8
|
76.7
|
1.0
|
CA
|
D:CYS239
|
4.8
|
60.7
|
1.0
|
O
|
D:CYS251
|
4.8
|
61.8
|
1.0
|
C
|
D:CYS242
|
4.8
|
57.0
|
1.0
|
C
|
D:CYS251
|
4.9
|
61.9
|
1.0
|
N
|
D:THR241
|
4.9
|
57.6
|
1.0
|
CB
|
D:LYS244
|
4.9
|
61.8
|
1.0
|
|
Reference:
P.P.Damke,
L.Celma,
S.M.Kondekar,
A.M.Di Guilmi,
S.Marsin,
J.Depagne,
X.Veaute,
P.Legrand,
H.Walbott,
J.Vercruyssen,
R.Guerois,
S.Quevillon-Cheruel,
J.P.Radicella.
Comfc Mediates Transport and Handling of Single-Stranded Dna During Natural Transformation. Nat Commun V. 13 1961 2022.
ISSN: ESSN 2041-1723
PubMed: 35414142
DOI: 10.1038/S41467-022-29494-Z
Page generated: Wed Oct 30 08:58:14 2024
|