Zinc in PDB 8dzf: Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2)
Zinc Binding Sites:
The binding sites of Zinc atom in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2)
(pdb code 8dzf). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2), PDB code: 8dzf:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 8dzf
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Zinc Binding Sites List in 8dzf
Zinc binding site 1 out
of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2)
![](/pictures/ZN/pdb/dz/8dzf-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/dz/8dzf-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 Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn601
b:188.2
occ:1.00
|
SG
|
A:CYS403
|
2.3
|
158.2
|
1.0
|
SG
|
A:CYS406
|
2.3
|
169.8
|
1.0
|
SG
|
A:CYS445
|
2.3
|
185.3
|
1.0
|
SG
|
A:CYS446
|
2.3
|
172.2
|
1.0
|
CB
|
A:CYS406
|
3.2
|
169.8
|
1.0
|
CB
|
A:CYS445
|
3.2
|
185.3
|
1.0
|
CB
|
A:CYS446
|
3.3
|
172.2
|
1.0
|
CB
|
A:CYS403
|
3.4
|
158.2
|
1.0
|
C
|
A:CYS445
|
3.5
|
185.3
|
1.0
|
N
|
A:CYS406
|
3.7
|
169.8
|
1.0
|
N
|
A:CYS446
|
3.7
|
172.2
|
1.0
|
O
|
A:CYS445
|
3.7
|
185.3
|
1.0
|
CA
|
A:CYS445
|
4.0
|
185.3
|
1.0
|
CA
|
A:CYS406
|
4.0
|
169.8
|
1.0
|
CA
|
A:CYS446
|
4.1
|
172.2
|
1.0
|
CB
|
A:GLN405
|
4.3
|
169.1
|
1.0
|
C
|
A:GLN405
|
4.5
|
169.1
|
1.0
|
CA
|
A:GLN405
|
4.8
|
169.1
|
1.0
|
CA
|
A:CYS403
|
4.8
|
158.2
|
1.0
|
N
|
A:GLN405
|
4.9
|
169.1
|
1.0
|
N
|
A:CYS445
|
5.0
|
185.3
|
1.0
|
|
Zinc binding site 2 out
of 6 in 8dzf
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Zinc Binding Sites List in 8dzf
Zinc binding site 2 out
of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2)
![](/pictures/ZN/pdb/dz/8dzf-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/dz/8dzf-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 Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn601
b:184.5
occ:1.00
|
SG
|
B:CYS406
|
2.3
|
166.6
|
1.0
|
SG
|
B:CYS403
|
2.3
|
155.6
|
1.0
|
SG
|
B:CYS445
|
2.3
|
183.7
|
1.0
|
SG
|
B:CYS446
|
2.3
|
170.6
|
1.0
|
CB
|
B:CYS406
|
3.2
|
166.6
|
1.0
|
CB
|
B:CYS445
|
3.2
|
183.7
|
1.0
|
CB
|
B:CYS446
|
3.3
|
170.6
|
1.0
|
CB
|
B:CYS403
|
3.4
|
155.6
|
1.0
|
C
|
B:CYS445
|
3.5
|
183.7
|
1.0
|
N
|
B:CYS406
|
3.7
|
166.6
|
1.0
|
N
|
B:CYS446
|
3.7
|
170.6
|
1.0
|
O
|
B:CYS445
|
3.7
|
183.7
|
1.0
|
CA
|
B:CYS445
|
4.0
|
183.7
|
1.0
|
CA
|
B:CYS406
|
4.0
|
166.6
|
1.0
|
CA
|
B:CYS446
|
4.1
|
170.6
|
1.0
|
CB
|
B:GLN405
|
4.3
|
166.1
|
1.0
|
C
|
B:GLN405
|
4.5
|
166.1
|
1.0
|
CA
|
B:GLN405
|
4.8
|
166.1
|
1.0
|
CA
|
B:CYS403
|
4.8
|
155.6
|
1.0
|
N
|
B:GLN405
|
4.9
|
166.1
|
1.0
|
N
|
B:CYS445
|
5.0
|
183.7
|
1.0
|
|
Zinc binding site 3 out
of 6 in 8dzf
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Zinc Binding Sites List in 8dzf
Zinc binding site 3 out
of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2)
![](/pictures/ZN/pdb/dz/8dzf-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/dz/8dzf-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 Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn601
b:190.4
occ:1.00
|
SG
|
C:CYS406
|
2.3
|
168.8
|
1.0
|
SG
|
C:CYS403
|
2.3
|
161.2
|
1.0
|
SG
|
C:CYS445
|
2.3
|
184.6
|
1.0
|
SG
|
C:CYS446
|
2.3
|
171.4
|
1.0
|
CB
|
C:CYS406
|
3.2
|
168.8
|
1.0
|
CB
|
C:CYS445
|
3.2
|
184.6
|
1.0
|
CB
|
C:CYS446
|
3.3
|
171.4
|
1.0
|
CB
|
C:CYS403
|
3.4
|
161.2
|
1.0
|
C
|
C:CYS445
|
3.5
|
184.6
|
1.0
|
N
|
C:CYS406
|
3.7
|
168.8
|
1.0
|
N
|
C:CYS446
|
3.7
|
171.4
|
1.0
|
O
|
C:CYS445
|
3.7
|
184.6
|
1.0
|
CA
|
C:CYS445
|
4.0
|
184.6
|
1.0
|
CA
|
C:CYS406
|
4.0
|
168.8
|
1.0
|
CA
|
C:CYS446
|
4.1
|
171.4
|
1.0
|
CB
|
C:GLN405
|
4.3
|
171.2
|
1.0
|
C
|
C:GLN405
|
4.5
|
171.2
|
1.0
|
CA
|
C:GLN405
|
4.8
|
171.2
|
1.0
|
CA
|
C:CYS403
|
4.8
|
161.2
|
1.0
|
N
|
C:GLN405
|
4.9
|
171.2
|
1.0
|
N
|
C:CYS445
|
5.0
|
184.6
|
1.0
|
|
Zinc binding site 4 out
of 6 in 8dzf
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Zinc Binding Sites List in 8dzf
Zinc binding site 4 out
of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2)
![](/pictures/ZN/pdb/dz/8dzf-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/dz/8dzf-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 Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn601
b:189.1
occ:1.00
|
SG
|
D:CYS403
|
2.3
|
158.5
|
1.0
|
SG
|
D:CYS406
|
2.3
|
169.8
|
1.0
|
SG
|
D:CYS445
|
2.3
|
186.9
|
1.0
|
SG
|
D:CYS446
|
2.3
|
174.4
|
1.0
|
CB
|
D:CYS406
|
3.2
|
169.8
|
1.0
|
CB
|
D:CYS445
|
3.2
|
186.9
|
1.0
|
CB
|
D:CYS446
|
3.3
|
174.4
|
1.0
|
CB
|
D:CYS403
|
3.4
|
158.5
|
1.0
|
C
|
D:CYS445
|
3.5
|
186.9
|
1.0
|
N
|
D:CYS406
|
3.7
|
169.8
|
1.0
|
N
|
D:CYS446
|
3.7
|
174.4
|
1.0
|
O
|
D:CYS445
|
3.7
|
186.9
|
1.0
|
CA
|
D:CYS445
|
4.0
|
186.9
|
1.0
|
CA
|
D:CYS406
|
4.0
|
169.8
|
1.0
|
CA
|
D:CYS446
|
4.1
|
174.4
|
1.0
|
CB
|
D:GLN405
|
4.3
|
168.2
|
1.0
|
C
|
D:GLN405
|
4.5
|
168.2
|
1.0
|
CA
|
D:GLN405
|
4.8
|
168.2
|
1.0
|
CA
|
D:CYS403
|
4.8
|
158.5
|
1.0
|
N
|
D:GLN405
|
4.9
|
168.2
|
1.0
|
N
|
D:CYS445
|
5.0
|
186.9
|
1.0
|
|
Zinc binding site 5 out
of 6 in 8dzf
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Zinc Binding Sites List in 8dzf
Zinc binding site 5 out
of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2)
![](/pictures/ZN/pdb/dz/8dzf-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/dz/8dzf-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn601
b:183.9
occ:1.00
|
SG
|
E:CYS406
|
2.3
|
166.2
|
1.0
|
SG
|
E:CYS403
|
2.3
|
155.2
|
1.0
|
SG
|
E:CYS445
|
2.3
|
184.7
|
1.0
|
SG
|
E:CYS446
|
2.3
|
171.6
|
1.0
|
CB
|
E:CYS406
|
3.2
|
166.2
|
1.0
|
CB
|
E:CYS445
|
3.2
|
184.7
|
1.0
|
CB
|
E:CYS446
|
3.3
|
171.6
|
1.0
|
CB
|
E:CYS403
|
3.4
|
155.2
|
1.0
|
C
|
E:CYS445
|
3.5
|
184.7
|
1.0
|
N
|
E:CYS406
|
3.7
|
166.2
|
1.0
|
N
|
E:CYS446
|
3.7
|
171.6
|
1.0
|
O
|
E:CYS445
|
3.7
|
184.7
|
1.0
|
CA
|
E:CYS445
|
4.0
|
184.7
|
1.0
|
CA
|
E:CYS406
|
4.0
|
166.2
|
1.0
|
CA
|
E:CYS446
|
4.1
|
171.6
|
1.0
|
CB
|
E:GLN405
|
4.3
|
164.8
|
1.0
|
C
|
E:GLN405
|
4.5
|
164.8
|
1.0
|
CA
|
E:GLN405
|
4.8
|
164.8
|
1.0
|
CA
|
E:CYS403
|
4.8
|
155.2
|
1.0
|
N
|
E:GLN405
|
4.9
|
164.8
|
1.0
|
N
|
E:CYS445
|
5.0
|
184.7
|
1.0
|
|
Zinc binding site 6 out
of 6 in 8dzf
Go back to
Zinc Binding Sites List in 8dzf
Zinc binding site 6 out
of 6 in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2)
![](/pictures/ZN/pdb/dz/8dzf-ZN-sphere_06.jpg) Mono view
![](/pictures/ZN/pdb/dz/8dzf-ZN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Amp-Pnp (Class-2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn601
b:187.4
occ:1.00
|
SG
|
F:CYS406
|
2.3
|
168.5
|
1.0
|
SG
|
F:CYS403
|
2.3
|
161.6
|
1.0
|
SG
|
F:CYS445
|
2.3
|
184.2
|
1.0
|
SG
|
F:CYS446
|
2.3
|
170.3
|
1.0
|
CB
|
F:CYS406
|
3.2
|
168.5
|
1.0
|
CB
|
F:CYS445
|
3.2
|
184.2
|
1.0
|
CB
|
F:CYS446
|
3.3
|
170.3
|
1.0
|
CB
|
F:CYS403
|
3.4
|
161.6
|
1.0
|
C
|
F:CYS445
|
3.5
|
184.2
|
1.0
|
N
|
F:CYS406
|
3.7
|
168.5
|
1.0
|
N
|
F:CYS446
|
3.7
|
170.3
|
1.0
|
O
|
F:CYS445
|
3.7
|
184.2
|
1.0
|
CA
|
F:CYS445
|
4.0
|
184.2
|
1.0
|
CA
|
F:CYS406
|
4.0
|
168.5
|
1.0
|
CA
|
F:CYS446
|
4.1
|
170.3
|
1.0
|
CB
|
F:GLN405
|
4.3
|
169.7
|
1.0
|
C
|
F:GLN405
|
4.5
|
169.7
|
1.0
|
CA
|
F:GLN405
|
4.8
|
169.7
|
1.0
|
CA
|
F:CYS403
|
4.8
|
161.6
|
1.0
|
N
|
F:GLN405
|
4.9
|
169.7
|
1.0
|
N
|
F:CYS445
|
5.0
|
184.2
|
1.0
|
|
Reference:
A.R.Nayak,
P.K.Singh,
J.Zhao,
M.Samso,
M.S.Donnenberg.
Cryo-Em Structure of the Type IV Pilus Extension Atpase From Enteropathogenic Escherichia Coli. Mbio V. 13 2022.
ISSN: ESSN 2150-7511
PubMed: 36326250
DOI: 10.1128/MBIO.02270-22
Page generated: Sat Apr 8 08:22:09 2023
|