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 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)


Mono view


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 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)


Mono view


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 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)


Mono view


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 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)


Mono view


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 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)


Mono view


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

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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)


Mono view


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

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