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

Go back to 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)


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

Go back to 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)


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

Go back to 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)


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

Go back to 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)


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

Go back to 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)


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

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)


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: Wed Oct 30 19:22:54 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy