Zinc in PDB 8dzg: Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp

The structure of Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Bundle-Forming Pilus Extension Atpase From E.Coli in the Presence of Adp (pdb code 8dzg). 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 Adp, PDB code: 8dzg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:103.5 occ:1.00 SG A:CYS446 2.3 90.1 1.0 SG A:CYS445 2.3 94.7 1.0 SG A:CYS406 2.3 85.7 1.0 SG A:CYS403 2.3 76.4 1.0 CB A:CYS446 3.3 90.1 1.0 CB A:CYS403 3.4 76.4 1.0 N A:CYS446 3.8 90.1 1.0 CB A:CYS406 3.9 85.7 1.0 CB A:CYS445 3.9 94.7 1.0 N A:CYS406 4.1 85.7 1.0 CA A:CYS446 4.2 90.1 1.0 C A:CYS445 4.4 94.7 1.0 CA A:CYS406 4.6 85.7 1.0 CB A:GLN405 4.6 81.9 1.0 CA A:CYS445 4.7 94.7 1.0 CB A:LYS443 4.7 94.5 1.0 CA A:CYS403 4.8 76.4 1.0 CD A:LYS443 5.0 94.5 1.0

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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:106.9 occ:1.00 SG B:CYS446 2.3 95.7 1.0 SG B:CYS445 2.3 100.2 1.0 SG B:CYS406 2.3 88.4 1.0 SG B:CYS403 2.3 78.7 1.0 CB B:CYS446 3.3 95.7 1.0 CB B:CYS403 3.4 78.7 1.0 N B:CYS446 3.8 95.7 1.0 CB B:CYS406 3.9 88.4 1.0 CB B:CYS445 3.9 100.2 1.0 N B:CYS406 4.1 88.4 1.0 CA B:CYS446 4.2 95.7 1.0 C B:CYS445 4.4 100.2 1.0 CA B:CYS406 4.6 88.4 1.0 CB B:GLN405 4.6 85.1 1.0 CA B:CYS445 4.7 100.2 1.0 CB B:LYS443 4.7 100.8 1.0 CA B:CYS403 4.8 78.7 1.0 CD B:LYS443 5.0 100.8 1.0

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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn603 b:110.8 occ:1.00 SG C:CYS446 2.3 95.8 1.0 SG C:CYS445 2.3 100.6 1.0 SG C:CYS406 2.3 91.7 1.0 SG C:CYS403 2.3 80.7 1.0 CB C:CYS446 3.3 95.8 1.0 CB C:CYS403 3.4 80.7 1.0 N C:CYS446 3.8 95.8 1.0 CB C:CYS406 3.9 91.7 1.0 CB C:CYS445 3.9 100.6 1.0 N C:CYS406 4.1 91.7 1.0 CA C:CYS446 4.2 95.8 1.0 C C:CYS445 4.4 100.6 1.0 CA C:CYS406 4.6 91.7 1.0 CB C:GLN405 4.6 89.5 1.0 CA C:CYS445 4.7 100.6 1.0 CB C:LYS443 4.7 101.9 1.0 CA C:CYS403 4.8 80.7 1.0 CD C:LYS443 5.0 101.9 1.0

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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn603 b:105.0 occ:1.00 SG D:CYS446 2.3 91.2 1.0 SG D:CYS445 2.3 95.7 1.0 SG D:CYS406 2.3 85.5 1.0 SG D:CYS403 2.3 76.4 1.0 CB D:CYS446 3.3 91.2 1.0 CB D:CYS403 3.4 76.4 1.0 N D:CYS446 3.8 91.2 1.0 CB D:CYS406 3.9 85.5 1.0 CB D:CYS445 3.9 95.7 1.0 N D:CYS406 4.1 85.5 1.0 CA D:CYS446 4.2 91.2 1.0 C D:CYS445 4.4 95.7 1.0 CA D:CYS406 4.6 85.5 1.0 CB D:GLN405 4.6 81.8 1.0 CA D:CYS445 4.7 95.7 1.0 CB D:LYS443 4.7 95.0 1.0 CA D:CYS403 4.8 76.4 1.0 CD D:LYS443 5.0 95.0 1.0

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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn603 b:106.3 occ:1.00 SG E:CYS446 2.3 95.4 1.0 SG E:CYS445 2.3 99.8 1.0 SG E:CYS406 2.3 89.1 1.0 SG E:CYS403 2.3 80.0 1.0 CB E:CYS446 3.3 95.4 1.0 CB E:CYS403 3.4 80.0 1.0 N E:CYS446 3.8 95.4 1.0 CB E:CYS406 3.9 89.1 1.0 CB E:CYS445 3.9 99.8 1.0 N E:CYS406 4.1 89.1 1.0 CA E:CYS446 4.2 95.4 1.0 C E:CYS445 4.4 99.8 1.0 CA E:CYS406 4.6 89.1 1.0 CB E:GLN405 4.6 86.4 1.0 CA E:CYS445 4.7 99.8 1.0 CB E:LYS443 4.7 100.3 1.0 CA E:CYS403 4.8 80.0 1.0 CD E:LYS443 5.0 100.3 1.0

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 Adp


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 Adp within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn603 b:110.5 occ:1.00 SG F:CYS446 2.3 94.8 1.0 SG F:CYS445 2.3 99.6 1.0 SG F:CYS406 2.3 91.2 1.0 SG F:CYS403 2.3 80.2 1.0 CB F:CYS446 3.3 94.8 1.0 CB F:CYS403 3.4 80.2 1.0 N F:CYS446 3.8 94.8 1.0 CB F:CYS406 3.9 91.2 1.0 CB F:CYS445 3.9 99.6 1.0 N F:CYS406 4.1 91.2 1.0 CA F:CYS446 4.2 94.8 1.0 C F:CYS445 4.4 99.6 1.0 CA F:CYS406 4.6 91.2 1.0 CB F:GLN405 4.6 89.1 1.0 CA F:CYS445 4.7 99.6 1.0 CB F:LYS443 4.7 100.9 1.0 CA F:CYS403 4.8 80.2 1.0 CD F:LYS443 5.0 100.9 1.0

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