Zinc in PDB 6hms: Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna

All present enzymatic activity of Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna:
2.7.7.7; 3.1.11.1;

The structure of Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna (pdb code 6hms). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna, PDB code: 6hms:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:66.4 occ:1.00 CA A:HIS560 3.4 56.0 1.0 FE A:FE701 3.5 60.7 1.0 CA A:ASN450 4.4 52.6 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:72.3 occ:1.00 CA B:HIS711 3.6 62.9 1.0 CA B:CYS709 3.9 76.9 1.0 CA B:CYS706 4.2 58.8 1.0 CA B:CYS718 4.6 62.3 1.0 CA B:GLY710 4.9 69.8 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:99.4 occ:1.00 CA B:CYS753 2.6 86.7 1.0 CA B:CYS750 4.3 74.4 1.0 CA B:CYS734 4.4 80.6 1.0 CA B:LYS752 4.6 89.0 1.0 CA B:CYS731 4.9 72.3 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Map of Dna Polymerase D From Pyrococcus Abyssi in Complex with Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1303 b:66.5 occ:1.00 CA B:CYS1142 4.0 68.4 1.0 CA B:LYS1125 4.0 62.0 1.0 CA B:PRO1140 4.2 68.4 1.0 CA B:CYS1126 4.4 64.4 1.0 CA B:CYS1139 4.9 64.5 1.0

P.Raia, M.Carroni, E.Henry, G.Pehau-Arnaudet, S.Brule, P.Beguin, G.Henneke, E.Lindahl, M.Delarue, L.Sauguet. Structure of the DP1-DP2 Pold Complex Bound with Dna and Its Implications For the Evolutionary History of Dna and Rna Polymerases. Plos Biol. V. 17 00122 2019.
ISSN: ESSN 1545-7885
PubMed: 30657780
DOI: 10.1371/JOURNAL.PBIO.3000122