Zinc in PDB 8ppu: Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches

The structure of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Zinc atom in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches (pdb code 8ppu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches, PDB code: 8ppu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:159.7 occ:1.00 SG B:CYS706 2.3 60.9 1.0 SG B:CYS709 2.3 86.3 1.0 SG B:CYS718 2.3 71.8 1.0 SG B:CYS721 2.3 88.2 1.0 CB B:CYS718 3.1 57.4 1.0 CB B:CYS706 3.2 48.2 1.0 CB B:CYS709 4.0 83.5 1.0 CB B:CYS721 4.1 83.0 1.0 N B:CYS709 4.3 81.7 1.0 N B:CYS721 4.3 79.1 1.0 CB B:ASN720 4.5 68.6 1.0 CG2 B:THR723 4.5 47.7 1.0 CA B:CYS718 4.5 55.5 1.0 CA B:CYS706 4.7 43.2 1.0 CA B:CYS709 4.7 82.9 1.0 CA B:CYS721 4.8 81.8 1.0 N B:GLY710 4.8 66.6 1.0 CB B:HIS711 4.9 39.7 1.0

Zinc binding site 2 out of 3 in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:142.1 occ:1.00 CB B:CYS753 2.2 88.8 1.0 SG B:CYS731 2.3 85.3 1.0 SG B:CYS734 2.3 67.9 1.0 SG B:CYS753 2.3 92.7 1.0 CB B:CYS734 3.1 70.0 1.0 N B:CYS734 3.3 73.4 1.0 CA B:CYS753 3.6 88.0 1.0 CB B:ARG733 3.7 85.9 1.0 CA B:CYS734 3.9 71.1 1.0 SG B:CYS750 3.9 70.2 1.0 CB B:CYS731 3.9 73.3 1.0 C B:ARG733 4.0 84.2 1.0 N B:CYS753 4.1 86.8 1.0 CG2 B:VAL755 4.2 77.0 1.0 CA B:ARG733 4.2 85.9 1.0 N B:ARG733 4.4 85.9 1.0 CG B:ARG733 4.6 87.6 1.0 CB B:CYS750 4.6 63.7 1.0 C B:CYS753 4.7 88.2 1.0 CD B:ARG733 4.8 88.8 1.0 N B:ASN754 4.9 81.0 1.0 C B:CYS734 4.9 72.0 1.0 O B:ARG733 5.0 83.6 1.0

Zinc binding site 3 out of 3 in the Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1303 b:160.6 occ:1.00 SG B:CYS1142 2.3 90.9 1.0 SG B:CYS1123 2.3 66.5 1.0 SG B:CYS1139 2.3 90.0 1.0 SG B:CYS1126 2.3 65.3 1.0 CB B:CYS1139 3.0 82.7 1.0 CB B:CYS1123 3.3 54.3 1.0 CB B:CYS1142 3.3 88.2 1.0 CB B:CYS1126 3.4 65.9 1.0 N B:CYS1126 3.9 66.8 1.0 CG2 B:VAL1141 4.3 82.2 1.0 CA B:CYS1126 4.3 66.4 1.0 N B:CYS1142 4.3 87.9 1.0 CA B:CYS1142 4.4 87.5 1.0 CA B:CYS1139 4.5 81.4 1.0 N B:GLY1144 4.7 78.2 1.0 CA B:CYS1123 4.8 53.8 1.0 CB B:LYS1125 4.8 63.8 1.0 C B:CYS1142 4.9 88.3 1.0 CA B:GLY1144 5.0 75.2 1.0

L.Betancurt-Anzola, K.M.Zatopek, M.Martinez-Carranza, A.F.Gardner, L.Sauguet. Molecular Basis For Proof-Reading By Family-D Dna Polymerases To Be Published.