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

Enzymatic activity of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing A Mismatch

All present enzymatic activity of Pyrococcus Abyssi Dna Polymerase D (Pold) in Its Editing Mode Bound to A Primer/Template Substrate Containing A Mismatch:
2.7.7.7; 3.1.11.1;

Other elements in 8ppt:

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

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

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 A Mismatch (pdb code 8ppt). 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 A Mismatch, PDB code: 8ppt:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8ppt

Go back to Zinc Binding Sites List in 8ppt
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 A Mismatch


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 A Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:237.8
occ:1.00
 SG B:CYS709 2.3 100.9 1.0
SG B:CYS718 2.3 64.8 1.0
SG B:CYS721 2.3 75.4 1.0
SG B:CYS706 2.3 54.1 1.0
CB B:CYS718 3.1 45.8 1.0
CB B:CYS706 3.2 52.2 1.0
CB B:CYS709 3.9 101.5 1.0
CB B:CYS721 4.1 74.5 1.0
N B:CYS709 4.3 97.5 1.0
N B:CYS721 4.4 72.1 1.0
CA B:CYS718 4.6 43.7 1.0
CA B:CYS706 4.6 48.7 1.0
CA B:CYS709 4.7 98.7 1.0
CB B:ASN720 4.7 65.8 1.0
CB B:HIS711 4.7 39.6 1.0
CA B:CYS721 4.8 74.0 1.0
N B:GLY710 4.9 74.2 1.0
N B:HIS711 4.9 46.0 1.0

Zinc binding site 2 out of 3 in 8ppt

Go back to Zinc Binding Sites List in 8ppt
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 A Mismatch


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 A Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1302

b:234.7
occ:1.00
 CB B:CYS734 2.1 96.6 1.0
SG B:CYS750 2.3 97.1 1.0
SG B:CYS753 2.3 124.8 1.0
SG B:CYS731 2.3 85.2 1.0
SG B:CYS734 2.3 95.2 1.0
CB B:CYS731 3.1 77.2 1.0
CB B:CYS753 3.3 122.6 1.0
CB B:CYS750 3.4 91.3 1.0
CA B:CYS734 3.5 95.8 1.0
N B:CYS734 3.9 96.5 1.0
C B:CYS734 4.1 97.3 1.0
N B:CYS753 4.3 122.3 1.0
CA B:CYS753 4.4 122.7 1.0
O B:CYS734 4.5 99.5 1.0
CA B:CYS731 4.6 72.1 1.0
OH B:TYR738 4.7 65.8 1.0
CD B:LYS752 4.7 121.0 1.0
N B:ASN735 4.7 84.7 1.0
CA B:CYS750 4.8 90.7 1.0

Zinc binding site 3 out of 3 in 8ppt

Go back to Zinc Binding Sites List in 8ppt
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 A Mismatch


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 A Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1303

b:193.3
occ:1.00
 SG B:CYS1126 2.3 76.1 1.0
SG B:CYS1142 2.3 107.7 1.0
SG B:CYS1139 2.3 96.7 1.0
SG B:CYS1123 2.3 70.8 1.0
CB B:CYS1142 2.9 107.4 1.0
CB B:CYS1123 3.2 58.6 1.0
CB B:CYS1139 3.2 96.3 1.0
CB B:CYS1126 3.6 75.4 1.0
N B:CYS1126 3.8 74.2 1.0
CA B:CYS1142 4.2 106.9 1.0
CB B:LYS1125 4.3 68.9 1.0
CA B:CYS1126 4.4 73.4 1.0
N B:CYS1142 4.4 106.2 1.0
CG1 B:VAL1141 4.6 102.3 1.0
C B:VAL1141 4.6 102.2 1.0
CG2 B:THR1128 4.6 64.2 1.0
O B:VAL1141 4.6 102.8 1.0
CA B:CYS1139 4.7 95.0 1.0
CA B:CYS1123 4.7 55.5 1.0
C B:LYS1125 4.8 69.3 1.0
CA B:LYS1125 4.9 66.6 1.0
N B:LYS1125 5.0 68.7 1.0

Reference:

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.
Page generated: Fri Aug 22 12:25:02 2025

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