Zinc in PDB 8ppv: Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches

Enzymatic activity of Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches

Other elements in 8ppv:

Zinc Binding Sites:

Zinc binding site 1 out of 3 in 8ppv

Zinc Binding Sites List in 8ppv

Zinc binding site 1 out of 3 in the Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) 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 Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:112.9 occ:1.00 SG B:CYS718 2.3 63.2 1.0 SG B:CYS709 2.3 76.8 1.0 SG B:CYS706 2.3 60.6 1.0 SG B:CYS721 2.3 68.1 1.0 CB B:CYS718 3.1 46.1 1.0 CB B:CYS706 3.2 51.9 1.0 CB B:CYS709 4.0 67.8 1.0 CB B:CYS721 4.1 60.5 1.0 N B:CYS709 4.2 68.2 1.0 N B:CYS721 4.4 61.8 1.0 OG1 B:THR723 4.4 52.1 1.0 CA B:CYS718 4.5 42.9 1.0 CA B:CYS706 4.6 45.2 1.0 CA B:CYS709 4.7 68.8 1.0 CB B:HIS711 4.7 45.7 1.0 CB B:ASN720 4.8 57.1 1.0 N B:GLY710 4.8 58.8 1.0 CA B:CYS721 4.8 60.6 1.0 CB B:LYS708 4.9 66.1 1.0 N B:HIS711 4.9 49.0 1.0

Zinc binding site 2 out of 3 in 8ppv

Zinc Binding Sites List in 8ppv

Zinc binding site 2 out of 3 in the Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) 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 Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:135.4 occ:1.00 SG B:CYS750 2.3 73.7 1.0 SG B:CYS734 2.3 79.4 1.0 SG B:CYS731 2.3 77.9 1.0 SG B:CYS753 2.3 91.0 1.0 CB B:CYS750 3.2 72.5 1.0 CB B:CYS731 3.3 69.8 1.0 CB B:CYS753 3.5 84.0 1.0 CB B:CYS734 3.6 77.7 1.0 N B:CYS734 3.9 75.1 1.0 N B:CYS753 4.1 84.0 1.0 CA B:CYS734 4.3 77.2 1.0 CA B:CYS753 4.5 82.0 1.0 CB B:LYS752 4.6 85.0 1.0 CB B:ARG733 4.6 82.0 1.0 C B:LYS752 4.6 84.0 1.0 CA B:CYS750 4.7 74.2 1.0 CA B:CYS731 4.7 67.5 1.0 C B:ARG733 4.9 79.1 1.0 CD B:LYS752 5.0 82.1 1.0 CA B:LYS752 5.0 84.7 1.0 C B:CYS734 5.0 78.2 1.0

Zinc binding site 3 out of 3 in 8ppv

Zinc Binding Sites List in 8ppv

Zinc binding site 3 out of 3 in the Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) 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 Intermediate Conformer of Pyrococcus Abyssi Dna Polymerase D (Pold) Bound to A Primer/Template Substrate Containing Three Consecutive Mismatches within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1303 b:131.8 occ:1.00 CB B:CYS1142 2.1 90.0 1.0 SG B:CYS1142 2.3 92.2 1.0 SG B:CYS1123 2.3 82.0 1.0 SG B:CYS1139 2.3 88.5 1.0 CB B:CYS1139 3.2 83.5 1.0 SG B:CYS1126 3.3 81.5 1.0 CB B:CYS1123 3.3 71.7 1.0 CA B:CYS1142 3.6 85.9 1.0 CB B:CYS1126 4.2 75.8 1.0 N B:CYS1142 4.3 86.7 1.0 N B:CYS1126 4.4 77.4 1.0 C B:CYS1142 4.4 86.2 1.0 CA B:CYS1139 4.6 82.8 1.0 O B:PRO1140 4.7 83.4 1.0 CG2 B:THR1128 4.7 69.8 1.0 O B:VAL1141 4.7 84.4 1.0 CA B:CYS1123 4.7 71.3 1.0 O B:CYS1139 4.7 84.7 1.0 N B:GLY1143 4.8 88.5 1.0 C B:VAL1141 4.8 86.0 1.0 CB B:LYS1125 4.8 79.4 1.0 C B:CYS1139 4.9 83.2 1.0 N B:GLY1144 5.0 89.2 1.0 CA B:CYS1126 5.0 78.2 1.0

Reference: