Zinc in PDB 6t8h: Cryo-Em Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi

All present enzymatic activity of Cryo-Em Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi:
2.7.7.7; 3.1.11.1;

The structure of Cryo-Em Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi (pdb code 6t8h). 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 Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi, PDB code: 6t8h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cryo-Em Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi


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 the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:97.9 occ:1.00 OD2 A:ASP404 2.0 58.1 1.0 ND1 A:HIS560 2.0 66.2 1.0 NE2 A:HIS497 2.0 56.2 1.0 OD1 A:ASP404 2.0 58.1 1.0 CG A:ASP404 2.2 58.1 1.0 CE1 A:HIS560 2.4 66.2 1.0 OD1 A:ASN450 2.7 54.5 1.0 CD2 A:HIS497 2.8 56.2 1.0 CE1 A:HIS497 3.1 56.2 1.0 CG A:HIS560 3.3 66.2 1.0 N A:ASN450 3.5 54.5 1.0 CG A:ASN450 3.6 54.5 1.0 NE2 A:HIS560 3.7 66.2 1.0 CB A:ASP404 3.7 58.1 1.0 CG A:HIS497 3.9 56.2 1.0 CB A:HIS560 4.0 66.2 1.0 ND1 A:HIS497 4.0 56.2 1.0 CD2 A:HIS560 4.1 66.2 1.0 OD1 A:ASP360 4.1 64.3 1.0 CA A:GLY449 4.2 50.3 1.0 N A:ALA451 4.3 47.2 1.0 C A:GLY449 4.3 50.3 1.0 ND2 A:ASN450 4.4 54.5 1.0 FE A:FE701 4.4 86.1 1.0 CA A:ASN450 4.4 54.5 1.0 CB A:ASN450 4.4 54.5 1.0 N A:ASP404 4.5 58.1 1.0 CA A:ASP404 4.5 58.1 1.0 CA A:HIS560 4.6 66.2 1.0 C A:ASN450 4.7 54.5 1.0 CB A:ALA451 4.9 47.2 1.0

Zinc binding site 2 out of 4 in the Cryo-Em Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi


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 the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:0.5 occ:1.00 SG B:CYS709 2.2 0.9 1.0 SG B:CYS706 2.3 99.4 1.0 SG B:CYS718 2.3 95.9 1.0 SG B:CYS721 2.3 97.4 1.0 CB B:CYS709 2.6 0.9 1.0 CB B:ASN720 2.9 94.9 1.0 N B:CYS721 3.0 97.4 1.0 CB B:CYS721 3.1 97.4 1.0 N B:CYS709 3.5 0.9 1.0 CB B:CYS718 3.6 95.9 1.0 CA B:CYS721 3.7 97.4 1.0 CA B:CYS709 3.7 0.9 1.0 C B:ASN720 3.7 94.9 1.0 CA B:ASN720 3.7 94.9 1.0 CB B:CYS706 3.8 99.4 1.0 CG B:ASN720 3.9 94.9 1.0 OD1 B:ASN720 4.0 94.9 1.0 N B:ASN720 4.1 94.9 1.0 CB B:LYS708 4.1 0.2 1.0 CG B:LYS708 4.4 0.2 1.0 C B:LYS708 4.5 0.2 1.0 C B:CYS721 4.6 97.4 1.0 N B:GLY722 4.6 91.5 1.0 C B:CYS709 4.8 0.9 1.0 O B:ASN720 4.8 94.9 1.0 CA B:LYS708 4.8 0.2 1.0 N B:GLY710 4.9 97.2 1.0 CA B:CYS718 4.9 95.9 1.0

Zinc binding site 3 out of 4 in the Cryo-Em Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi


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 the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1302 b:0.3 occ:1.00 SG B:CYS734 1.9 0.1 1.0 SG B:CYS753 2.2 0.7 1.0 SG B:CYS750 2.3 0.2 1.0 SG B:CYS731 2.3 0.9 1.0 CB B:CYS753 2.5 0.7 1.0 CB B:CYS734 2.9 0.1 1.0 CB B:CYS750 3.1 0.2 1.0 CB B:CYS731 3.3 0.9 1.0 N B:CYS734 3.5 0.1 1.0 CA B:CYS753 3.6 0.7 1.0 N B:CYS753 3.7 0.7 1.0 CA B:CYS734 3.8 0.1 1.0 C B:LYS752 4.3 0.9 1.0 CB B:ARG733 4.4 0.3 1.0 CG2 B:VAL755 4.5 0.9 1.0 CA B:CYS750 4.5 0.2 1.0 C B:CYS753 4.6 0.7 1.0 C B:ARG733 4.6 0.3 1.0 C B:CYS734 4.7 0.1 1.0 O B:LYS752 4.7 0.9 1.0 O B:CYS753 4.8 0.7 1.0 CA B:CYS731 4.8 0.9 1.0 CB B:ALA736 5.0 0.8 1.0 CA B:ARG733 5.0 0.3 1.0 CG B:ARG733 5.0 0.3 1.0 NH1 B:ARG733 5.0 0.3 1.0

Zinc binding site 4 out of 4 in the Cryo-Em Structure of the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi


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 the Dna-Bound Pold-Pcna Processive Complex From P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1303 b:0.9 occ:1.00 SG B:CYS1126 2.1 0.2 1.0 SG B:CYS1142 2.3 0.3 1.0 CB B:CYS1142 2.6 0.3 1.0 CB B:CYS1139 2.6 0.1 1.0 SG B:CYS1123 2.7 0.3 1.0 SG B:CYS1139 2.8 0.1 1.0 CB B:CYS1123 3.0 0.3 1.0 CB B:CYS1126 3.2 0.2 1.0 N B:CYS1126 3.4 0.2 1.0 CA B:CYS1126 3.9 0.2 1.0 O B:PRO1140 3.9 0.3 1.0 CA B:CYS1142 4.0 0.3 1.0 CA B:CYS1139 4.0 0.1 1.0 C B:CYS1139 4.3 0.1 1.0 N B:CYS1142 4.4 0.3 1.0 C B:LYS1125 4.4 0.3 1.0 CA B:CYS1123 4.6 0.3 1.0 CD B:PRO1140 4.6 0.3 1.0 N B:PRO1140 4.6 0.3 1.0 O B:CYS1126 4.6 0.2 1.0 CB B:LYS1125 4.7 0.3 1.0 C B:CYS1126 4.7 0.2 1.0 N B:LYS1125 4.7 0.3 1.0 C B:CYS1142 4.7 0.3 1.0 O B:CYS1139 4.7 0.1 1.0 N B:CYS1139 4.8 0.1 1.0 CA B:LYS1125 4.8 0.3 1.0 N B:GLY1144 4.9 0.2 1.0 C B:PRO1140 4.9 0.3 1.0 O B:LYS1145 5.0 99.4 1.0 O B:CYS1142 5.0 0.3 1.0

C.Madru, P.Raia, I.Hugonneau Beaufet, M.Delarue, M.Carroni, L.Sauguet. Structure of Pcna Bound to Cpip Motif of DP2 From P. Abyssi To Be Published.