Zinc in PDB 6knc: Pold-Pcna-Dna (Form B)

All present enzymatic activity of Pold-Pcna-Dna (Form B):
2.7.7.7; 3.1.11.1;

The structure of Pold-Pcna-Dna (Form B) also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Pold-Pcna-Dna (Form B) (pdb code 6knc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Pold-Pcna-Dna (Form B), PDB code: 6knc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Pold-Pcna-Dna (Form B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pold-Pcna-Dna (Form B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:0.7 occ:1.00 CE1 A:HIS610 1.9 0.6 1.0 NE2 A:HIS610 2.2 0.6 1.0 ND1 A:HIS673 2.2 0.5 1.0 OD2 A:ASP517 2.3 0.9 1.0 OD1 A:ASP473 2.7 0.1 1.0 CG A:HIS673 2.9 0.5 1.0 CB A:HIS673 3.0 0.5 1.0 CA A:HIS673 3.0 0.5 1.0 ND1 A:HIS610 3.2 0.6 1.0 CE1 A:HIS673 3.4 0.5 1.0 CG A:ASP473 3.5 0.1 1.0 CD2 A:HIS610 3.5 0.6 1.0 OD2 A:ASP473 3.5 0.1 1.0 N A:HIS673 3.5 0.5 1.0 CG A:ASP517 3.5 0.9 1.0 CG A:HIS610 4.0 0.6 1.0 FE A:FE801 4.0 0.2 1.0 CD2 A:HIS673 4.2 0.5 1.0 C A:HIS673 4.3 0.5 1.0 NE2 A:HIS673 4.3 0.5 1.0 CB A:ASP517 4.4 0.9 1.0 OD1 A:ASP517 4.4 0.9 1.0 C A:GLY672 4.7 0.5 1.0 O A:HIS673 4.7 0.5 1.0 CB A:ASP473 4.9 0.1 1.0

Zinc binding site 2 out of 4 in the Pold-Pcna-Dna (Form B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pold-Pcna-Dna (Form B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1401 b:0.7 occ:1.00 SG B:CYS715 2.3 0.1 1.0 SG B:CYS727 2.3 0.8 1.0 SG B:CYS718 2.4 0.8 1.0 CB B:CYS727 2.5 0.8 1.0 SG B:CYS730 2.5 0.2 1.0 CB B:CYS718 2.8 0.8 1.0 OG1 B:THR732 3.3 0.0 1.0 CB B:CYS715 3.5 0.1 1.0 CB B:CYS730 3.5 0.2 1.0 O B:THR732 3.6 0.0 1.0 CA B:CYS727 3.9 0.8 1.0 CA B:CYS718 4.0 0.8 1.0 N B:CYS718 4.2 0.8 1.0 C B:THR732 4.5 0.0 1.0 CB B:HIS720 4.5 0.8 1.0 CA B:CYS730 4.6 0.2 1.0 N B:GLY719 4.6 0.2 1.0 N B:CYS730 4.6 0.2 1.0 CB B:THR732 4.7 0.0 1.0 N B:THR732 4.7 0.0 1.0 N B:CYS727 4.7 0.8 1.0 N B:HIS720 4.7 0.8 1.0 C B:CYS718 4.8 0.8 1.0 CA B:CYS715 4.8 0.1 1.0 C B:CYS727 4.9 0.8 1.0 CA B:THR732 4.9 0.0 1.0 C B:CYS730 4.9 0.2 1.0

Zinc binding site 3 out of 4 in the Pold-Pcna-Dna (Form B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pold-Pcna-Dna (Form B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1402 b:0.2 occ:1.00 CB B:CYS1150 2.3 0.3 1.0 SG B:CYS1131 2.3 0.2 1.0 SG B:CYS1147 2.4 0.8 1.0 SG B:CYS1150 2.6 0.3 1.0 N B:CYS1150 3.0 0.3 1.0 CA B:CYS1150 3.1 0.3 1.0 CB B:CYS1131 3.2 0.2 1.0 SG B:CYS1134 3.4 0.7 1.0 CB B:CYS1147 3.5 0.8 1.0 O B:CYS1150 3.8 0.3 1.0 CB B:CYS1134 3.8 0.7 1.0 C B:CYS1150 3.8 0.3 1.0 C B:LYS1149 4.1 0.0 1.0 N B:CYS1134 4.1 0.7 1.0 CB B:LYS1149 4.3 0.0 1.0 CA B:CYS1134 4.6 0.7 1.0 CA B:LYS1149 4.6 0.0 1.0 CA B:CYS1131 4.7 0.2 1.0 CB B:LYS1133 4.7 0.5 1.0 N B:LYS1149 4.8 0.0 1.0 CG B:LYS1149 4.8 0.0 1.0 N B:GLY1151 4.9 0.6 1.0 CA B:CYS1147 4.9 0.8 1.0

Zinc binding site 4 out of 4 in the Pold-Pcna-Dna (Form B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pold-Pcna-Dna (Form B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1403 b:78.5 occ:1.00 SG B:CYS762 2.2 0.1 1.0 SG B:CYS759 2.2 0.4 1.0 SG B:CYS743 2.2 0.6 1.0 SG B:CYS740 2.5 0.0 1.0 CB B:CYS740 2.7 0.0 1.0 CB B:CYS743 3.0 0.6 1.0 CB B:CYS759 3.0 0.4 1.0 CB B:CYS762 3.7 0.1 1.0 N B:CYS743 3.7 0.6 1.0 CA B:CYS743 3.9 0.6 1.0 CA B:CYS740 4.2 0.0 1.0 N B:CYS762 4.3 0.1 1.0 CE2 B:TYR747 4.5 1.0 1.0 CA B:CYS759 4.5 0.4 1.0 OH B:TYR747 4.6 1.0 1.0 CA B:CYS762 4.6 0.1 1.0 C B:CYS740 4.7 0.0 1.0 C B:CYS743 4.7 0.6 1.0 O B:CYS762 4.8 0.1 1.0 O B:CYS740 4.9 0.0 1.0 C B:LYS742 4.9 0.0 1.0

K.Mayanagi, Y.Ishino. Molecular Architecture and Switching Mechanism of Dna Polymerase D in Replisome As Revealed By Cryo-Electron Microscopy To Be Published.