Zinc in PDB 6knb: Pold-Pcna-Dna (Form A)

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

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

Iron

(Fe)

1 atom

The binding sites of Zinc atom in the Pold-Pcna-Dna (Form A) (pdb code 6knb). 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 A), PDB code: 6knb:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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 A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn802 b:0.8 occ:1.00 OD1 A:ASP473 2.0 21.1 1.0 OD1 A:ASN563 2.0 10.2 1.0 OD2 A:ASP517 2.3 21.5 1.0 ND1 A:HIS673 2.3 28.9 1.0 NE2 A:HIS610 2.3 11.3 1.0 CG A:ASN563 2.5 10.2 1.0 ND2 A:ASN563 2.5 10.2 1.0 CE1 A:HIS610 2.8 11.3 1.0 CG A:HIS673 2.8 28.9 1.0 CB A:HIS673 3.0 28.9 1.0 CG A:ASP473 3.2 21.1 1.0 CE1 A:HIS673 3.3 28.9 1.0 CG A:ASP517 3.4 21.5 1.0 FE A:FE801 3.5 86.2 1.0 CD2 A:HIS610 3.5 11.3 1.0 CA A:HIS673 3.6 28.9 1.0 N A:HIS673 3.7 28.9 1.0 OD2 A:ASP473 3.7 21.1 1.0 CB A:ASN563 3.9 10.2 1.0 CD2 A:HIS673 4.0 28.9 1.0 OD1 A:ASP517 4.0 21.5 1.0 ND1 A:HIS610 4.1 11.3 1.0 ND1 A:HIS564 4.1 7.8 1.0 NE2 A:HIS673 4.2 28.9 1.0 CE1 A:HIS475 4.4 21.8 1.0 CB A:ASP473 4.4 21.1 1.0 CG A:HIS610 4.4 11.3 1.0 C A:GLY672 4.4 16.7 1.0 NE2 A:HIS475 4.5 21.8 1.0 N A:ASN563 4.5 10.2 1.0 CE1 A:HIS564 4.6 7.8 1.0 CB A:ASP517 4.6 21.5 1.0 CA A:ASN563 4.8 10.2 1.0 N A:HIS564 4.9 7.8 1.0 CA A:ASP473 4.9 21.1 1.0

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


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 A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1401 b:0.9 occ:1.00 SG B:CYS718 2.2 41.2 1.0 SG B:CYS730 2.3 76.3 1.0 SG B:CYS727 2.3 85.3 1.0 SG B:CYS715 2.3 33.8 1.0 CB B:CYS715 2.9 33.8 1.0 CB B:CYS718 3.1 41.2 1.0 CB B:CYS727 3.2 85.3 1.0 CB B:CYS730 3.5 76.3 1.0 N B:CYS718 3.9 41.2 1.0 CA B:CYS718 4.1 41.2 1.0 N B:CYS730 4.1 76.3 1.0 CA B:CYS715 4.3 33.8 1.0 CA B:CYS730 4.4 76.3 1.0 CA B:CYS727 4.7 85.3 1.0 N B:GLY719 4.7 26.5 1.0 C B:CYS718 4.9 41.2 1.0 OG1 B:THR732 4.9 47.3 1.0

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


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 A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1402 b:0.9 occ:1.00 CB B:CYS1134 1.6 14.8 1.0 SG B:CYS1150 2.3 10.1 1.0 SG B:CYS1147 2.3 7.2 1.0 SG B:CYS1131 2.4 12.8 1.0 SG B:CYS1134 2.4 14.8 1.0 CA B:CYS1134 3.0 14.8 1.0 CB B:CYS1131 3.0 12.8 1.0 N B:CYS1134 3.5 14.8 1.0 CB B:CYS1147 3.7 7.2 1.0 O B:CYS1134 3.9 14.8 1.0 CB B:CYS1150 3.9 10.1 1.0 C B:CYS1134 3.9 14.8 1.0 NH2 B:ARG1139 4.1 8.1 1.0 CB B:LYS1149 4.4 7.2 1.0 N B:CYS1150 4.4 10.1 1.0 CA B:CYS1131 4.5 12.8 1.0 C B:LYS1149 4.6 7.2 1.0 CB B:LYS1137 4.7 11.8 1.0 CA B:CYS1150 4.8 10.1 1.0 C B:LYS1133 4.8 8.1 1.0 O B:LYS1137 4.9 11.8 1.0 CA B:LYS1149 4.9 7.2 1.0

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


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 A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1403 b:94.4 occ:1.00 SG B:CYS762 2.2 47.0 1.0 SG B:CYS743 2.3 53.0 1.0 SG B:CYS740 2.3 44.6 1.0 SG B:CYS759 2.3 50.5 1.0 CB B:CYS740 2.5 44.6 1.0 CB B:CYS759 2.6 50.5 1.0 CB B:CYS743 3.6 53.0 1.0 O B:CYS762 3.7 47.0 1.0 N B:CYS762 3.8 47.0 1.0 CB B:CYS762 3.8 47.0 1.0 CA B:CYS740 4.0 44.6 1.0 CA B:CYS759 4.1 50.5 1.0 CA B:CYS762 4.2 47.0 1.0 C B:CYS762 4.5 47.0 1.0 CB B:LYS761 4.5 47.7 1.0 N B:CYS743 4.6 53.0 1.0 CA B:CYS743 4.6 53.0 1.0 CB B:ALA745 4.6 29.1 1.0 C B:CYS759 4.7 50.5 1.0 N B:CYS740 4.7 44.6 1.0 C B:CYS740 4.8 44.6 1.0 C B:LYS761 4.8 47.7 1.0 N B:LYS761 4.9 47.7 1.0 O B:CYS759 4.9 50.5 1.0 N B:CYS759 4.9 50.5 1.0 O B:CYS740 5.0 44.6 1.0 CA B:LYS761 5.0 47.7 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.