Calcium in PDB 6v93: Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex

All present enzymatic activity of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex:
2.7.7.7;

The structure of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Calcium atom in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex (pdb code 6v93). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex, PDB code: 6v93:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1602 b:50.7 occ:1.00 O A:PHE976 2.4 42.0 1.0 O2B A:DCP1604 2.4 45.9 1.0 OD1 A:ASP975 2.4 48.1 1.0 O1A A:DCP1604 2.4 45.9 1.0 O2G A:DCP1604 2.5 45.9 1.0 OD2 A:ASP1144 2.6 47.5 1.0 CG A:ASP975 3.0 48.1 1.0 OD2 A:ASP975 3.0 48.1 1.0 CG A:ASP1144 3.6 47.5 1.0 PB A:DCP1604 3.6 45.9 1.0 C A:PHE976 3.6 42.0 1.0 O A:HOH1749 3.6 43.7 1.0 PA A:DCP1604 3.7 45.9 1.0 PG A:DCP1604 3.7 45.9 1.0 O3A A:DCP1604 4.0 45.9 1.0 O3B A:DCP1604 4.1 45.9 1.0 O A:HOH1745 4.1 42.8 1.0 CB A:ASP1144 4.1 47.5 1.0 O3G A:DCP1604 4.2 45.9 1.0 N A:PHE976 4.2 42.0 1.0 C5' A:DCP1604 4.2 45.9 1.0 CA A:CA1603 4.4 58.1 1.0 CB A:ASP975 4.4 48.1 1.0 CA A:PHE976 4.4 42.0 1.0 O5' A:DCP1604 4.5 45.9 1.0 OD1 A:ASP1144 4.5 47.5 1.0 N A:GLN977 4.6 46.0 1.0 CA A:GLN977 4.7 46.0 1.0 C A:ASP975 4.7 48.1 1.0 O2A A:DCP1604 4.8 45.9 1.0 N A:SER978 4.8 45.0 1.0 O1B A:DCP1604 4.9 45.9 1.0 CB A:PHE976 4.9 42.0 1.0 CA A:ASP975 4.9 48.1 1.0 O1G A:DCP1604 4.9 45.9 1.0

Calcium binding site 2 out of 2 in the Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Dna Polymerase Zeta/Dna/Dntp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1603 b:58.1 occ:1.00 O A:HOH1749 2.5 43.7 1.0 O A:HOH1710 2.6 48.5 1.0 OD1 A:ASP1144 2.8 47.5 1.0 OG A:SER1145 2.9 46.0 1.0 OD2 A:ASP1144 3.1 47.5 1.0 C5' P:DC115 3.2 48.0 1.0 CG A:ASP1144 3.3 47.5 1.0 OD2 A:ASP975 3.7 48.1 1.0 OD1 A:ASP975 3.7 48.1 1.0 C4' P:DC115 3.8 48.0 1.0 CG A:ASP975 3.9 48.1 1.0 O1A A:DCP1604 3.9 45.9 1.0 C3' P:DC115 4.0 48.0 1.0 CB A:SER1145 4.3 46.0 1.0 O5' P:DC115 4.3 48.0 1.0 OP1 P:DC115 4.4 48.0 1.0 CA A:CA1602 4.4 50.7 1.0 O A:ASP1142 4.6 50.2 1.0 P P:DC115 4.7 48.0 1.0 OP2 P:DC115 4.7 48.0 1.0 O A:HOH1745 4.7 42.8 1.0 CB A:ASP1144 4.8 47.5 1.0 N A:SER1145 4.8 46.0 1.0 CB A:ASP975 4.9 48.1 1.0

R.Malik, M.Kopylov, Y.Gomez-Llorente, R.Jain, R.E.Johnson, L.Prakash, S.Prakash, I.Ubarretxena-Belandia, A.K.Aggarwal. Structure and Mechanism of B-Family Dna Polymerase Zeta Specialized For Translesion Dna Synthesis. Nat.Struct.Mol.Biol. V. 27 913 2020.
ISSN: ESSN 1545-9985
PubMed: 32807989
DOI: 10.1038/S41594-020-0476-7