Zinc in PDB 7icp: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar), PDB code: 7icp was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.810, 57.743, 48.517, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / n/a

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar) (pdb code 7icp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar), PDB code: 7icp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn340 b:0.0 occ:1.00 OD1 A:ASP192 3.0 59.5 1.0 CG A:ASP192 3.4 45.9 1.0 CG A:ASP190 3.5 39.3 1.0 OD2 A:ASP256 3.7 28.8 1.0 O A:HOH549 3.7 74.8 1.0 OD2 A:ASP190 3.8 49.3 1.0 OD1 A:ASP190 3.8 46.3 1.0 CB A:ASP192 3.8 29.9 1.0 CB A:ASP190 3.9 16.2 1.0 OD2 A:ASP192 4.0 44.2 1.0 O A:HOH661 4.1 40.4 1.0 CG A:ASP256 4.3 22.4 1.0 CA A:ASP192 4.6 17.4 1.0 N A:ASP192 4.6 13.0 1.0 CB A:ASP256 4.7 11.3 1.0 C A:MET191 4.8 12.6 1.0 O A:MET191 4.9 17.0 1.0 NH1 A:ARG258 4.9 79.1 1.0

Zinc binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of ZNCL2 (0.01 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn343 b:93.7 occ:1.00 ND1 A:HIS51 2.7 44.5 1.0 CG A:HIS51 3.2 46.5 1.0 CB A:HIS51 3.3 42.1 1.0 CE1 A:HIS51 3.6 43.0 1.0 CD2 A:HIS51 4.2 44.9 1.0 CA A:HIS51 4.3 31.5 1.0 NE2 A:HIS51 4.4 43.2 1.0 N A:LYS52 4.7 29.3 1.0

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta. Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566