Zinc in PDB 7ico: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2, PDB code: 7ico 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 / 3.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.143, 57.535, 48.490, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 (pdb code 7ico). 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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2, PDB code: 7ico:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2


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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn340 b:67.0 occ:1.00 OD1 A:ASP256 2.6 44.1 1.0 O A:HOH632 3.0 51.3 1.0 OD1 A:ASP190 3.1 44.1 1.0 CG A:ASP190 3.3 40.3 1.0 CG A:ASP192 3.5 25.5 1.0 OD2 A:ASP192 3.5 27.6 1.0 CB A:ASP192 3.6 14.7 1.0 OD2 A:ASP190 3.6 45.8 1.0 CG A:ASP256 3.8 39.0 1.0 OD1 A:ASP192 4.1 30.1 1.0 CB A:ASP190 4.2 29.8 1.0 OD2 A:ASP256 4.2 37.7 1.0 CA A:ASP192 4.5 9.4 1.0 O A:HOH586 4.6 30.2 1.0 O A:HOH619 4.7 68.3 1.0 N A:ASP192 4.8 17.1 1.0 O A:MET191 5.0 19.9 1.0

Zinc binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2


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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn343 b:73.7 occ:1.00 ND1 A:HIS51 2.2 49.7 1.0 CG A:HIS51 2.8 43.9 1.0 CB A:HIS51 2.8 41.4 1.0 CA A:HIS51 3.1 30.7 1.0 N A:LYS52 3.3 45.9 1.0 CE1 A:HIS51 3.4 49.4 1.0 C A:HIS51 3.8 30.3 1.0 CD2 A:HIS51 4.0 39.3 1.0 NE2 A:HIS51 4.2 46.7 1.0 N A:HIS51 4.2 27.2 1.0 O A:PRO50 4.2 36.7 1.0 CA A:LYS52 4.5 54.2 1.0 C A:PRO50 4.6 35.1 1.0 CB A:LYS52 4.6 63.7 1.0 O A:HIS51 5.0 16.9 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