Nickel in PDB 8icl: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar), PDB code: 8icl 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 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.721, 57.784, 48.382, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / n/a

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Nickel atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) (pdb code 8icl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar), PDB code: 8icl:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni339 b:30.0 occ:0.53 O1A A:DTP338 1.4 84.4 0.5 O1G A:DTP338 2.5 4.1 0.5 OD1 A:ASP190 2.6 30.4 1.0 PA A:DTP338 2.8 0.0 0.5 O2B A:DTP338 3.1 0.0 0.5 O3G A:DTP338 3.1 60.5 0.5 PG A:DTP338 3.2 30.9 0.5 NI A:NI340 3.2 30.0 0.5 O3B A:DTP338 3.3 71.0 0.5 O3A A:DTP338 3.4 85.9 0.5 OD2 A:ASP192 3.4 37.6 1.0 O A:HOH658 3.4 26.0 0.5 O A:ASP190 3.5 28.4 1.0 PB A:DTP338 3.5 93.2 0.5 CG A:ASP190 3.6 33.9 1.0 O5' A:DTP338 3.7 78.0 0.5 O2A A:DTP338 3.8 93.1 0.5 N A:ASP190 4.3 28.2 1.0 C A:ASP190 4.4 22.2 1.0 OD2 A:ASP190 4.4 48.6 1.0 O A:HOH502 4.6 8.7 1.0 O2G A:DTP338 4.6 80.8 0.5 CA A:ASP190 4.6 22.6 1.0 CB A:ASP190 4.7 25.6 1.0 CG A:ASP192 4.7 42.0 1.0 O1B A:DTP338 5.0 79.9 0.5

Nickel binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni340 b:30.0 occ:0.47 O3' P:DG7 2.2 0.0 1.0 OD2 A:ASP190 2.9 48.6 1.0 O1A A:DTP338 2.9 84.4 0.5 OD2 A:ASP192 3.0 37.6 1.0 OD1 A:ASP190 3.1 30.4 1.0 NI A:NI339 3.2 30.0 0.5 C3' P:DG7 3.3 0.0 1.0 CG A:ASP190 3.3 33.9 1.0 O A:HOH658 3.5 26.0 0.5 PA A:DTP338 3.7 0.0 0.5 OD1 A:ASP192 3.7 47.4 1.0 CG A:ASP192 3.8 42.0 1.0 O2A A:DTP338 3.8 93.1 0.5 C4' P:DG7 4.0 0.0 1.0 O5' A:DTP338 4.2 78.0 0.5 OD2 A:ASP256 4.3 32.2 1.0 C5' P:DG7 4.5 0.0 1.0 C2' P:DG7 4.6 0.0 1.0 CB A:ASP190 4.7 25.6 1.0 O5' P:DG7 4.7 0.0 1.0 O A:ASP190 5.0 28.4 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