Nickel in PDB 1zqr: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2, PDB code: 1zqr 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 / 3.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.686, 57.501, 47.920, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Nickel atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 (pdb code 1zqr). 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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2, PDB code: 1zqr:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2


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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni340 b:31.7 occ:1.00 OD1 A:ASP192 2.3 50.5 1.0 CG A:ASP192 2.8 49.0 1.0 CB A:ASP192 2.9 46.3 1.0 OD2 A:ASP190 3.0 21.6 1.0 CG A:ASP190 3.3 23.8 1.0 O A:MET191 3.4 20.6 1.0 CA A:ASP192 3.4 42.0 1.0 OD1 A:ASP190 3.4 26.9 1.0 C A:MET191 3.6 27.0 1.0 N A:ASP192 3.6 33.6 1.0 O3' P:DG7 3.9 86.9 1.0 OD2 A:ASP192 4.0 49.4 1.0 O A:ASP190 4.1 31.5 1.0 O A:HOH639 4.2 46.2 1.0 CB A:ASP190 4.4 22.0 1.0 C A:ASP190 4.4 27.6 1.0 CB A:ASP256 4.5 27.8 1.0 OD2 A:ASP256 4.6 43.2 1.0 O A:HOH502 4.6 1.0 1.0 CA A:MET191 4.6 32.1 1.0 N A:MET191 4.7 29.4 1.0 CG A:ASP256 4.7 34.6 1.0 C3' P:DG7 4.8 86.2 1.0 C A:ASP192 4.8 37.7 1.0 NH1 A:ARG258 5.0 92.7 1.0

Nickel binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2


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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni343 b:29.3 occ:1.00 ND1 A:HIS134 2.6 64.2 1.0 O A:HOH516 2.7 1.0 1.0 CE1 A:HIS134 3.0 66.7 1.0 CG A:HIS134 3.2 59.3 1.0 O A:HOH515 3.3 1.0 1.0 NE2 A:HIS134 3.7 65.8 1.0 CD2 A:HIS134 3.8 64.2 1.0 CB A:HIS134 3.8 46.9 1.0 O A:HOH509 4.7 87.5 1.0 CA A:HIS134 4.8 35.0 1.0

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I