Sodium 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:

Nickel

(Ni)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2, PDB code: 1zqr:

Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na341 b:60.8 occ:1.00 O A:THR101 1.5 9.2 1.0 O P:HOH588 2.4 0.0 1.0 O A:ILE106 2.4 8.8 1.0 C A:THR101 2.6 15.2 1.0 OP1 P:DT6 3.0 23.3 1.0 N A:ARG102 3.5 22.1 1.0 O A:VAL103 3.5 1.0 1.0 C A:ILE106 3.5 15.0 1.0 CA A:THR101 3.6 20.5 1.0 CA A:ARG102 3.8 39.4 1.0 N A:VAL103 3.8 46.1 1.0 C A:ARG102 3.8 52.9 1.0 C A:VAL103 3.9 5.5 1.0 P P:DT6 3.9 17.9 1.0 OP2 P:DT6 3.9 32.1 1.0 CG2 A:THR101 4.0 33.9 1.0 CA A:ILE106 4.2 10.8 1.0 CB A:THR101 4.3 28.9 1.0 N A:ILE106 4.3 11.6 1.0 CB A:ILE106 4.4 2.1 1.0 O A:ARG102 4.4 67.8 1.0 N A:SER104 4.4 1.0 1.0 CA A:VAL103 4.5 25.4 1.0 O A:LEU100 4.6 15.9 1.0 CA A:SER104 4.6 3.5 1.0 N A:GLY107 4.6 19.2 1.0 CG2 A:ILE106 4.7 1.0 1.0 N A:THR101 4.8 19.0 1.0 O5' P:DT6 4.9 6.8 1.0 N A:GLY105 4.9 3.9 1.0 OG1 A:THR101 5.0 23.7 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