Sodium 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:

Zinc

(Zn)

2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium 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 Sodium binding site number: 1; 2;

Sodium 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 Sodium with other atoms in the Na 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:Na341 b:9.7 occ:1.00 OP1 P:DG6 2.4 10.8 1.0 O A:ILE106 2.4 2.6 1.0 O A:VAL103 2.5 16.1 1.0 O A:THR101 2.5 2.0 1.0 O A:HOH601 2.9 0.0 1.0 OP2 P:DG6 3.0 20.8 1.0 C A:ILE106 3.1 1.0 1.0 P P:DG6 3.1 14.3 1.0 N A:ILE106 3.4 1.2 1.0 C A:VAL103 3.5 15.5 1.0 C A:THR101 3.6 8.0 1.0 CA A:ILE106 3.7 5.0 1.0 N A:GLY107 3.9 4.4 1.0 N A:GLY105 4.0 6.9 1.0 CA A:SER104 4.2 12.3 1.0 CA A:GLY107 4.2 1.0 1.0 O3' P:DT5 4.2 11.6 1.0 N A:SER104 4.2 10.5 1.0 CA A:THR101 4.2 10.1 1.0 C A:GLY105 4.3 9.5 1.0 C A:SER104 4.3 11.5 1.0 CB A:ILE106 4.3 10.6 1.0 N A:VAL103 4.3 27.2 1.0 O5' P:DG6 4.4 14.6 1.0 CA A:VAL103 4.5 22.8 1.0 C A:ARG102 4.6 21.4 1.0 N A:ARG102 4.7 10.1 1.0 CA A:GLY105 4.7 10.6 1.0 O A:ARG102 4.9 24.0 1.0 CB A:THR101 5.0 19.0 1.0 CG2 A:THR101 5.0 15.2 1.0 O A:LEU100 5.0 18.9 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na342 b:22.1 occ:1.00 OP2 P:DG3 3.8 52.3 1.0 OP1 P:DG3 3.8 35.7 1.0 O P:HOH615 4.2 71.5 1.0 P P:DG3 4.3 46.8 1.0 O P:HOH570 5.0 56.3 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