Sodium in PDB 7ici: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of CRCL3 (0.1 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 CRCL3 (0.1 Millimolar), PDB code: 7ici 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 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.539, 57.708, 48.489, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / n/a

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 CRCL3 (0.1 Millimolar) (pdb code 7ici). 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 CRCL3 (0.1 Millimolar), PDB code: 7ici:
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 CRCL3 (0.1 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 CRCL3 (0.1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:22.0 occ:1.00 O A:ILE106 2.2 10.1 1.0 O A:THR101 2.4 18.3 1.0 OP1 P:DG6 2.4 25.0 1.0 O A:VAL103 2.5 12.4 1.0 OP2 P:DG6 3.1 30.6 1.0 P P:DG6 3.2 24.9 1.0 C A:ILE106 3.3 5.8 1.0 O A:HOH601 3.3 85.1 1.0 C A:THR101 3.5 16.2 1.0 C A:VAL103 3.6 16.8 1.0 N A:ILE106 3.7 12.7 1.0 N A:GLY105 3.8 11.2 1.0 CA A:ILE106 4.1 7.1 1.0 CA A:THR101 4.1 12.7 1.0 CA A:SER104 4.1 15.2 1.0 O3' P:DT5 4.3 31.2 1.0 N A:GLY107 4.3 9.2 1.0 N A:SER104 4.3 13.1 1.0 N A:VAL103 4.3 21.1 1.0 O5' P:DG6 4.3 16.2 1.0 C A:SER104 4.4 13.0 1.0 C A:GLY105 4.5 17.1 1.0 C A:ARG102 4.5 21.1 1.0 CA A:GLY107 4.5 8.4 1.0 CA A:VAL103 4.6 22.9 1.0 N A:ARG102 4.6 17.6 1.0 CB A:ILE106 4.6 11.1 1.0 CA A:GLY105 4.7 15.8 1.0 CG2 A:THR101 4.8 26.8 1.0 CA A:ARG102 4.8 16.4 1.0 O A:ARG102 4.8 25.4 1.0 O A:LEU100 4.9 22.8 1.0 CB A:THR101 4.9 21.6 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 CRCL3 (0.1 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 CRCL3 (0.1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:46.8 occ:1.00 OP1 P:DG3 3.6 42.0 1.0 OP2 P:DG3 4.0 44.6 1.0 O P:HOH615 4.1 80.4 1.0 P P:DG3 4.3 51.6 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