Sodium in PDB 7icu: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (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 CDCL2 (0.1 Millimolar), PDB code: 7icu 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 / 3.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.493, 57.682, 48.510, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / 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 CDCL2 (0.1 Millimolar) also contains other interesting chemical elements:

Cadmium

(Cd)

1 atom

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 CDCL2 (0.1 Millimolar) (pdb code 7icu). 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 CDCL2 (0.1 Millimolar), PDB code: 7icu:
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 CDCL2 (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 CDCL2 (0.1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:20.5 occ:1.00 O A:THR101 1.9 23.8 1.0 OP1 P:DG6 2.5 25.1 1.0 O A:VAL103 2.6 1.0 1.0 O A:ILE106 2.7 1.0 1.0 C A:THR101 3.2 15.4 1.0 C A:VAL103 3.3 1.0 1.0 O A:HOH601 3.3 85.1 1.0 P P:DG6 3.5 20.0 1.0 C A:ARG102 3.6 12.0 1.0 O A:ARG102 3.6 11.1 1.0 OP2 P:DG6 3.7 21.6 1.0 N A:VAL103 3.8 10.8 1.0 C A:ILE106 3.9 1.0 1.0 N A:ILE106 3.9 1.0 1.0 N A:SER104 3.9 2.5 1.0 CA A:SER104 3.9 15.1 1.0 CA A:ARG102 4.0 16.2 1.0 N A:ARG102 4.0 14.3 1.0 N A:GLY105 4.1 17.7 1.0 CA A:VAL103 4.1 8.0 1.0 CA A:THR101 4.2 8.4 1.0 O5' P:DG6 4.4 23.8 1.0 CA A:ILE106 4.4 1.0 1.0 C A:SER104 4.5 18.9 1.0 CG2 A:THR101 4.6 15.4 1.0 CB A:ILE106 4.8 9.1 1.0 O3' P:DT5 4.8 18.5 1.0 C A:GLY105 4.8 7.5 1.0 CB A:THR101 4.9 14.5 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 CDCL2 (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 CDCL2 (0.1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:35.4 occ:1.00 OP2 P:DG3 2.8 48.8 1.0 OP1 P:DG3 3.5 44.6 1.0 P P:DG3 3.7 46.3 1.0 O P:HOH615 4.2 86.2 1.0 O5' P:DG3 4.8 44.9 1.0 O3' P:DA2 4.8 33.5 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