Sodium in PDB 7icf: 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) (Four-Day Soak)

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) (Four-Day Soak), PDB code: 7icf 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 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	177.179, 57.710, 48.519, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 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) (Four-Day Soak) also contains other interesting chemical elements:

Cadmium

(Cd)

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 CDCL2 (0.1 Millimolar) (Four-Day Soak) (pdb code 7icf). 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) (Four-Day Soak), PDB code: 7icf:
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) (Four-Day Soak)


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) (Four-Day Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:29.9 occ:1.00 O A:THR101 1.9 22.6 1.0 OP1 P:DG6 2.5 29.8 1.0 O A:VAL103 2.5 4.4 1.0 O A:ILE106 2.7 1.0 1.0 OP2 P:DG6 3.1 19.3 1.0 C A:THR101 3.1 18.5 1.0 O A:HOH601 3.1 81.6 1.0 P P:DG6 3.2 20.6 1.0 C A:VAL103 3.5 5.0 1.0 C A:ILE106 3.7 1.0 1.0 N A:ILE106 3.8 1.0 1.0 CA A:THR101 3.9 8.8 1.0 N A:VAL103 4.0 32.2 1.0 N A:GLY105 4.0 24.6 1.0 C A:ARG102 4.1 30.5 1.0 N A:ARG102 4.2 21.7 1.0 O3' P:DT5 4.2 19.5 1.0 CA A:VAL103 4.3 16.6 1.0 CA A:ILE106 4.3 1.0 1.0 N A:SER104 4.3 5.4 1.0 CA A:SER104 4.3 13.6 1.0 CG2 A:THR101 4.4 14.4 1.0 O5' P:DG6 4.5 23.0 1.0 CA A:ARG102 4.5 21.0 1.0 O A:ARG102 4.5 33.5 1.0 C A:GLY105 4.6 12.2 1.0 CB A:ILE106 4.6 3.1 1.0 N A:GLY107 4.7 1.0 1.0 CB A:THR101 4.7 16.2 1.0 CA A:GLY107 4.7 1.1 1.0 C A:SER104 4.8 22.5 1.0 CA A:GLY105 4.8 18.6 1.0 O A:LEU100 4.9 29.6 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 CDCL2 (0.1 Millimolar) (Four-Day Soak)


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) (Four-Day Soak) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:23.0 occ:1.00 OP2 P:DG3 2.7 37.3 1.0 P P:DG3 3.7 41.3 1.0 OP1 P:DG3 3.8 42.4 1.0 O P:HOH615 3.9 89.1 1.0 O5' P:DG3 4.8 45.2 1.0 O3' P:DA2 4.9 29.8 1.0 O P:HOH570 4.9 53.9 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