Sodium in PDB 9ick: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Artificial Mother Liquor

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Artificial Mother Liquor, PDB code: 9ick 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.540, 57.726, 48.473, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / n/a

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Artificial Mother Liquor (pdb code 9ick). 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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Artificial Mother Liquor, PDB code: 9ick:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Artificial Mother Liquor


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 Artificial Mother Liquor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:34.6 occ:1.00 O A:THR101 2.2 30.1 1.0 OP1 P:DG6 2.3 31.3 1.0 O A:VAL103 2.3 23.0 1.0 O A:ILE106 2.4 19.7 1.0 C A:VAL103 3.2 20.2 1.0 C A:THR101 3.3 19.4 1.0 O A:HOH601 3.3 86.3 1.0 C A:ILE106 3.4 12.5 1.0 P P:DG6 3.6 26.9 1.0 N A:ILE106 3.6 13.8 1.0 N A:VAL103 3.8 21.1 1.0 C A:ARG102 3.9 25.1 1.0 CA A:ILE106 4.0 12.6 1.0 N A:GLY105 4.0 20.6 1.0 N A:SER104 4.0 16.4 1.0 CA A:SER104 4.0 18.5 1.0 OP2 P:DG6 4.0 36.4 1.0 CA A:THR101 4.1 15.1 1.0 CA A:VAL103 4.1 24.9 1.0 N A:ARG102 4.2 20.3 1.0 O A:ARG102 4.2 33.3 1.0 C A:SER104 4.3 22.1 1.0 CA A:ARG102 4.3 20.4 1.0 CB A:ILE106 4.4 12.6 1.0 N A:GLY107 4.5 10.7 1.0 O5' P:DG6 4.5 20.7 1.0 O3' P:DT5 4.6 29.2 1.0 C A:GLY105 4.6 19.8 1.0 O A:LEU100 4.6 24.7 1.0 CA A:GLY107 4.9 6.5 1.0 CG2 A:THR101 4.9 19.1 1.0 CA A:GLY105 4.9 20.4 1.0 CB A:THR101 5.0 24.5 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Artificial Mother Liquor


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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Artificial Mother Liquor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:57.5 occ:1.00 OP1 P:DG3 3.5 39.0 1.0 OP2 P:DG3 4.0 42.9 1.0 P P:DG3 4.2 45.5 1.0 O P:HOH615 4.5 84.9 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