Sodium in PDB 8ico: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8ico 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 (°)	179.687, 57.631, 48.285, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / n/a

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar) also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8ico). 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 Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8ico:
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 Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 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 Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:23.3 occ:1.00 O A:VAL103 2.2 22.5 1.0 O A:THR101 2.3 21.5 1.0 O A:ILE106 2.3 13.0 1.0 O A:HOH601 2.4 59.6 1.0 OP1 P:DT6 2.5 20.0 1.0 C A:VAL103 3.2 16.0 1.0 C A:THR101 3.2 14.8 1.0 C A:ILE106 3.5 7.2 1.0 N A:VAL103 3.6 28.1 1.0 N A:ILE106 3.7 7.0 1.0 C A:ARG102 3.7 26.1 1.0 P P:DT6 3.8 19.8 1.0 N A:ARG102 4.0 17.5 1.0 CA A:SER104 4.0 14.7 1.0 N A:SER104 4.0 8.8 1.0 N A:GLY105 4.0 17.1 1.0 CA A:ARG102 4.0 22.4 1.0 CA A:VAL103 4.0 23.3 1.0 CA A:ILE106 4.1 4.0 1.0 CA A:THR101 4.1 15.1 1.0 O A:ARG102 4.2 31.1 1.0 OP2 P:DT6 4.3 13.2 1.0 CB A:ILE106 4.3 8.1 1.0 C A:SER104 4.3 16.3 1.0 N A:GLY107 4.5 8.5 1.0 O A:LEU100 4.6 25.0 1.0 C A:GLY105 4.6 13.0 1.0 O5' P:DT6 4.8 17.1 1.0 O3' P:DA5 4.8 16.5 1.0 CG2 A:THR101 4.9 5.7 1.0 CA A:GLY107 4.9 7.6 1.0 CA A:GLY105 4.9 10.0 1.0 CB A:VAL103 5.0 15.2 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 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 Seven Base Pairs of Dna; Soaked in the Presence of Azt-Tp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:65.2 occ:1.00 O A:LEU62 2.5 44.8 1.0 O A:LYS60 2.8 44.5 1.0 O A:VAL65 3.3 25.7 1.0 C A:LEU62 3.4 42.1 1.0 O A:LYS61 3.7 44.7 1.0 C A:LYS61 3.8 42.4 1.0 C A:LYS60 4.0 39.9 1.0 N A:PRO63 4.1 41.8 1.0 N A:LEU62 4.1 38.3 1.0 CA A:PRO63 4.2 40.7 1.0 CA A:LYS61 4.3 41.3 1.0 C A:VAL65 4.4 15.7 1.0 CA A:LEU62 4.4 36.0 1.0 N A:VAL65 4.5 28.9 1.0 N A:LYS61 4.6 37.3 1.0 N A:GLY64 4.6 45.3 1.0 C A:PRO63 4.8 46.9 1.0 CA A:VAL65 5.0 17.1 1.0 CG2 A:VAL65 5.0 21.0 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