Sodium in PDB 9ich: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dgtp (1 Millimolar) and ZNCL2 (1 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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9ich 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 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.221, 57.678, 48.500, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar) also contains other interesting chemical elements:

Zinc

(Zn)

3 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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar) (pdb code 9ich). 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 Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9ich:
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 Dgtp (1 Millimolar) and ZNCL2 (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 Seven Base Pairs of Dna; Soaked in the Presence of Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:24.3 occ:1.00 O A:THR101 2.1 23.6 1.0 O A:HOH601 2.3 83.2 1.0 O A:VAL103 2.4 18.0 1.0 OP1 P:DT6 2.6 19.7 1.0 O A:ILE106 2.7 1.6 1.0 C A:VAL103 3.0 18.2 1.0 C A:THR101 3.2 19.2 1.0 N A:VAL103 3.4 18.5 1.0 C A:ARG102 3.5 21.1 1.0 N A:SER104 3.6 16.9 1.0 CA A:VAL103 3.7 18.6 1.0 C A:ILE106 3.8 1.3 1.0 P P:DT6 3.8 16.4 1.0 CA A:SER104 3.9 18.4 1.0 N A:ILE106 3.9 4.9 1.0 CA A:ARG102 4.0 20.1 1.0 O A:ARG102 4.0 20.3 1.0 N A:ARG102 4.0 16.5 1.0 CA A:THR101 4.2 15.0 1.0 OP2 P:DT6 4.2 25.4 1.0 CA A:ILE106 4.3 4.8 1.0 N A:GLY105 4.3 20.9 1.0 C A:SER104 4.4 18.0 1.0 CB A:ILE106 4.6 8.1 1.0 O5' P:DT6 4.6 14.8 1.0 O A:LEU100 4.8 23.6 1.0 N A:GLY107 4.9 4.4 1.0 CB A:VAL103 4.9 14.0 1.0 CG2 A:THR101 4.9 18.5 1.0 C A:GLY105 5.0 11.7 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 Dgtp (1 Millimolar) and ZNCL2 (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 Seven Base Pairs of Dna; Soaked in the Presence of Dgtp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:49.0 occ:1.00 O A:LEU62 2.4 35.4 1.0 O A:LYS60 3.3 26.2 1.0 O A:VAL65 3.3 23.0 1.0 C A:LEU62 3.5 29.9 1.0 CA A:PRO63 4.1 31.5 1.0 O A:LYS61 4.1 48.7 1.0 N A:PRO63 4.2 29.4 1.0 C A:LYS61 4.3 40.7 1.0 C A:VAL65 4.4 16.4 1.0 N A:GLY64 4.5 45.0 1.0 C A:LYS60 4.5 28.0 1.0 N A:LEU62 4.6 27.1 1.0 CA A:LEU62 4.6 24.0 1.0 N A:VAL65 4.8 17.9 1.0 CG2 A:VAL65 4.8 24.7 1.0 C A:PRO63 4.8 36.6 1.0 CA A:LYS61 5.0 44.2 1.0

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I