Sodium in PDB 9icg: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (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 Dctp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9icg 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 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.890, 57.600, 48.430, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 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 Dctp (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 Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) (pdb code 9icg). 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 Dctp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9icg:
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 Dctp (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 Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:7.7 occ:1.00 O A:THR101 2.0 18.7 1.0 O A:HOH601 2.0 25.9 1.0 O A:VAL103 2.3 1.7 1.0 OP1 P:DT6 2.6 24.6 1.0 O A:ILE106 2.8 1.0 1.0 C A:VAL103 3.0 9.8 1.0 C A:THR101 3.1 7.4 1.0 N A:VAL103 3.5 16.5 1.0 N A:ILE106 3.6 2.1 1.0 C A:ARG102 3.6 17.5 1.0 N A:SER104 3.6 12.9 1.0 C A:ILE106 3.7 1.0 1.0 CA A:SER104 3.8 4.7 1.0 P P:DT6 3.8 11.6 1.0 CA A:VAL103 3.9 9.0 1.0 N A:ARG102 3.9 1.0 1.0 N A:GLY105 3.9 1.1 1.0 CA A:ARG102 4.0 10.0 1.0 CA A:ILE106 4.0 1.0 1.0 O A:ARG102 4.0 20.4 1.0 CA A:THR101 4.1 1.0 1.0 C A:SER104 4.2 1.0 1.0 OP2 P:DT6 4.3 15.1 1.0 CB A:ILE106 4.4 2.8 1.0 O5' P:DT6 4.5 11.8 1.0 C A:GLY105 4.6 1.0 1.0 CB A:VAL103 4.7 9.0 1.0 O A:LEU100 4.7 1.0 1.0 N A:GLY107 4.8 1.0 1.0 CB A:THR101 4.8 9.4 1.0 CA A:GLY105 4.9 1.0 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 Dctp (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 Dctp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:46.0 occ:1.00 O P:HOH615 4.0 28.4 1.0 OP1 P:DT3 4.0 32.1 1.0 OP2 P:DT3 4.4 32.2 1.0 P P:DT3 4.7 40.5 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