Sodium in PDB 9ice: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CUCL2 (0.1 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 Datp (1 Millimolar) and CUCL2 (0.1 Millimolar), PDB code: 9ice 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 / 3.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.839, 57.871, 48.625, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / n/a

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 Datp (1 Millimolar) and CUCL2 (0.1 Millimolar) (pdb code 9ice). 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 Datp (1 Millimolar) and CUCL2 (0.1 Millimolar), PDB code: 9ice:
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 Datp (1 Millimolar) and CUCL2 (0.1 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 Datp (1 Millimolar) and CUCL2 (0.1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:1.0 occ:1.00 O A:VAL103 2.3 11.0 1.0 O A:THR101 2.3 7.1 1.0 OP1 P:DT6 2.4 17.5 1.0 O A:ILE106 2.6 1.0 1.0 C A:VAL103 2.9 15.5 1.0 O A:HOH601 3.2 37.7 1.0 C A:THR101 3.4 12.4 1.0 P P:DT6 3.4 17.7 1.0 N A:ILE106 3.6 6.2 1.0 N A:VAL103 3.6 33.1 1.0 C A:ILE106 3.6 3.1 1.0 N A:SER104 3.6 16.2 1.0 OP2 P:DT6 3.7 14.5 1.0 C A:ARG102 3.7 34.3 1.0 CA A:SER104 3.8 24.8 1.0 CA A:VAL103 3.8 24.4 1.0 CA A:ILE106 4.0 4.9 1.0 O A:ARG102 4.0 31.3 1.0 N A:GLY105 4.1 22.5 1.0 CA A:THR101 4.3 16.1 1.0 CB A:ILE106 4.3 12.4 1.0 N A:ARG102 4.3 17.0 1.0 C A:SER104 4.3 23.1 1.0 CA A:ARG102 4.3 30.4 1.0 O5' P:DT6 4.5 21.6 1.0 O3' P:DA5 4.6 20.9 1.0 C A:GLY105 4.6 14.0 1.0 N A:GLY107 4.8 12.8 1.0 O A:LEU100 4.8 18.5 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 Datp (1 Millimolar) and CUCL2 (0.1 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 Datp (1 Millimolar) and CUCL2 (0.1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:24.9 occ:1.00 O A:LEU62 2.2 34.9 1.0 O A:LYS60 2.6 31.8 1.0 C A:LEU62 2.7 34.2 1.0 C A:LYS61 3.1 26.2 1.0 N A:LEU62 3.1 22.0 1.0 O A:LYS61 3.3 20.8 1.0 CA A:LEU62 3.3 29.2 1.0 O A:VAL65 3.6 8.7 1.0 N A:PRO63 3.6 35.9 1.0 C A:LYS60 3.7 36.8 1.0 CA A:LYS61 3.8 35.1 1.0 CA A:PRO63 4.0 33.5 1.0 N A:LYS61 4.2 36.7 1.0 CG2 A:VAL65 4.3 14.7 1.0 C A:VAL65 4.6 11.0 1.0 C A:PRO63 4.7 37.8 1.0 CB A:LEU62 4.7 31.9 1.0 N A:GLY64 4.8 49.5 1.0 N A:VAL65 4.8 25.3 1.0 CD A:PRO63 4.9 39.5 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