Sodium in PDB 8ica: 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 CACL2 (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 Datp (1 Millimolar) and CACL2 (5 Millimolar), PDB code: 8ica 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 (°)	179.839, 57.719, 48.175, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 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 Datp (1 Millimolar) and CACL2 (5 Millimolar) also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

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 CACL2 (5 Millimolar) (pdb code 8ica). 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 CACL2 (5 Millimolar), PDB code: 8ica:
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 CACL2 (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 Datp (1 Millimolar) and CACL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:4.3 occ:1.00 O A:THR101 2.0 14.9 1.0 OP1 P:DT6 2.1 16.6 1.0 O A:HOH601 2.3 68.1 1.0 O A:VAL103 2.4 4.0 1.0 O A:ILE106 2.6 22.1 1.0 C A:THR101 3.2 14.9 1.0 P P:DT6 3.5 17.7 1.0 C A:VAL103 3.5 6.4 1.0 C A:ILE106 3.6 13.4 1.0 N A:ILE106 3.7 14.4 1.0 N A:GLY105 3.9 13.8 1.0 C A:ARG102 4.0 26.7 1.0 N A:VAL103 4.0 24.4 1.0 CA A:SER104 4.1 12.3 1.0 CA A:ILE106 4.1 6.9 1.0 N A:ARG102 4.1 22.3 1.0 CA A:THR101 4.2 7.8 1.0 OP2 P:DT6 4.2 12.1 1.0 N A:SER104 4.2 3.9 1.0 CA A:ARG102 4.2 28.7 1.0 O A:ARG102 4.3 28.4 1.0 CB A:ILE106 4.4 4.3 1.0 O3' P:DA5 4.4 21.6 1.0 C A:SER104 4.4 10.1 1.0 CA A:VAL103 4.4 14.5 1.0 O5' P:DT6 4.5 14.1 1.0 CG2 A:THR101 4.5 4.2 1.0 C A:GLY105 4.6 17.8 1.0 N A:GLY107 4.6 12.5 1.0 CA A:GLY105 4.8 18.3 1.0 CB A:THR101 4.9 6.1 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 CACL2 (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 Datp (1 Millimolar) and CACL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:58.9 occ:1.00 O A:LYS60 2.5 45.0 1.0 O A:LEU62 2.6 46.6 1.0 O A:VAL65 2.9 29.8 1.0 C A:LEU62 3.5 46.0 1.0 C A:LYS60 3.7 44.9 1.0 C A:LYS61 3.9 38.1 1.0 N A:LEU62 4.0 36.5 1.0 O A:LYS61 4.0 35.2 1.0 C A:VAL65 4.0 23.9 1.0 CA A:LEU62 4.2 40.7 1.0 CA A:LYS61 4.4 44.3 1.0 N A:PRO63 4.4 44.2 1.0 N A:VAL65 4.5 24.1 1.0 N A:LYS61 4.5 45.4 1.0 CA A:VAL65 4.6 18.1 1.0 CE A:LYS60 4.6 61.3 1.0 CA A:PRO63 4.7 40.5 1.0 CG A:LYS60 4.7 47.8 1.0 CB A:VAL65 4.8 15.4 1.0 CA A:LYS60 4.8 39.2 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