Sodium in PDB 8ice: 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 CDCL2 (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 CDCL2 (1 Millimolar), PDB code: 8ice 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 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.260, 57.756, 48.255, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 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 Datp (1 Millimolar) and CDCL2 (1 Millimolar) also contains other interesting chemical elements:

Cadmium

(Cd)

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 Datp (1 Millimolar) and CDCL2 (1 Millimolar) (pdb code 8ice). 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 CDCL2 (1 Millimolar), PDB code: 8ice:
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 CDCL2 (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 CDCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:8.1 occ:1.00 OP1 P:DT6 1.5 8.2 1.0 O A:VAL103 2.2 12.3 1.0 O A:THR101 2.8 4.3 1.0 O A:ILE106 2.9 1.0 1.0 P P:DT6 3.0 9.9 1.0 O A:HOH601 3.1 57.6 1.0 C A:VAL103 3.3 13.6 1.0 N A:GLY105 3.3 18.4 1.0 N A:ILE106 3.5 1.2 1.0 C A:ILE106 3.6 1.0 1.0 O A:ARG102 3.7 20.3 1.0 CA A:SER104 3.7 15.9 1.0 OP2 P:DT6 3.9 1.0 1.0 C A:SER104 3.9 16.7 1.0 C A:THR101 3.9 8.7 1.0 O5' P:DT6 3.9 10.7 1.0 O3' P:DA5 3.9 14.7 1.0 N A:SER104 3.9 13.7 1.0 C A:ARG102 3.9 21.0 1.0 CA A:ILE106 4.0 1.0 1.0 C A:GLY105 4.0 9.1 1.0 CA A:GLY105 4.2 16.3 1.0 N A:VAL103 4.3 20.4 1.0 CA A:VAL103 4.3 16.0 1.0 N A:GLY107 4.5 4.5 1.0 CB A:ILE106 4.6 1.0 1.0 CA A:ARG102 4.6 20.6 1.0 N A:ARG102 4.7 15.6 1.0 CA A:THR101 4.8 6.6 1.0 O A:GLY105 4.9 12.0 1.0 O A:SER104 5.0 11.2 1.0 CA A:GLY107 5.0 6.7 1.0 CB A:SER104 5.0 12.6 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 CDCL2 (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 CDCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:37.7 occ:1.00 O A:LEU62 2.9 18.6 1.0 O A:LYS60 3.4 20.8 1.0 O A:VAL65 3.6 13.7 1.0 C A:LEU62 3.9 29.7 1.0 CE A:LYS60 4.2 63.4 1.0 CG A:LYS60 4.6 42.0 1.0 N A:PRO63 4.6 38.7 1.0 C A:LYS60 4.6 27.2 1.0 C A:VAL65 4.6 17.8 1.0 CA A:PRO63 4.7 43.2 1.0 N A:LEU62 4.8 38.8 1.0 C A:LYS61 4.8 42.7 1.0 N A:VAL65 4.9 26.5 1.0 CA A:LEU62 4.9 32.1 1.0 O A:LYS61 5.0 42.9 1.0 N A:GLY64 5.0 43.8 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