Sodium in PDB 8icz: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of of Datp (1 Millimolar), MNCL2 (5 Millimolar), and Lithium Sulfate (75 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 of Datp (1 Millimolar), MNCL2 (5 Millimolar), and Lithium Sulfate (75 Millimolar), PDB code: 8icz 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 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.583, 57.736, 48.471, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 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 of Datp (1 Millimolar), MNCL2 (5 Millimolar), and Lithium Sulfate (75 Millimolar) (pdb code 8icz). 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 of Datp (1 Millimolar), MNCL2 (5 Millimolar), and Lithium Sulfate (75 Millimolar), PDB code: 8icz:
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 of Datp (1 Millimolar), MNCL2 (5 Millimolar), and Lithium Sulfate (75 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 of Datp (1 Millimolar), MNCL2 (5 Millimolar), and Lithium Sulfate (75 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:7.2 occ:1.00 O A:THR101 2.0 21.1 1.0 OP1 P:DT6 2.4 16.8 1.0 O A:ILE106 2.5 10.1 1.0 O A:VAL103 2.7 7.4 1.0 O P:HOH601 2.8 92.5 1.0 C A:THR101 3.2 17.3 1.0 C A:VAL103 3.2 11.8 1.0 P P:DT6 3.5 18.8 1.0 C A:ILE106 3.5 4.9 1.0 N A:VAL103 3.7 23.9 1.0 C A:ARG102 3.7 25.2 1.0 N A:ILE106 3.8 8.0 1.0 OP2 P:DT6 3.8 17.1 1.0 N A:SER104 3.8 17.4 1.0 CA A:SER104 3.9 25.2 1.0 N A:ARG102 4.0 18.2 1.0 CA A:ARG102 4.0 23.9 1.0 CA A:ILE106 4.0 2.9 1.0 O A:ARG102 4.0 27.8 1.0 CA A:VAL103 4.1 19.4 1.0 N A:GLY105 4.1 27.4 1.0 CA A:THR101 4.2 16.1 1.0 O5' P:DT6 4.3 14.4 1.0 CB A:ILE106 4.5 2.7 1.0 C A:SER104 4.5 29.5 1.0 N A:GLY107 4.7 4.3 1.0 O3' P:DA5 4.8 18.5 1.0 CG2 A:THR101 4.8 10.2 1.0 C A:GLY105 4.8 12.3 1.0 O A:LEU100 4.9 26.2 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 of Datp (1 Millimolar), MNCL2 (5 Millimolar), and Lithium Sulfate (75 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 of Datp (1 Millimolar), MNCL2 (5 Millimolar), and Lithium Sulfate (75 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:55.0 occ:1.00 O A:LEU62 2.6 18.9 1.0 O A:LYS60 3.1 31.0 1.0 C A:LEU62 3.5 24.4 1.0 O A:VAL65 3.6 28.2 1.0 C A:LYS61 4.2 27.6 1.0 N A:LEU62 4.2 18.5 1.0 C A:LYS60 4.2 26.1 1.0 N A:PRO63 4.3 28.1 1.0 O A:LYS61 4.3 28.4 1.0 C A:VAL65 4.4 21.7 1.0 CA A:PRO63 4.5 26.8 1.0 CA A:LEU62 4.5 20.9 1.0 CG2 A:VAL65 4.5 17.3 1.0 CA A:LYS61 4.6 33.1 1.0 N A:VAL65 4.6 11.0 1.0 N A:GLY64 4.8 39.1 1.0 N A:LYS61 4.9 27.3 1.0 CA A:VAL65 5.0 12.2 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