Sodium in PDB 8icb: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Artificial Mother Liquor

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 Artificial Mother Liquor, PDB code: 8icb 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 (°)	178.627, 57.775, 48.076, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 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 Artificial Mother Liquor (pdb code 8icb). 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 Artificial Mother Liquor, PDB code: 8icb:
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 Artificial Mother Liquor


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 Artificial Mother Liquor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:10.9 occ:1.00 OP1 P:DT6 2.0 4.0 1.0 O A:THR101 2.1 17.6 1.0 O A:HOH601 2.3 0.0 1.0 O A:VAL103 2.4 1.0 1.0 O A:ILE106 2.6 10.7 1.0 C A:THR101 3.3 14.3 1.0 C A:VAL103 3.3 1.0 1.0 P P:DT6 3.4 12.5 1.0 C A:ILE106 3.7 5.3 1.0 CA A:SER104 3.8 6.1 1.0 C A:ARG102 3.8 24.6 1.0 N A:GLY105 3.9 13.0 1.0 OP2 P:DT6 4.0 6.4 1.0 N A:VAL103 4.0 17.2 1.0 N A:SER104 4.0 1.0 1.0 O A:ARG102 4.0 26.6 1.0 N A:ILE106 4.1 7.6 1.0 N A:ARG102 4.2 21.8 1.0 CA A:ARG102 4.2 23.8 1.0 CA A:THR101 4.2 2.1 1.0 CA A:ILE106 4.3 4.2 1.0 CA A:VAL103 4.3 6.6 1.0 O5' P:DT6 4.3 11.1 1.0 C A:SER104 4.4 10.3 1.0 O3' P:DA5 4.4 8.2 1.0 CB A:ILE106 4.5 1.0 1.0 C A:GLY105 4.7 7.5 1.0 N A:GLY107 4.7 2.3 1.0 CG2 A:THR101 4.8 1.0 1.0 O A:LEU100 4.9 10.1 1.0 CB A:THR101 4.9 1.0 1.0 CG2 A:ILE106 5.0 1.0 1.0 CA A:GLY105 5.0 10.7 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 Artificial Mother Liquor


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 Artificial Mother Liquor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:44.9 occ:1.00 O A:LEU62 2.2 42.9 1.0 O A:LYS60 2.8 25.9 1.0 C A:LEU62 3.3 36.3 1.0 O A:VAL65 3.4 20.9 1.0 O A:LYS61 3.8 37.5 1.0 C A:LYS61 3.9 29.8 1.0 C A:LYS60 4.1 29.0 1.0 N A:LEU62 4.1 28.5 1.0 N A:PRO63 4.2 34.0 1.0 CA A:PRO63 4.2 31.6 1.0 C A:VAL65 4.2 14.2 1.0 CA A:LEU62 4.3 28.8 1.0 N A:VAL65 4.3 11.5 1.0 CA A:LYS61 4.4 28.3 1.0 CA A:VAL65 4.5 8.2 1.0 N A:GLY64 4.6 40.9 1.0 N A:LYS61 4.7 26.4 1.0 C A:PRO63 4.8 32.7 1.0 CB A:VAL65 5.0 13.7 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