Sodium in PDB 1zqg: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of A Sodium-Free Artificial Mother Liquor at pH 6.5

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 A Sodium-Free Artificial Mother Liquor at pH 6.5, PDB code: 1zqg 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 (°)	179.044, 57.691, 48.334, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 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 A Sodium-Free Artificial Mother Liquor at pH 6.5 (pdb code 1zqg). 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 A Sodium-Free Artificial Mother Liquor at pH 6.5, PDB code: 1zqg:
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 A Sodium-Free Artificial Mother Liquor at pH 6.5


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 A Sodium-Free Artificial Mother Liquor at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:9.9 occ:1.00 O A:THR101 2.1 22.2 1.0 O A:HOH601 2.4 83.3 1.0 OP1 P:DT6 2.6 21.6 1.0 O A:VAL103 2.6 13.2 1.0 O A:ILE106 2.6 11.8 1.0 C A:THR101 3.2 13.5 1.0 C A:VAL103 3.6 8.7 1.0 P P:DT6 3.6 11.5 1.0 C A:ILE106 3.8 4.5 1.0 OP2 P:DT6 3.9 4.3 1.0 C A:ARG102 4.0 22.5 1.0 N A:VAL103 4.0 14.2 1.0 CA A:THR101 4.1 1.3 1.0 N A:ARG102 4.1 18.3 1.0 N A:ILE106 4.2 5.6 1.0 CA A:SER104 4.2 15.8 1.0 N A:GLY105 4.2 13.4 1.0 CA A:ARG102 4.3 24.6 1.0 N A:SER104 4.3 12.0 1.0 O A:ARG102 4.4 19.4 1.0 CA A:VAL103 4.5 8.1 1.0 CA A:ILE106 4.5 6.4 1.0 O5' P:DT6 4.6 13.1 1.0 CG2 A:THR101 4.7 3.0 1.0 O3' P:DA5 4.7 5.2 1.0 CB A:ILE106 4.8 7.9 1.0 CB A:THR101 4.8 1.0 1.0 C A:SER104 4.8 13.4 1.0 N A:GLY107 4.8 1.0 1.0 CA A:GLY107 4.9 1.0 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 A Sodium-Free Artificial Mother Liquor at pH 6.5


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 A Sodium-Free Artificial Mother Liquor at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:48.1 occ:1.00 O A:LEU62 2.3 38.7 1.0 O A:LYS60 3.2 33.5 1.0 C A:LEU62 3.5 35.6 1.0 O A:VAL65 3.9 13.9 1.0 C A:LYS61 4.2 33.3 1.0 O A:LYS61 4.3 35.6 1.0 N A:LEU62 4.3 26.9 1.0 N A:PRO63 4.4 34.8 1.0 C A:LYS60 4.4 30.6 1.0 CA A:PRO63 4.4 32.7 1.0 CA A:LEU62 4.5 30.7 1.0 N A:VAL65 4.5 14.4 1.0 C A:VAL65 4.6 12.6 1.0 N A:GLY64 4.7 42.9 1.0 CA A:LYS61 4.7 34.4 1.0 CA A:VAL65 4.8 10.7 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