Sodium in PDB 1zqh: 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 7.5

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 7.5, PDB code: 1zqh 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 (°)	178.007, 58.502, 48.701, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 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 7.5 (pdb code 1zqh). 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 7.5, PDB code: 1zqh:
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 7.5


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 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:1.0 occ:1.00 O P:HOH601 2.1 99.8 1.0 OP1 P:DT6 2.2 28.7 1.0 O A:THR101 2.3 12.9 1.0 O A:ILE106 3.1 10.3 1.0 O A:VAL103 3.1 19.8 1.0 C A:THR101 3.5 12.1 1.0 P P:DT6 3.6 21.6 1.0 C A:VAL103 3.7 16.9 1.0 C A:ARG102 3.8 23.6 1.0 O A:ARG102 3.9 25.9 1.0 CA A:SER104 3.9 17.2 1.0 N A:SER104 4.1 13.3 1.0 CA A:ARG102 4.1 22.0 1.0 N A:VAL103 4.1 21.5 1.0 N A:ARG102 4.2 13.6 1.0 OP2 P:DT6 4.3 24.3 1.0 C A:ILE106 4.3 9.4 1.0 O5' P:DT6 4.4 6.9 1.0 N A:GLY105 4.4 21.6 1.0 CA A:VAL103 4.6 17.6 1.0 N A:ILE106 4.6 8.3 1.0 CA A:THR101 4.7 5.4 1.0 C A:SER104 4.7 11.2 1.0 O3' P:DA5 4.8 9.2 1.0 CB A:SER104 4.9 25.4 1.0 O P:HOH566 4.9 32.6 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 A Sodium-Free Artificial Mother Liquor at pH 7.5


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 7.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:3.0 occ:1.00 O A:LEU62 2.6 30.4 1.0 O A:LYS60 3.1 16.4 1.0 O A:LYS61 3.1 11.4 1.0 C A:LEU62 3.3 23.9 1.0 C A:LYS61 3.6 15.9 1.0 N A:PRO63 3.8 26.1 1.0 CA A:PRO63 3.9 16.7 1.0 O A:VAL65 3.9 29.8 1.0 N A:LEU62 4.1 15.9 1.0 CA A:LEU62 4.2 12.0 1.0 C A:LYS60 4.2 14.9 1.0 CA A:LYS61 4.4 25.9 1.0 N A:GLY64 4.7 35.4 1.0 C A:VAL65 4.7 30.1 1.0 C A:PRO63 4.7 17.3 1.0 CD A:PRO63 4.7 23.8 1.0 N A:VAL65 4.8 37.0 1.0 N A:LYS61 4.8 14.7 1.0 CB A:PRO63 4.9 16.0 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