Sodium in PDB 1zqo: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of CACL2 (15 Millimolar) and Nacl (15 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 CACL2 (15 Millimolar) and Nacl (15 Millimolar), PDB code: 1zqo 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 (°)	178.691, 57.741, 48.171, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 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 CACL2 (15 Millimolar) and Nacl (15 Millimolar) (pdb code 1zqo). 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 CACL2 (15 Millimolar) and Nacl (15 Millimolar), PDB code: 1zqo:
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 CACL2 (15 Millimolar) and Nacl (15 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 CACL2 (15 Millimolar) and Nacl (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:13.4 occ:1.00 O A:THR101 1.9 7.2 1.0 OP1 P:DT6 2.3 8.9 1.0 O P:HOH601 2.4 91.3 1.0 O A:ILE106 2.4 8.5 1.0 O A:VAL103 2.6 1.1 1.0 C A:THR101 3.2 11.9 1.0 C A:VAL103 3.5 1.5 1.0 P P:DT6 3.6 10.1 1.0 C A:ILE106 3.6 9.1 1.0 OP2 P:DT6 3.9 5.5 1.0 N A:VAL103 4.0 24.9 1.0 C A:ARG102 4.0 31.1 1.0 CA A:THR101 4.1 3.7 1.0 N A:GLY105 4.1 10.0 1.0 N A:ILE106 4.1 2.1 1.0 CA A:SER104 4.1 6.7 1.0 N A:ARG102 4.2 16.6 1.0 CA A:ILE106 4.2 5.1 1.0 N A:SER104 4.3 2.5 1.0 CA A:ARG102 4.3 27.3 1.0 CB A:ILE106 4.4 1.0 1.0 O A:ARG102 4.4 35.8 1.0 CA A:VAL103 4.4 15.5 1.0 CG2 A:THR101 4.5 7.2 1.0 O5' P:DT6 4.6 10.8 1.0 C A:SER104 4.6 7.6 1.0 O3' P:DA5 4.6 7.2 1.0 N A:GLY107 4.7 7.1 1.0 CB A:THR101 4.8 1.0 1.0 O A:LEU100 5.0 12.1 1.0 CA A:GLY107 5.0 2.6 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 CACL2 (15 Millimolar) and Nacl (15 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 CACL2 (15 Millimolar) and Nacl (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:32.2 occ:1.00 O A:LEU62 2.2 41.7 1.0 O A:LYS60 3.1 27.3 1.0 C A:LEU62 3.3 41.0 1.0 O A:VAL65 3.8 29.3 1.0 O A:LYS61 3.9 46.1 1.0 C A:LYS61 4.0 37.4 1.0 N A:LEU62 4.2 28.1 1.0 N A:PRO63 4.2 40.2 1.0 C A:LYS60 4.3 27.9 1.0 CA A:LEU62 4.3 32.9 1.0 CA A:PRO63 4.3 36.0 1.0 N A:VAL65 4.4 18.8 1.0 C A:VAL65 4.6 22.9 1.0 CA A:LYS61 4.6 38.9 1.0 N A:GLY64 4.8 44.1 1.0 CA A:VAL65 4.9 12.1 1.0 N A:LYS61 5.0 32.8 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