Sodium in PDB 1zqq: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of MNCL2 (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 MNCL2 (15 Millimolar) and Nacl (15 Millimolar), PDB code: 1zqq 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 / 3.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.065, 57.369, 47.788, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / n/a

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 MNCL2 (15 Millimolar) and Nacl (15 Millimolar) also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

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 MNCL2 (15 Millimolar) and Nacl (15 Millimolar) (pdb code 1zqq). 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 MNCL2 (15 Millimolar) and Nacl (15 Millimolar), PDB code: 1zqq:
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 MNCL2 (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 MNCL2 (15 Millimolar) and Nacl (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:4.2 occ:1.00 O A:THR101 2.1 19.9 1.0 OP1 P:DT6 2.2 23.6 1.0 O A:ILE106 2.5 25.6 1.0 O A:VAL103 2.7 6.7 1.0 O A:HOH588 3.1 75.5 1.0 C A:THR101 3.3 16.1 1.0 C A:ILE106 3.5 20.5 1.0 P P:DT6 3.5 17.4 1.0 N A:ILE106 3.6 14.6 1.0 C A:VAL103 3.8 11.2 1.0 CA A:ILE106 3.9 21.0 1.0 OP2 P:DT6 3.9 18.8 1.0 N A:GLY105 4.1 16.4 1.0 CA A:SER104 4.1 12.5 1.0 CA A:THR101 4.1 5.9 1.0 CB A:ILE106 4.2 20.4 1.0 C A:ARG102 4.3 12.9 1.0 N A:ARG102 4.3 23.1 1.0 N A:VAL103 4.4 4.7 1.0 N A:SER104 4.5 16.2 1.0 O3' P:DA5 4.5 14.6 1.0 CA A:ARG102 4.5 22.1 1.0 O A:ARG102 4.5 13.9 1.0 O5' P:DT6 4.6 13.8 1.0 N A:GLY107 4.6 11.7 1.0 C A:SER104 4.6 12.1 1.0 C A:GLY105 4.7 9.0 1.0 CA A:VAL103 4.8 5.8 1.0 CB A:THR101 4.9 3.1 1.0 CG2 A:THR101 4.9 11.1 1.0 CA A:GLY105 5.0 10.2 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 MNCL2 (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 MNCL2 (15 Millimolar) and Nacl (15 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:23.4 occ:1.00 O A:LEU62 2.3 23.8 1.0 O A:VAL65 3.0 12.9 1.0 C A:LEU62 3.2 24.1 1.0 O A:LYS60 3.2 29.1 1.0 N A:PRO63 3.9 21.7 1.0 C A:VAL65 4.0 10.1 1.0 N A:VAL65 4.0 16.0 1.0 O A:LYS61 4.0 35.4 1.0 CA A:PRO63 4.1 22.4 1.0 C A:LYS61 4.2 36.4 1.0 N A:GLY64 4.2 29.6 1.0 CA A:LEU62 4.3 23.4 1.0 N A:LEU62 4.3 30.8 1.0 C A:LYS60 4.3 29.7 1.0 CA A:VAL65 4.4 11.6 1.0 CB A:VAL65 4.5 12.2 1.0 C A:PRO63 4.5 28.3 1.0 CD A:PRO63 4.9 23.3 1.0 CA A:LYS61 5.0 43.4 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