Sodium in PDB 1bpx: Dna Polymerase Beta/Dna Complex

All present enzymatic activity of Dna Polymerase Beta/Dna Complex:
2.7.7.7;

The structure of Dna Polymerase Beta/Dna Complex, PDB code: 1bpx was solved by M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, H.Pelletier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.767, 79.395, 54.622, 90.00, 106.35, 90.00
R / Rfree (%)	25.3 / n/a

The binding sites of Sodium atom in the Dna Polymerase Beta/Dna Complex (pdb code 1bpx). 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/Dna Complex, PDB code: 1bpx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta/Dna Complex


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/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Na342 b:54.2 occ:1.00 O A:HOH502 1.8 76.8 1.0 O A:LEU62 2.4 34.4 1.0 O A:VAL65 2.5 60.7 1.0 OP1 D:DC3 2.5 33.1 1.0 O A:LYS60 2.6 44.1 1.0 OP2 D:DC3 2.8 34.4 1.0 P D:DC3 3.1 44.3 1.0 C A:LEU62 3.6 27.9 1.0 C A:VAL65 3.6 49.3 1.0 C A:LYS60 3.9 40.0 1.0 N A:GLY64 3.9 59.3 1.0 CG A:LYS60 4.0 55.5 1.0 O3' D:DT2 4.1 53.0 1.0 CA A:PRO63 4.1 33.8 1.0 N A:VAL65 4.1 50.1 1.0 N A:PRO63 4.2 22.8 1.0 CA A:VAL65 4.3 42.5 1.0 O5' D:DC3 4.5 41.2 1.0 C A:PRO63 4.5 52.5 1.0 N A:GLY66 4.6 50.8 1.0 CA A:GLY66 4.6 47.7 1.0 C A:LYS61 4.6 54.0 1.0 N A:LEU62 4.6 47.3 1.0 CB A:VAL65 4.7 42.9 1.0 O A:LYS61 4.7 59.9 1.0 CA A:LYS60 4.7 40.0 1.0 CA A:LEU62 4.8 36.4 1.0 C A:GLY64 4.8 55.8 1.0 CD A:LYS60 4.8 63.5 1.0 N A:LYS61 4.9 39.7 1.0 C3' D:DT2 4.9 41.6 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta/Dna Complex


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/Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:29.9 occ:1.00 OP1 P:DG9 2.0 48.7 1.0 O A:THR101 2.0 37.6 1.0 O A:ILE106 2.1 28.2 1.0 O P:HOH501 2.6 42.3 1.0 O A:HOH500 2.7 36.0 1.0 O A:VAL103 2.8 53.6 1.0 P P:DG9 3.2 46.4 1.0 C A:THR101 3.2 41.4 1.0 C A:ILE106 3.2 38.3 1.0 OP2 P:DG9 3.4 45.9 1.0 C A:VAL103 3.4 47.7 1.0 O A:HOH539 3.5 70.8 1.0 CA A:THR101 3.8 43.6 1.0 N A:ILE106 3.8 27.6 1.0 N A:SER104 4.0 41.4 1.0 CA A:SER104 4.0 32.3 1.0 N A:GLY105 4.0 38.8 1.0 CA A:ILE106 4.0 32.6 1.0 C A:ARG102 4.2 33.6 1.0 N A:VAL103 4.2 35.9 1.0 O5' P:DG9 4.3 38.2 1.0 O A:ARG102 4.3 36.2 1.0 N A:GLY107 4.3 35.3 1.0 O3' P:DC8 4.3 43.2 1.0 N A:ARG102 4.4 28.0 1.0 CA A:VAL103 4.4 45.1 1.0 CB A:THR101 4.4 35.0 1.0 CB A:ILE106 4.4 37.5 1.0 C A:SER104 4.5 41.0 1.0 CA A:GLY107 4.6 47.8 1.0 C A:GLY105 4.7 34.8 1.0 CA A:ARG102 4.7 27.5 1.0 O A:LEU100 4.8 41.3 1.0 CG2 A:ILE106 5.0 33.8 1.0 CA A:GLY105 5.0 25.4 1.0

M.R.Sawaya, R.Prasad, S.H.Wilson, J.Kraut, H.Pelletier. Crystal Structures of Human Dna Polymerase Beta Complexed with Gapped and Nicked Dna: Evidence For An Induced Fit Mechanism. Biochemistry V. 36 11205 1997.
ISSN: ISSN 0006-2960
PubMed: 9287163
DOI: 10.1021/BI9703812