Sodium in PDB 1bpy: Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp

All present enzymatic activity of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp:
2.7.7.7;

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

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.543, 79.817, 54.942, 90.00, 107.11, 90.00
R / Rfree (%)	23.2 / 33

The structure of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp (pdb code 1bpy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp, PDB code: 1bpy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:29.5 occ:1.00 O A:ILE106 2.3 39.5 1.0 O A:THR101 2.3 51.6 1.0 OP1 P:DG9 2.9 51.5 1.0 O A:VAL103 2.9 46.8 1.0 O A:HOH617 3.0 33.4 1.0 O P:HOH766 3.0 59.8 1.0 C A:THR101 3.4 49.8 1.0 C A:ILE106 3.5 47.4 1.0 C A:VAL103 3.5 42.9 1.0 OP2 P:DG9 3.5 47.5 1.0 P P:DG9 3.6 48.8 1.0 CA A:SER104 3.9 42.1 1.0 N A:SER104 3.9 44.4 1.0 O P:HOH751 3.9 60.9 1.0 N A:ILE106 4.0 28.0 1.0 N A:VAL103 4.0 37.8 1.0 O A:HOH618 4.1 61.2 1.0 CA A:THR101 4.1 47.6 1.0 N A:GLY105 4.2 34.0 1.0 CA A:ILE106 4.2 34.2 1.0 C A:ARG102 4.4 37.1 1.0 N A:ARG102 4.4 32.3 1.0 CA A:VAL103 4.4 39.5 1.0 C A:SER104 4.5 38.6 1.0 N A:GLY107 4.5 46.8 1.0 O3' P:DC8 4.5 42.7 1.0 CA A:ARG102 4.6 24.3 1.0 CB A:ILE106 4.7 41.3 1.0 CB A:THR101 4.8 29.4 1.0 CA A:GLY107 4.8 44.3 1.0 C A:GLY105 5.0 30.0 1.0 O A:ARG102 5.0 36.6 1.0 O A:LEU100 5.0 46.7 1.0

Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Complexed with Gapped Dna and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:38.9 occ:1.00 O A:LEU62 2.2 36.3 1.0 O A:VAL65 2.3 60.7 1.0 OP1 D:DC3 2.4 32.7 1.0 O A:LYS60 2.5 55.4 1.0 O D:HOH588 2.9 46.0 1.0 O D:HOH587 3.0 47.4 1.0 C A:LEU62 3.3 34.5 1.0 P D:DC3 3.4 45.4 1.0 C A:VAL65 3.5 47.7 1.0 OP2 D:DC3 3.6 36.9 1.0 C A:LYS60 3.6 44.3 1.0 N A:VAL65 3.8 39.4 1.0 N A:GLY64 4.0 56.9 1.0 CA A:PRO63 4.0 42.2 1.0 N A:PRO63 4.0 34.6 1.0 N A:LEU62 4.1 49.6 1.0 CA A:VAL65 4.1 37.0 1.0 O D:HOH595 4.2 57.9 1.0 O3' D:DT2 4.3 55.0 1.0 CA A:LYS60 4.3 33.4 1.0 CA A:LEU62 4.4 36.2 1.0 C A:PRO63 4.4 54.6 1.0 CB A:VAL65 4.4 39.1 1.0 C A:LYS61 4.5 49.9 1.0 C A:GLY64 4.5 41.8 1.0 N A:GLY66 4.5 41.9 1.0 CG A:LYS60 4.6 30.9 1.0 N A:LYS61 4.7 40.6 1.0 O5' D:DC3 4.7 46.8 1.0 CA A:GLY66 4.8 28.2 1.0 CA A:LYS61 4.9 40.7 1.0 CA A:GLY64 4.9 47.3 1.0 O A:LYS61 4.9 47.6 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