Sodium in PDB 4r65: Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta

All present enzymatic activity of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta, PDB code: 4r65 was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.74 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.810, 79.940, 55.480, 90.00, 107.30, 90.00
R / Rfree (%)	18.7 / 22.2

The structure of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta (pdb code 4r65). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta, PDB code: 4r65:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:18.3 occ:1.00 OP1 P:DG9 2.5 18.6 1.0 O A:ILE106 2.5 14.4 1.0 O A:THR101 2.5 17.9 1.0 O A:VAL103 2.6 17.1 1.0 O P:HOH102 2.7 19.9 1.0 O A:HOH544 2.9 22.7 1.0 C A:THR101 3.4 16.0 1.0 P P:DG9 3.4 18.4 1.0 C A:ILE106 3.4 15.4 1.0 OP2 P:DG9 3.4 20.7 1.0 C A:VAL103 3.5 17.7 1.0 N A:ILE106 3.7 14.5 1.0 N A:GLY105 3.9 16.3 1.0 CA A:THR101 3.9 19.5 1.0 CA A:SER104 4.0 15.7 1.0 N A:VAL103 4.1 15.9 1.0 CA A:ILE106 4.1 15.9 1.0 N A:SER104 4.1 15.8 1.0 C A:SER104 4.3 16.2 1.0 C A:ARG102 4.3 19.9 1.0 N A:GLY107 4.4 16.5 1.0 N A:ARG102 4.4 20.1 1.0 O3' P:DC8 4.4 17.1 1.0 CA A:VAL103 4.4 17.8 1.0 O A:HOH731 4.5 30.2 1.0 CB A:THR101 4.5 18.5 1.0 CB A:ILE106 4.5 18.2 1.0 C A:GLY105 4.6 19.3 1.0 CA A:GLY107 4.6 15.8 1.0 O5' P:DG9 4.6 20.7 1.0 CA A:ARG102 4.6 20.3 1.0 CA A:GLY105 4.8 19.6 1.0 O A:ARG102 4.9 21.4 1.0 O A:LEU100 4.9 16.3 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:31.6 occ:1.00 O A:LEU62 2.6 26.8 1.0 O A:VAL65 2.7 22.2 1.0 OP1 D:DC3 2.7 24.3 1.0 O A:LYS60 2.7 26.5 1.0 O A:HOH825 2.8 32.0 1.0 O A:HOH561 3.0 30.1 1.0 C A:LEU62 3.6 25.8 1.0 P D:DC3 3.6 24.7 1.0 OP2 D:DC3 3.7 21.0 1.0 C A:LYS60 3.7 26.4 1.0 C A:VAL65 3.7 24.3 1.0 O D:HOH106 3.8 32.6 1.0 N A:VAL65 4.0 24.7 1.0 CA A:PRO63 4.0 27.6 1.0 N A:GLY64 4.1 21.8 1.0 O A:LYS61 4.1 29.4 1.0 C A:LYS61 4.1 30.3 1.0 N A:PRO63 4.2 27.7 1.0 N A:LEU62 4.3 27.6 1.0 CA A:VAL65 4.3 23.7 1.0 CG A:LYS60 4.4 27.2 1.0 CA A:LYS60 4.4 23.1 1.0 C A:PRO63 4.5 24.1 1.0 CB A:VAL65 4.5 23.9 1.0 CA A:LEU62 4.6 24.6 1.0 N A:LYS61 4.6 23.5 1.0 O3' D:DT2 4.6 27.3 1.0 CA A:LYS61 4.7 27.5 1.0 N A:GLY66 4.7 20.6 1.0 O5' D:DC3 4.8 27.9 1.0 NZ A:LYS60 4.9 29.7 1.0 C A:GLY64 4.9 23.8 1.0 CA A:GLY66 4.9 25.6 1.0

W.A.Beard, D.D.Shock, V.K.Batra, R.Prasad, S.H.Wilson. Substrate-Induced Dna Polymerase Beta Activation. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25261471
DOI: 10.1074/JBC.M114.607432