Sodium in PDB 4jwm: Ternary Complex of D256E Mutant of Dna Polymerase Beta

All present enzymatic activity of Ternary Complex of D256E Mutant of Dna Polymerase Beta:
2.7.7.7;

The structure of Ternary Complex of D256E Mutant of Dna Polymerase Beta, PDB code: 4jwm was solved by V.K.Batra, L.Perera, L.Ping, D.D.Shock, W.A.Beard, L.C.Pedersen, L.G.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.57 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.660, 79.760, 55.640, 90.00, 107.47, 90.00
R / Rfree (%)	19.2 / 23.3

The structure of Ternary Complex of D256E Mutant of Dna Polymerase Beta also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Ternary Complex of D256E Mutant of Dna Polymerase Beta (pdb code 4jwm). 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 of D256E Mutant of Dna Polymerase Beta, PDB code: 4jwm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex of D256E 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 of D256E Mutant of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:17.1 occ:1.00 O A:THR101 2.3 19.2 1.0 OP1 P:DG9 2.4 19.5 1.0 O A:HOH545 2.4 22.0 1.0 O A:VAL103 2.5 15.1 1.0 O A:ILE106 2.5 15.9 1.0 O P:HOH104 2.6 23.7 1.0 C A:THR101 3.3 18.5 1.0 P P:DG9 3.4 21.3 1.0 C A:VAL103 3.4 17.6 1.0 C A:ILE106 3.5 16.7 1.0 OP2 P:DG9 3.6 22.2 1.0 N A:ILE106 3.7 18.1 1.0 CA A:THR101 3.9 19.7 1.0 N A:GLY105 3.9 18.3 1.0 CA A:SER104 4.0 18.1 1.0 O A:HOH712 4.0 34.1 1.0 N A:VAL103 4.1 17.1 1.0 N A:SER104 4.1 17.1 1.0 CA A:ILE106 4.1 16.5 1.0 N A:ARG102 4.3 17.6 1.0 C A:ARG102 4.3 18.0 1.0 C A:SER104 4.3 19.1 1.0 CA A:VAL103 4.4 17.6 1.0 N A:GLY107 4.5 12.6 1.0 CB A:THR101 4.5 21.3 1.0 O3' P:DC8 4.5 20.2 1.0 O5' P:DG9 4.5 24.5 1.0 CB A:ILE106 4.5 17.9 1.0 CA A:ARG102 4.6 16.9 1.0 C A:GLY105 4.6 18.8 1.0 CA A:GLY107 4.7 16.9 1.0 O A:LEU100 4.7 16.9 1.0 O A:ARG102 4.8 15.8 1.0 CA A:GLY105 4.8 19.6 1.0 O A:HOH718 4.9 45.6 1.0

Sodium binding site 2 out of 2 in the Ternary Complex of D256E 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 of D256E Mutant of Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:32.8 occ:1.00 O A:LEU62 2.3 29.1 1.0 O A:VAL65 2.3 26.8 1.0 O A:LYS60 2.5 30.7 1.0 OP1 D:DC3 2.6 31.1 1.0 O D:HOH104 2.6 30.3 1.0 O A:HOH644 2.7 37.0 1.0 C A:LEU62 3.4 29.6 1.0 C A:VAL65 3.4 28.0 1.0 C A:LYS60 3.5 30.6 1.0 P D:DC3 3.6 33.4 1.0 OP2 D:DC3 3.8 29.8 1.0 N A:VAL65 3.8 26.7 1.0 O D:HOH109 4.0 41.5 1.0 CA A:VAL65 4.0 26.3 1.0 CA A:PRO63 4.1 27.1 1.0 N A:PRO63 4.1 28.5 1.0 N A:LEU62 4.1 31.3 1.0 N A:GLY64 4.1 27.0 1.0 C A:LYS61 4.1 32.1 1.0 CA A:LYS60 4.2 28.8 1.0 CB A:VAL65 4.3 26.5 1.0 O A:LYS61 4.3 31.4 1.0 CG A:LYS60 4.4 30.6 1.0 CA A:LEU62 4.4 29.9 1.0 N A:LYS61 4.5 32.1 1.0 N A:GLY66 4.5 28.2 1.0 C A:PRO63 4.5 26.6 1.0 O3' D:DT2 4.6 31.4 1.0 CA A:LYS61 4.6 32.6 1.0 CA A:GLY66 4.8 28.5 1.0 O5' D:DC3 4.8 35.1 1.0 C A:GLY64 4.8 27.9 1.0 O A:ALA59 4.9 24.8 1.0 CB A:LYS60 4.9 29.8 1.0

V.K.Batra, L.Perera, P.Lin, D.D.Shock, W.A.Beard, L.C.Pedersen, L.G.Pedersen, S.H.Wilson. Amino Acid Substitution in the Active Site of Dna Polymerase Beta Explains the Energy Barrier of the Nucleotidyl Transfer Reaction. J.Am.Chem.Soc. V. 135 8078 2013.
ISSN: ISSN 0002-7863
PubMed: 23647366
DOI: 10.1021/JA403842J