Sodium in PDB 4klm: Dna Polymerase Beta Matched Product Complex with MG2+, 11 H

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MG2+, 11 H:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 11 H, PDB code: 4klm was solved by B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.83 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.588, 79.760, 55.338, 90.00, 107.70, 90.00
R / Rfree (%)	18.8 / 23.9

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 11 H also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Matched Product Complex with MG2+, 11 H (pdb code 4klm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta Matched Product Complex with MG2+, 11 H, PDB code: 4klm:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta Matched Product Complex with MG2+, 11 H


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 Matched Product Complex with MG2+, 11 H within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:19.9 occ:1.00 OD1 A:ASP192 2.1 18.5 1.0 OD2 A:ASP190 2.2 25.6 1.0 OD2 A:ASP256 2.2 25.2 1.0 O3' P:DC10 2.3 26.5 1.0 OP1 P:DC11 2.4 20.8 1.0 P P:DC11 2.9 29.1 1.0 CG A:ASP190 3.0 21.4 1.0 OD1 A:ASP190 3.1 22.9 1.0 CG A:ASP192 3.2 16.3 1.0 CG A:ASP256 3.3 22.4 1.0 MG A:MG405 3.5 19.5 1.0 OD2 A:ASP192 3.6 15.8 1.0 C3' P:DC10 3.6 19.6 1.0 CB A:ASP256 3.8 22.1 1.0 C4' P:DC10 3.8 22.4 1.0 OP2 P:DC11 4.0 24.6 1.0 O5' P:DC11 4.0 20.6 1.0 C5' P:DC10 4.1 26.1 1.0 C5' P:DC11 4.2 19.2 1.0 CB A:ASP190 4.3 21.6 1.0 OD1 A:ASP256 4.4 20.1 1.0 CB A:ASP192 4.5 17.6 1.0 C2' P:DC10 4.6 23.6 1.0 O A:HOH512 4.6 23.3 1.0 O A:MET191 4.7 18.8 1.0 NH2 A:ARG254 4.8 19.4 1.0 O P:HOH107 4.8 36.8 1.0 O5' P:DC10 4.8 21.8 1.0 CA A:ASP192 4.9 16.7 1.0 C A:MET191 4.9 15.6 1.0 N A:ASP256 4.9 18.1 1.0 OP1 P:DC10 4.9 19.1 1.0 N A:ASP192 5.0 17.4 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Matched Product Complex with MG2+, 11 H


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 Matched Product Complex with MG2+, 11 H within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:30.0 occ:1.00 O A:LYS60 2.3 30.3 1.0 O A:LEU62 2.3 29.1 1.0 O A:HOH667 2.5 37.0 1.0 O A:VAL65 2.6 29.3 1.0 O D:HOH103 2.7 38.6 1.0 OP1 D:DC3 2.8 28.4 1.0 C A:LEU62 3.3 29.4 1.0 C A:LYS60 3.3 30.4 1.0 C A:VAL65 3.7 28.8 1.0 N A:LEU62 3.8 30.9 1.0 P D:DC3 3.9 30.0 1.0 C A:LYS61 3.9 35.2 1.0 N A:VAL65 4.0 23.5 1.0 N A:PRO63 4.0 33.2 1.0 OP2 D:DC3 4.0 26.8 1.0 CA A:PRO63 4.1 33.3 1.0 CA A:LYS60 4.1 29.4 1.0 CA A:LEU62 4.2 27.2 1.0 CA A:VAL65 4.2 24.0 1.0 N A:LYS61 4.3 29.3 1.0 O A:LYS61 4.3 36.1 1.0 N A:GLY64 4.3 29.2 1.0 CA A:LYS61 4.4 31.4 1.0 CG A:LYS60 4.4 34.8 1.0 CB A:VAL65 4.4 26.8 1.0 C A:PRO63 4.6 26.1 1.0 O3' D:DT2 4.7 29.2 1.0 O A:ALA59 4.8 27.3 1.0 N A:GLY66 4.8 26.6 1.0 CB A:LYS60 4.9 30.7 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Matched Product Complex with MG2+, 11 H


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta Matched Product Complex with MG2+, 11 H within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:30.0 occ:1.00 O A:THR101 2.2 21.0 1.0 O A:HOH548 2.5 25.4 1.0 O A:ILE106 2.5 20.6 1.0 O A:VAL103 2.5 21.3 1.0 O P:HOH102 2.5 26.3 1.0 OP1 P:DG9 2.5 23.2 1.0 C A:THR101 3.2 18.7 1.0 C A:VAL103 3.4 19.3 1.0 C A:ILE106 3.5 21.1 1.0 P P:DG9 3.6 23.6 1.0 OP2 P:DG9 3.7 24.7 1.0 N A:ILE106 3.8 19.7 1.0 CA A:THR101 3.9 20.9 1.0 O A:HOH676 3.9 35.8 1.0 CA A:SER104 4.0 22.5 1.0 N A:SER104 4.1 17.4 1.0 N A:GLY105 4.1 16.9 1.0 N A:VAL103 4.1 18.9 1.0 CA A:ILE106 4.2 19.8 1.0 N A:ARG102 4.3 19.8 1.0 C A:ARG102 4.3 22.8 1.0 C A:SER104 4.4 21.0 1.0 CA A:VAL103 4.4 18.4 1.0 CB A:THR101 4.4 19.9 1.0 N A:GLY107 4.5 19.7 1.0 CB A:ILE106 4.5 21.4 1.0 CA A:ARG102 4.5 23.4 1.0 O3' P:DC8 4.6 26.3 1.0 O A:ARG102 4.7 24.0 1.0 CA A:GLY107 4.7 21.7 1.0 C A:GLY105 4.7 22.4 1.0 O5' P:DG9 4.7 23.5 1.0 O A:LEU100 4.8 20.4 1.0 O A:HOH750 4.9 39.5 1.0 CA A:GLY105 5.0 21.5 1.0

B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson. Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048