Sodium in PDB 4klj: Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min, PDB code: 4klj 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)	31.99 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.000, 80.600, 55.500, 90.00, 107.90, 90.00
R / Rfree (%)	17.9 / 22.7

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min (pdb code 4klj). 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+, 5 Min, PDB code: 4klj:
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+, 5 Min


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+, 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:20.6 occ:1.00 O A:THR101 2.3 21.4 1.0 O A:ILE106 2.4 16.5 1.0 O P:HOH203 2.4 24.7 1.0 O A:HOH799 2.5 26.8 1.0 OP1 P:DG9 2.5 22.2 1.0 O A:VAL103 2.5 20.0 1.0 C A:THR101 3.3 19.3 1.0 C A:VAL103 3.4 17.7 1.0 C A:ILE106 3.5 19.2 1.0 P P:DG9 3.5 21.7 1.0 OP2 P:DG9 3.7 22.6 1.0 N A:ILE106 3.9 19.8 1.0 CA A:THR101 3.9 21.4 1.0 O A:HOH609 4.0 36.4 1.0 CA A:SER104 4.0 17.3 1.0 N A:GLY105 4.0 17.9 1.0 N A:SER104 4.1 16.6 1.0 N A:VAL103 4.1 19.3 1.0 CA A:ILE106 4.2 18.2 1.0 C A:ARG102 4.3 23.4 1.0 N A:ARG102 4.4 21.2 1.0 C A:SER104 4.4 21.9 1.0 CA A:VAL103 4.4 17.6 1.0 N A:GLY107 4.4 18.8 1.0 O3' P:DC8 4.5 23.2 1.0 CB A:THR101 4.5 20.2 1.0 CB A:ILE106 4.6 18.3 1.0 CA A:ARG102 4.6 22.0 1.0 CA A:GLY107 4.7 21.1 1.0 C A:GLY105 4.7 22.5 1.0 O5' P:DG9 4.8 20.1 1.0 O A:HOH703 4.8 32.5 1.0 O A:ARG102 4.9 23.4 1.0 O A:LEU100 4.9 17.9 1.0 CA A:GLY105 5.0 22.4 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min


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+, 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:20.8 occ:1.00 OD1 A:ASP192 2.2 18.5 1.0 OD2 A:ASP256 2.2 23.9 1.0 OD2 A:ASP190 2.3 23.0 1.0 O3' P:DC10 2.5 20.1 1.0 OP1 P:DC11 2.5 16.0 1.0 OD1 A:ASP190 2.8 21.6 1.0 CG A:ASP190 2.8 22.1 1.0 P P:DC11 3.0 20.6 1.0 CG A:ASP192 3.2 14.4 1.0 CG A:ASP256 3.3 17.9 1.0 MG A:MG401 3.5 16.3 1.0 OD2 A:ASP192 3.6 15.1 1.0 C3' P:DC10 3.7 16.7 1.0 CB A:ASP256 3.8 19.4 1.0 C4' P:DC10 3.9 19.5 1.0 C5' P:DC10 4.1 20.6 1.0 OP2 P:DC11 4.1 17.9 1.0 CB A:ASP190 4.2 21.6 1.0 O5' P:DC11 4.2 18.1 1.0 C5' P:DC11 4.3 16.6 1.0 OD1 A:ASP256 4.4 22.2 1.0 CB A:ASP192 4.5 15.1 1.0 O A:MET191 4.5 17.4 1.0 O A:HOH502 4.6 23.8 1.0 C2' P:DC10 4.7 17.7 1.0 CA A:ASP192 4.8 15.3 1.0 C A:MET191 4.8 17.8 1.0 N A:ASP256 4.8 17.5 1.0 NH2 A:ARG254 4.9 17.3 1.0 N A:ASP192 4.9 15.5 1.0 CA A:ASP256 5.0 15.9 1.0 O5' P:DC10 5.0 19.1 1.0 O P:HOH201 5.0 32.7 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Matched Product Complex with MG2+, 5 Min


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+, 5 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:30.0 occ:1.00 O A:VAL65 2.4 26.5 1.0 O A:HOH596 2.5 33.9 1.0 O A:LYS60 2.5 30.1 1.0 O A:LEU62 2.5 31.6 1.0 O D:HOH103 2.5 36.3 1.0 OP1 D:DC3 2.6 25.8 1.0 C A:LEU62 3.4 27.9 1.0 C A:LYS60 3.5 27.7 1.0 C A:VAL65 3.5 24.5 1.0 P D:DC3 3.6 29.0 1.0 OP2 D:DC3 3.8 24.2 1.0 N A:VAL65 3.9 19.8 1.0 CA A:PRO63 4.0 34.2 1.0 N A:PRO63 4.1 33.9 1.0 N A:LEU62 4.1 26.2 1.0 C A:LYS61 4.1 33.4 1.0 CA A:VAL65 4.2 23.5 1.0 N A:GLY64 4.2 25.9 1.0 CA A:LYS60 4.3 27.6 1.0 O A:LYS61 4.4 33.3 1.0 CA A:LEU62 4.4 27.6 1.0 CG A:LYS60 4.4 33.6 1.0 N A:LYS61 4.4 29.2 1.0 CB A:VAL65 4.4 25.1 1.0 C A:PRO63 4.5 28.0 1.0 O3' D:DT2 4.5 29.9 1.0 CA A:LYS61 4.6 28.6 1.0 N A:GLY66 4.6 26.6 1.0 CA A:GLY66 4.8 28.8 1.0 O5' D:DC3 4.9 26.7 1.0 C A:GLY64 4.9 25.5 1.0 O A:ALA59 4.9 25.7 1.0 CB A:LYS60 5.0 30.9 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