Sodium in PDB 4kli: Dna Polymerase Beta Matched Product Complex with MG2+, 90 S

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MG2+, 90 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 90 S, PDB code: 4kli 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)	32.02 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.940, 80.506, 55.498, 90.00, 107.87, 90.00
R / Rfree (%)	18.5 / 22.2

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 90 S 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+, 90 S (pdb code 4kli). 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+, 90 S, PDB code: 4kli:
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+, 90 S


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+, 90 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:17.4 occ:1.00 OD1 A:ASP192 2.2 16.8 1.0 OD2 A:ASP190 2.2 23.1 1.0 OD2 A:ASP256 2.3 21.3 1.0 OP1 P:DC11 2.4 14.0 1.0 O3' P:DC10 2.5 15.3 1.0 CG A:ASP190 2.8 20.5 1.0 OD1 A:ASP190 2.8 17.1 1.0 P P:DC11 3.0 14.7 1.0 CG A:ASP192 3.2 15.5 1.0 CG A:ASP256 3.4 17.9 1.0 MG A:MG401 3.5 12.6 1.0 OD2 A:ASP192 3.6 13.9 1.0 C3' P:DC10 3.8 12.9 1.0 CB A:ASP256 3.9 15.0 1.0 C4' P:DC10 4.0 15.8 1.0 OP2 P:DC11 4.0 15.6 1.0 C5' P:DC10 4.1 17.7 1.0 CB A:ASP190 4.1 14.3 1.0 O5' P:DC11 4.2 12.6 1.0 C5' P:DC11 4.4 13.1 1.0 O A:HOH502 4.4 21.1 1.0 OD1 A:ASP256 4.4 19.0 1.0 CB A:ASP192 4.5 11.3 1.0 O A:HOH772 4.5 34.3 1.0 O A:MET191 4.6 13.9 1.0 C2' P:DC10 4.7 14.3 1.0 C A:MET191 4.8 15.2 1.0 CA A:ASP192 4.8 12.2 1.0 N A:ASP256 4.9 14.3 1.0 O P:HOH201 4.9 24.7 1.0 O5' P:DC10 4.9 15.5 1.0 N A:ASP192 4.9 13.1 1.0 NH2 A:ARG254 5.0 14.7 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Matched Product Complex with MG2+, 90 S


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+, 90 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:30.0 occ:1.00 O A:LEU62 2.4 22.0 1.0 O A:VAL65 2.4 24.3 1.0 O A:HOH631 2.4 30.7 1.0 O A:LYS60 2.5 25.5 1.0 O D:HOH102 2.5 28.1 1.0 OP1 D:DC3 2.6 25.0 1.0 C A:LEU62 3.4 22.3 1.0 C A:LYS60 3.5 21.3 1.0 C A:VAL65 3.5 24.8 1.0 P D:DC3 3.6 25.5 1.0 OP2 D:DC3 3.8 25.2 1.0 N A:VAL65 3.8 17.0 1.0 O D:HOH106 4.0 35.9 1.0 N A:LEU62 4.0 21.9 1.0 C A:LYS61 4.1 28.2 1.0 N A:PRO63 4.1 28.6 1.0 N A:GLY64 4.1 23.8 1.0 CA A:PRO63 4.1 28.7 1.0 CA A:VAL65 4.2 18.6 1.0 CA A:LYS60 4.3 27.2 1.0 CA A:LEU62 4.3 23.0 1.0 CB A:VAL65 4.4 23.9 1.0 O A:LYS61 4.4 30.3 1.0 N A:LYS61 4.4 24.8 1.0 CG A:LYS60 4.5 25.7 1.0 O3' D:DT2 4.5 24.9 1.0 C A:PRO63 4.5 23.9 1.0 CA A:LYS61 4.5 25.3 1.0 N A:GLY66 4.6 23.8 1.0 C A:GLY64 4.8 22.5 1.0 CA A:GLY66 4.8 24.4 1.0 O5' D:DC3 4.9 25.5 1.0 O A:ALA59 4.9 21.0 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Matched Product Complex with MG2+, 90 S


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+, 90 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:30.0 occ:1.00 O A:THR101 2.4 16.5 1.0 OP1 P:DG9 2.4 17.4 1.0 O A:ILE106 2.4 14.9 1.0 O A:VAL103 2.5 15.3 1.0 O P:HOH204 2.5 22.1 1.0 O A:HOH560 2.5 23.3 1.0 C A:THR101 3.4 16.4 1.0 C A:VAL103 3.4 14.0 1.0 C A:ILE106 3.5 14.9 1.0 P P:DG9 3.5 18.2 1.0 OP2 P:DG9 3.7 21.1 1.0 N A:ILE106 3.8 17.2 1.0 O A:HOH647 3.9 33.8 1.0 CA A:THR101 3.9 13.7 1.0 CA A:SER104 4.0 13.4 1.0 N A:GLY105 4.0 14.3 1.0 N A:SER104 4.1 14.6 1.0 CA A:ILE106 4.1 15.5 1.0 N A:VAL103 4.2 15.3 1.0 C A:SER104 4.4 13.9 1.0 C A:ARG102 4.4 17.8 1.0 N A:ARG102 4.4 17.5 1.0 CA A:VAL103 4.4 12.7 1.0 O3' P:DC8 4.4 20.9 1.0 N A:GLY107 4.5 15.0 1.0 CB A:THR101 4.5 15.0 1.0 CB A:ILE106 4.6 15.4 1.0 C A:GLY105 4.7 15.8 1.0 CA A:ARG102 4.7 17.3 1.0 O5' P:DG9 4.7 15.9 1.0 CA A:GLY107 4.7 20.2 1.0 O A:HOH652 4.9 32.2 1.0 O A:LEU100 4.9 17.2 1.0 O A:ARG102 4.9 21.1 1.0 CA A:GLY105 4.9 17.5 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