Sodium in PDB 4klg: Dna Polymerase Beta Matched Product Complex with MG2+, 40 S

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MG2+, 40 S:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 40 S, PDB code: 4klg 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 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	51.109, 80.478, 55.529, 90.00, 107.78, 90.00
R / Rfree (%)	18.8 / 22.9

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 40 S also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Dna Polymerase Beta Matched Product Complex with MG2+, 40 S (pdb code 4klg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Dna Polymerase Beta Matched Product Complex with MG2+, 40 S, PDB code: 4klg:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Dna Polymerase Beta Matched Product Complex with MG2+, 40 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+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ T:Na101 b:30.0 occ:1.00 O A:HOH765 2.1 30.0 1.0 O T:HOH255 2.2 30.0 1.0 O A:HOH685 2.2 37.8 1.0 O D:HOH105 2.3 39.5 1.0 O T:HOH234 2.4 42.6 1.0 O A:HOH729 2.5 46.8 1.0 O T:HOH236 4.1 38.0 1.0 O D:HOH104 4.2 32.4 1.0 N3 T:DA4 4.3 26.1 1.0 O4' T:DC5 4.4 30.3 1.0 O A:HOH576 4.4 30.9 1.0 C4' T:DC5 4.5 32.2 1.0 O2 D:DC3 4.6 36.6 1.0 C5' T:DC5 4.6 30.1 1.0 O T:HOH245 4.6 41.0 1.0 OE2 A:GLU288 4.7 49.4 1.0 C2 T:DA4 4.8 28.2 1.0 N2 T:DG3 5.0 32.8 1.0

Sodium binding site 2 out of 4 in the Dna Polymerase Beta Matched Product Complex with MG2+, 40 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+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:14.7 occ:1.00 OD1 A:ASP192 2.2 17.1 1.0 OD2 A:ASP190 2.2 29.6 1.0 OD2 A:ASP256 2.2 26.1 1.0 OP1 P:DC11 2.4 16.1 1.0 O3' P:DC10 2.5 17.3 1.0 OD1 A:ASP190 2.8 18.2 1.0 CG A:ASP190 2.8 22.7 1.0 P P:DC11 3.0 16.5 1.0 CG A:ASP192 3.2 16.7 1.0 CG A:ASP256 3.4 22.1 1.0 MG A:MG401 3.6 9.2 1.0 OD2 A:ASP192 3.6 15.1 1.0 C3' P:DC10 3.8 13.8 1.0 CB A:ASP256 3.9 16.9 1.0 C4' P:DC10 4.0 17.6 1.0 OP2 P:DC11 4.1 17.1 1.0 C5' P:DC10 4.2 21.5 1.0 O5' P:DC11 4.2 14.4 1.0 CB A:ASP190 4.2 15.2 1.0 C5' P:DC11 4.4 15.3 1.0 OD1 A:ASP256 4.4 20.6 1.0 CB A:ASP192 4.5 12.0 1.0 O A:HOH503 4.5 17.1 0.6 O A:MET191 4.6 17.1 1.0 C2' P:DC10 4.8 14.9 1.0 C A:MET191 4.9 14.8 1.0 CA A:ASP192 4.9 15.5 1.0 O A:HOH504 4.9 26.7 1.0 N A:ASP256 4.9 15.1 1.0 NH2 A:ARG254 4.9 17.3 1.0 O5' P:DC10 5.0 15.3 1.0 N A:ASP192 5.0 12.1 1.0

Sodium binding site 3 out of 4 in the Dna Polymerase Beta Matched Product Complex with MG2+, 40 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+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:30.0 occ:1.00 O A:THR101 2.4 17.1 1.0 O P:HOH203 2.4 21.1 1.0 O P:HOH223 2.4 30.0 1.0 OP1 P:DG9 2.4 19.8 1.0 O A:ILE106 2.5 15.5 1.0 O A:VAL103 2.6 16.2 1.0 C A:THR101 3.4 16.1 1.0 P P:DG9 3.5 20.1 1.0 C A:VAL103 3.5 16.4 1.0 C A:ILE106 3.6 17.0 1.0 OP2 P:DG9 3.6 19.9 1.0 O A:HOH618 3.7 36.1 1.0 N A:ILE106 3.9 15.2 1.0 CA A:THR101 4.0 15.9 1.0 N A:GLY105 4.0 15.1 1.0 CA A:SER104 4.1 16.8 1.0 N A:SER104 4.2 16.5 1.0 N A:VAL103 4.2 17.0 1.0 CA A:ILE106 4.3 14.9 1.0 C A:ARG102 4.4 20.8 1.0 N A:ARG102 4.4 14.4 1.0 C A:SER104 4.4 15.7 1.0 O3' P:DC8 4.4 22.6 1.0 CA A:VAL103 4.5 15.1 1.0 CB A:THR101 4.5 15.9 1.0 N A:GLY107 4.6 16.6 1.0 CA A:ARG102 4.6 16.8 1.0 CB A:ILE106 4.7 14.6 1.0 O A:HOH658 4.7 34.3 1.0 O5' P:DG9 4.7 16.1 1.0 C A:GLY105 4.8 16.6 1.0 CA A:GLY107 4.8 19.3 1.0 O A:ARG102 4.9 19.4 1.0 O A:LEU100 4.9 16.0 1.0 CA A:GLY105 5.0 17.3 1.0

Sodium binding site 4 out of 4 in the Dna Polymerase Beta Matched Product Complex with MG2+, 40 S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dna Polymerase Beta Matched Product Complex with MG2+, 40 S within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:30.0 occ:1.00 O A:HOH597 2.4 31.8 1.0 O A:LEU62 2.4 26.1 1.0 O A:LYS60 2.5 27.9 1.0 O A:VAL65 2.5 24.9 1.0 OP1 D:DC3 2.6 25.5 1.0 O D:HOH103 2.6 35.8 1.0 C A:LEU62 3.4 23.0 1.0 C A:LYS60 3.5 24.5 1.0 C A:VAL65 3.6 24.2 1.0 P D:DC3 3.7 25.6 1.0 OP2 D:DC3 3.8 24.8 1.0 N A:VAL65 3.9 17.1 1.0 O D:HOH106 3.9 37.4 1.0 CA A:PRO63 4.0 28.0 1.0 N A:LEU62 4.0 27.9 1.0 N A:PRO63 4.1 32.0 1.0 C A:LYS61 4.1 31.0 1.0 N A:GLY64 4.1 25.8 1.0 CA A:VAL65 4.2 19.8 1.0 CA A:LYS60 4.3 25.9 1.0 CA A:LEU62 4.4 26.9 1.0 O A:LYS61 4.4 30.9 1.0 N A:LYS61 4.4 26.9 1.0 CB A:VAL65 4.4 23.0 1.0 C A:PRO63 4.5 27.8 1.0 CG A:LYS60 4.5 30.3 1.0 CA A:LYS61 4.5 28.0 1.0 O3' D:DT2 4.6 25.7 1.0 N A:GLY66 4.6 21.7 1.0 C A:GLY64 4.8 23.4 1.0 O5' D:DC3 4.9 27.8 1.0 O A:ALA59 4.9 25.0 1.0 CA A:GLY66 4.9 23.9 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