Sodium in PDB 4klo: Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min

All present enzymatic activity of Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min, PDB code: 4klo 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)	22.62 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.814, 79.966, 55.380, 90.00, 107.75, 90.00
R / Rfree (%)	18.2 / 23

The structure of Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 Min (pdb code 4klo). 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 Nick Complex with MG2+ and Ppi, 30 Min, PDB code: 4klo:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 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 Nick Complex with MG2+ and Ppi, 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:17.9 occ:1.00 OD2 A:ASP256 2.2 23.6 1.0 OD1 A:ASP192 2.2 16.4 1.0 OD2 A:ASP190 2.3 23.2 1.0 OP1 P:DC11 2.5 15.8 1.0 O3' P:DC10 2.6 20.0 1.0 CG A:ASP190 2.9 22.1 1.0 OD1 A:ASP190 2.9 18.7 1.0 P P:DC11 3.1 19.8 1.0 CG A:ASP192 3.2 13.8 1.0 CG A:ASP256 3.3 18.9 1.0 MG A:MG404 3.5 17.4 1.0 OD2 A:ASP192 3.6 14.3 1.0 C3' P:DC10 3.8 18.3 1.0 CB A:ASP256 3.8 15.5 1.0 C4' P:DC10 3.9 20.6 1.0 C5' P:DC10 4.1 22.8 1.0 OP2 P:DC11 4.1 22.4 1.0 CB A:ASP190 4.2 18.8 1.0 O5' P:DC11 4.2 18.5 1.0 OD1 A:ASP256 4.3 17.6 1.0 C5' P:DC11 4.3 17.5 1.0 O P:HOH221 4.4 33.7 1.0 CB A:ASP192 4.5 14.2 1.0 O A:MET191 4.6 15.7 1.0 O A:HOH533 4.7 25.2 1.0 C2' P:DC10 4.7 18.9 1.0 N A:ASP256 4.7 16.6 1.0 CA A:ASP192 4.8 16.2 1.0 NH2 A:ARG254 4.8 22.2 1.0 C A:MET191 4.8 14.0 1.0 O5' P:DC10 4.9 19.7 1.0 CA A:ASP256 4.9 15.6 1.0 N A:ASP192 5.0 18.0 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 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 Nick Complex with MG2+ and Ppi, 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:27.2 occ:1.00 O A:LEU62 2.6 26.9 1.0 O A:LYS60 2.6 29.7 1.0 O A:VAL65 2.6 26.6 1.0 O A:HOH635 2.7 34.8 1.0 OP1 D:DC3 2.7 27.1 1.0 O D:HOH104 2.9 37.1 1.0 C A:LEU62 3.4 28.4 1.0 C A:LYS60 3.6 28.4 1.0 C A:VAL65 3.7 28.8 1.0 P D:DC3 3.7 28.2 1.0 O D:HOH108 3.8 40.4 1.0 OP2 D:DC3 3.8 23.1 1.0 N A:LEU62 3.9 26.8 1.0 N A:VAL65 4.0 24.9 1.0 C A:LYS61 4.0 29.2 1.0 N A:PRO63 4.1 30.0 1.0 N A:GLY64 4.2 25.3 1.0 CA A:PRO63 4.2 32.2 1.0 CA A:VAL65 4.3 22.1 1.0 CA A:LEU62 4.3 25.0 1.0 O A:LYS61 4.3 32.8 1.0 CA A:LYS60 4.3 27.6 1.0 N A:LYS61 4.4 27.3 1.0 CB A:VAL65 4.5 22.2 1.0 CG A:LYS60 4.5 31.4 1.0 CA A:LYS61 4.5 31.9 1.0 C A:PRO63 4.6 25.6 1.0 O3' D:DT2 4.6 28.5 1.0 N A:GLY66 4.8 23.7 1.0 O A:ALA59 4.9 26.1 1.0 C A:GLY64 4.9 25.9 1.0 O5' D:DC3 5.0 30.5 1.0 CA A:GLY66 5.0 30.0 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta Matched Nick Complex with MG2+ and Ppi, 30 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 Nick Complex with MG2+ and Ppi, 30 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:21.6 occ:1.00 O A:THR101 2.5 25.9 1.0 O A:ILE106 2.5 18.6 1.0 OP1 P:DG9 2.6 20.1 1.0 O P:HOH202 2.6 24.9 1.0 O A:VAL103 2.6 19.3 1.0 O A:HOH837 2.7 26.6 1.0 C A:THR101 3.4 18.6 1.0 C A:VAL103 3.5 17.2 1.0 C A:ILE106 3.5 20.1 1.0 P P:DG9 3.6 21.7 1.0 OP2 P:DG9 3.7 22.0 1.0 O A:HOH667 3.8 35.3 1.0 N A:ILE106 3.8 18.3 1.0 CA A:THR101 3.9 20.5 1.0 CA A:SER104 4.0 20.2 1.0 N A:GLY105 4.0 16.3 1.0 N A:SER104 4.1 17.4 1.0 N A:VAL103 4.1 18.7 1.0 CA A:ILE106 4.2 19.6 1.0 C A:ARG102 4.3 24.0 1.0 C A:SER104 4.4 20.5 1.0 N A:ARG102 4.4 21.1 1.0 CA A:VAL103 4.4 17.8 1.0 CB A:THR101 4.4 21.6 1.0 N A:GLY107 4.5 16.2 1.0 CB A:ILE106 4.5 18.6 1.0 O3' P:DC8 4.6 25.3 1.0 CA A:ARG102 4.6 24.9 1.0 C A:GLY105 4.7 18.8 1.0 CA A:GLY107 4.7 23.3 1.0 O A:HOH772 4.8 35.9 1.0 O5' P:DG9 4.8 20.0 1.0 O A:ARG102 4.8 21.8 1.0 O A:LEU100 4.9 19.9 1.0 CA A:GLY105 5.0 18.4 1.0 O A:HOH721 5.0 34.0 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