Sodium in PDB 4kll: Dna Polymerase Beta Matched Product Complex with MG2+, 45 Min

All present enzymatic activity of Dna Polymerase Beta Matched Product Complex with MG2+, 45 Min:
2.7.7.7;

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 45 Min, PDB code: 4kll 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)	23.76 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.423, 79.570, 55.226, 90.00, 107.69, 90.00
R / Rfree (%)	17.9 / 23

The structure of Dna Polymerase Beta Matched Product Complex with MG2+, 45 Min 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+, 45 Min (pdb code 4kll). 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+, 45 Min, PDB code: 4kll:
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+, 45 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+, 45 Min within 5.0Å range: probe atom residue distance (Å) B Occ T:Na101 b:39.6 occ:1.00 O T:HOH204 2.2 32.7 1.0 O A:HOH758 2.3 36.5 1.0 O D:HOH110 2.3 38.3 1.0 O A:HOH682 2.3 38.5 1.0 O A:HOH665 2.3 31.8 1.0 O T:HOH202 2.3 33.4 1.0 O A:HOH594 4.0 35.0 1.0 O2 D:DC3 4.3 33.7 1.0 O D:HOH102 4.3 30.6 1.0 O T:HOH220 4.4 36.1 1.0 O A:HOH619 4.4 33.0 1.0 O A:HOH650 4.4 37.4 1.0 OE2 A:GLU288 4.5 41.0 1.0 O T:HOH235 4.5 41.6 1.0 O A:HOH697 4.5 39.0 1.0 N3 T:DA4 4.6 30.0 1.0 O4' T:DC5 4.7 30.2 1.0 C4' T:DC5 4.8 36.8 1.0 C5' D:DG4 4.9 30.7 1.0 C5' T:DC5 4.9 31.1 1.0 O4' D:DG4 5.0 35.8 1.0

Sodium binding site 2 out of 4 in the Dna Polymerase Beta Matched Product Complex with MG2+, 45 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+, 45 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:21.9 occ:1.00 OD2 A:ASP256 2.2 27.1 1.0 OD1 A:ASP192 2.2 19.1 1.0 OD2 A:ASP190 2.2 28.9 1.0 OP1 P:DC11 2.4 19.3 1.0 O3' P:DC10 2.4 22.8 1.0 P P:DC11 2.9 21.7 1.0 CG A:ASP190 2.9 25.8 1.0 OD1 A:ASP190 3.1 24.1 1.0 CG A:ASP192 3.2 17.6 1.0 CG A:ASP256 3.3 23.1 1.0 MG A:MG402 3.5 20.1 1.0 OD2 A:ASP192 3.6 18.4 1.0 C3' P:DC10 3.6 21.4 1.0 CB A:ASP256 3.8 17.6 1.0 C4' P:DC10 3.8 23.2 1.0 OP2 P:DC11 3.9 26.9 1.0 C5' P:DC10 4.0 27.6 1.0 O5' P:DC11 4.1 20.4 1.0 CB A:ASP190 4.3 21.1 1.0 C5' P:DC11 4.3 17.5 1.0 OD1 A:ASP256 4.3 21.4 1.0 CB A:ASP192 4.5 16.5 1.0 O A:MET191 4.6 21.0 1.0 C2' P:DC10 4.6 23.2 1.0 O A:HOH672 4.7 30.9 1.0 NH2 A:ARG254 4.8 25.9 1.0 O5' P:DC10 4.8 24.4 1.0 CA A:ASP192 4.9 18.5 1.0 C A:MET191 4.9 18.0 1.0 N A:ASP256 4.9 21.8 1.0 O P:HOH103 5.0 35.2 1.0 CA A:ASP256 5.0 18.3 1.0

Sodium binding site 3 out of 4 in the Dna Polymerase Beta Matched Product Complex with MG2+, 45 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+, 45 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:30.0 occ:1.00 O A:LYS60 2.2 27.7 1.0 O A:LEU62 2.4 30.2 1.0 O A:VAL65 2.5 31.0 1.0 O A:HOH595 2.5 30.7 1.0 O D:HOH103 2.6 34.6 1.0 OP1 D:DC3 2.8 31.0 1.0 C A:LYS60 3.3 29.3 1.0 C A:LEU62 3.3 24.4 1.0 C A:VAL65 3.6 28.9 1.0 N A:LEU62 3.8 29.2 1.0 P D:DC3 3.8 28.1 1.0 C A:LYS61 3.9 35.6 1.0 OP2 D:DC3 3.9 24.3 1.0 N A:VAL65 4.0 24.1 1.0 O D:HOH108 4.0 34.4 1.0 CA A:LYS60 4.1 30.4 1.0 N A:PRO63 4.1 28.5 1.0 CA A:LEU62 4.2 24.1 1.0 N A:LYS61 4.2 30.8 1.0 CA A:PRO63 4.3 31.9 1.0 CA A:VAL65 4.3 22.6 1.0 CG A:LYS60 4.3 28.7 1.0 O A:LYS61 4.3 35.5 1.0 CA A:LYS61 4.4 36.0 1.0 N A:GLY64 4.4 24.9 1.0 CB A:VAL65 4.5 27.9 1.0 C A:PRO63 4.7 29.9 1.0 N A:GLY66 4.7 25.0 1.0 O3' D:DT2 4.7 28.3 1.0 O A:ALA59 4.7 29.4 1.0 CB A:LYS60 4.8 30.9 1.0 CA A:GLY66 5.0 28.0 1.0 NZ A:LYS60 5.0 38.4 1.0

Sodium binding site 4 out of 4 in the Dna Polymerase Beta Matched Product Complex with MG2+, 45 Min


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+, 45 Min within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:30.0 occ:1.00 O P:HOH102 2.3 28.1 1.0 O A:THR101 2.4 26.4 1.0 OP1 P:DG9 2.5 24.1 1.0 O A:ILE106 2.5 20.6 1.0 O A:HOH742 2.5 27.2 1.0 O A:VAL103 2.6 19.8 1.0 C A:THR101 3.4 19.5 1.0 P P:DG9 3.5 24.8 1.0 C A:ILE106 3.5 21.2 1.0 C A:VAL103 3.5 21.7 1.0 OP2 P:DG9 3.6 26.6 1.0 N A:ILE106 3.9 21.0 1.0 N A:GLY105 4.0 20.5 1.0 CA A:THR101 4.0 20.9 1.0 CA A:SER104 4.0 22.9 1.0 N A:SER104 4.2 18.6 1.0 CA A:ILE106 4.2 21.6 1.0 N A:VAL103 4.3 21.6 1.0 C A:SER104 4.4 21.4 1.0 C A:ARG102 4.4 24.5 1.0 N A:ARG102 4.4 23.7 1.0 N A:GLY107 4.5 20.3 1.0 O3' P:DC8 4.5 25.9 1.0 CB A:THR101 4.5 19.3 1.0 CA A:VAL103 4.6 19.9 1.0 O5' P:DG9 4.6 25.0 1.0 CB A:ILE106 4.6 21.9 1.0 CA A:ARG102 4.7 26.7 1.0 CA A:GLY107 4.7 20.3 1.0 C A:GLY105 4.7 24.0 1.0 O A:ARG102 4.8 22.8 1.0 CA A:GLY105 4.9 22.7 1.0 O A:LEU100 5.0 24.1 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