Sodium in PDB 4f5q: Closed Ternary Complex of R283K Dna Polymerase Beta

All present enzymatic activity of Closed Ternary Complex of R283K Dna Polymerase Beta:
2.7.7.7;

The structure of Closed Ternary Complex of R283K Dna Polymerase Beta, PDB code: 4f5q was solved by B.D.Freudenthal, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.11 / 2.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.139, 77.629, 54.953, 90.00, 114.20, 90.00
R / Rfree (%)	21.4 / 28.2

The structure of Closed Ternary Complex of R283K Dna Polymerase Beta also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Manganese	(Mn)	2 atoms

The binding sites of Sodium atom in the Closed Ternary Complex of R283K Dna Polymerase Beta (pdb code 4f5q). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Closed Ternary Complex of R283K Dna Polymerase Beta, PDB code: 4f5q:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Closed Ternary Complex of R283K Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Closed Ternary Complex of R283K Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:30.0 occ:1.00 O A:VAL65 2.2 49.5 1.0 O A:HOH573 2.4 30.0 1.0 O A:LEU62 2.5 37.9 1.0 O A:LYS60 2.5 42.9 1.0 OP1 D:DC3 2.7 32.0 1.0 C A:VAL65 3.2 39.3 1.0 C A:LEU62 3.4 41.2 1.0 C A:LYS60 3.5 40.3 1.0 P D:DC3 3.7 42.9 1.0 OP2 D:DC3 3.7 39.4 1.0 N A:VAL65 3.8 31.5 1.0 CA A:VAL65 3.9 37.0 1.0 N A:LEU62 4.0 42.0 1.0 CA A:LYS60 4.1 38.8 1.0 CB A:VAL65 4.1 39.2 1.0 C A:LYS61 4.2 47.1 1.0 N A:GLY66 4.2 43.9 1.0 N A:PRO63 4.2 34.5 1.0 CA A:LEU62 4.3 43.2 1.0 CA A:PRO63 4.3 27.5 1.0 N A:GLY64 4.3 35.0 1.0 CG A:LYS60 4.3 47.4 1.0 CA A:GLY66 4.5 30.6 1.0 N A:LYS61 4.5 42.1 1.0 O3' D:DT2 4.6 37.1 1.0 O A:LYS61 4.6 46.9 1.0 O A:ALA59 4.7 40.3 1.0 C A:PRO63 4.7 42.7 1.0 CA A:LYS61 4.8 49.2 1.0 C A:GLY64 4.8 39.0 1.0 CB A:LYS60 4.9 48.8 1.0 NZ A:LYS60 4.9 43.4 1.0 CG1 A:VAL65 4.9 48.3 1.0 O5' D:DC3 5.0 33.9 1.0

Sodium binding site 2 out of 2 in the Closed Ternary Complex of R283K Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Closed Ternary Complex of R283K Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:30.0 occ:1.00 O A:HOH536 2.1 30.9 1.0 O A:THR101 2.2 38.5 1.0 O A:VAL103 2.3 24.0 1.0 OP1 P:DG9 2.6 22.6 1.0 O A:ILE106 2.8 15.9 1.0 O P:HOH106 2.9 34.2 1.0 C A:THR101 3.2 32.6 1.0 C A:VAL103 3.3 28.4 1.0 P P:DG9 3.6 26.6 1.0 C A:ILE106 3.7 13.8 1.0 CA A:SER104 3.8 24.8 1.0 OP2 P:DG9 3.8 43.3 1.0 N A:SER104 3.9 31.3 1.0 CA A:THR101 3.9 30.2 1.0 N A:ILE106 3.9 26.3 1.0 N A:GLY105 3.9 23.6 1.0 N A:VAL103 4.1 21.3 1.0 C A:SER104 4.2 30.3 1.0 C A:ARG102 4.2 20.2 1.0 N A:ARG102 4.3 27.6 1.0 CA A:VAL103 4.3 19.6 1.0 CA A:ILE106 4.3 20.5 1.0 CB A:THR101 4.5 20.0 1.0 CA A:ARG102 4.5 16.9 1.0 O3' P:DC8 4.6 27.0 1.0 CB A:ILE106 4.7 18.1 1.0 O A:ARG102 4.7 28.8 1.0 N A:GLY107 4.7 19.5 1.0 C A:GLY105 4.8 19.2 1.0 O A:LEU100 4.9 33.3 1.0 O5' P:DG9 4.9 19.4 1.0 CA A:GLY105 5.0 18.9 1.0 O A:HOH557 5.0 40.1 1.0

B.D.Freudenthal, W.A.Beard, S.H.Wilson. Structures of Dntp Intermediate States During Dna Polymerase Active Site Assembly. Structure V. 20 1829 2012.
ISSN: ISSN 0969-2126
PubMed: 22959623
DOI: 10.1016/J.STR.2012.08.008