Sodium in PDB 5j2h: Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus:
2.7.7.7;

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus, PDB code: 5j2h was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.800, 79.700, 55.400, 90.00, 107.50, 90.00
R / Rfree (%)	20.5 / 26.6

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus (pdb code 5j2h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus, PDB code: 5j2h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:23.6 occ:1.00 O A:THR101 2.2 25.8 1.0 OP1 P:DG9 2.4 20.8 1.0 O P:HOH106 2.4 25.4 1.0 O A:ILE106 2.6 21.4 1.0 O A:VAL103 2.9 17.6 1.0 O A:HOH698 3.1 41.2 1.0 C A:THR101 3.1 24.4 1.0 P P:DG9 3.5 22.3 1.0 C A:VAL103 3.6 18.0 1.0 C A:ILE106 3.6 22.4 1.0 OP2 P:DG9 3.7 24.9 1.0 CA A:THR101 3.8 24.5 1.0 N A:ILE106 4.0 23.9 1.0 CA A:SER104 4.1 18.2 1.0 N A:VAL103 4.1 19.1 1.0 N A:ARG102 4.1 22.8 1.0 N A:GLY105 4.2 18.8 1.0 N A:SER104 4.2 17.4 1.0 C A:ARG102 4.2 20.9 1.0 CA A:ILE106 4.3 21.9 1.0 CA A:ARG102 4.4 22.5 1.0 CB A:THR101 4.4 21.8 1.0 C A:SER104 4.5 17.9 1.0 O3' P:DC8 4.5 21.3 1.0 CA A:VAL103 4.6 19.0 1.0 O5' P:DG9 4.6 26.5 1.0 N A:GLY107 4.6 22.9 1.0 CB A:ILE106 4.7 22.3 1.0 O A:ARG102 4.7 22.9 1.0 CA A:GLY107 4.8 23.5 1.0 O A:LEU100 4.8 28.1 1.0 C A:GLY105 4.9 22.9 1.0 O A:HOH671 4.9 37.8 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:T Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:54.6 occ:1.00 O A:LYS60 2.2 30.4 1.0 O A:VAL65 2.3 30.4 1.0 O A:LEU62 2.5 33.3 1.0 OP1 D:DC3 2.8 33.2 1.0 C A:LYS60 3.3 31.3 1.0 C A:VAL65 3.5 28.9 1.0 C A:LEU62 3.6 33.1 1.0 O D:HOH108 3.8 32.2 1.0 P D:DC3 3.8 32.8 1.0 OP2 D:DC3 3.9 32.5 1.0 CA A:LYS60 3.9 30.6 1.0 N A:VAL65 3.9 29.2 1.0 CG A:LYS60 3.9 33.6 1.0 C A:LYS61 4.1 33.5 1.0 CA A:VAL65 4.2 29.5 1.0 CA A:PRO63 4.2 33.3 1.0 N A:GLY64 4.3 32.0 1.0 N A:LYS61 4.3 31.8 1.0 N A:LEU62 4.3 32.9 1.0 O A:LYS61 4.3 33.4 1.0 N A:PRO63 4.3 33.1 1.0 CB A:VAL65 4.5 29.4 1.0 N A:GLY66 4.5 29.7 1.0 CA A:LYS61 4.5 33.5 1.0 CB A:LYS60 4.6 31.6 1.0 CA A:LEU62 4.6 32.6 1.0 C A:PRO63 4.6 32.2 1.0 CA A:GLY66 4.7 30.9 1.0 O3' D:DT2 4.7 30.0 1.0 O A:ALA59 4.7 27.1 1.0 C A:GLY64 4.9 30.0 1.0 NZ A:LYS60 5.0 38.9 1.0

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006