Sodium in PDB 5j2a: Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus, PDB code: 5j2a 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 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.420, 79.220, 55.340, 90.00, 107.07, 90.00
R / Rfree (%)	22.5 / 29.6

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

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

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C Mismatch at the Primer Terminus (pdb code 5j2a). 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 A:C Mismatch at the Primer Terminus, PDB code: 5j2a:
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 A:C 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 A:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:26.4 occ:1.00 O A:LEU62 2.3 25.0 1.0 O A:VAL65 2.4 23.7 1.0 O A:LYS60 2.7 32.4 1.0 O A:HOH576 2.9 26.3 1.0 OP1 D:DC3 3.1 32.5 1.0 C A:LYS60 3.3 31.3 1.0 C A:LEU62 3.3 25.4 1.0 C A:VAL65 3.4 23.9 1.0 N A:VAL65 3.7 22.7 1.0 CA A:LYS60 3.9 30.5 1.0 C A:LYS61 3.9 30.2 1.0 N A:LEU62 4.0 28.2 1.0 CA A:PRO63 4.0 23.2 1.0 N A:PRO63 4.0 24.8 1.0 N A:GLY64 4.0 22.5 1.0 CA A:VAL65 4.0 22.7 1.0 N A:LYS61 4.0 30.7 1.0 P D:DC3 4.1 33.9 1.0 O A:LYS61 4.1 32.6 1.0 OP2 D:DC3 4.1 31.8 1.0 CA A:LEU62 4.3 26.6 1.0 CB A:VAL65 4.3 22.9 1.0 CG A:LYS60 4.3 29.4 1.0 CA A:LYS61 4.3 30.2 1.0 O A:ALA59 4.4 30.0 1.0 N A:GLY66 4.4 24.6 1.0 C A:PRO63 4.5 22.7 1.0 CB A:LYS60 4.7 29.5 1.0 CA A:GLY66 4.7 25.9 1.0 C A:GLY64 4.8 23.3 1.0 O3' D:DT2 4.9 30.8 1.0 O D:HOH104 5.0 26.4 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A:C 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 A:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:42.9 occ:1.00 O A:HOH551 1.9 8.2 1.0 O A:THR101 2.5 19.0 1.0 OP1 P:DG9 2.6 19.2 1.0 O A:ILE106 3.0 16.8 1.0 O P:HOH214 3.0 26.1 1.0 OP2 P:DG9 3.2 20.3 1.0 P P:DG9 3.3 21.6 1.0 C A:THR101 3.5 17.3 1.0 O A:VAL103 3.8 19.9 1.0 C A:ILE106 3.9 15.2 1.0 CA A:THR101 4.2 16.7 1.0 O5' P:DG9 4.3 22.9 1.0 N A:ILE106 4.4 15.1 1.0 C A:VAL103 4.5 17.2 1.0 N A:ARG102 4.5 17.8 1.0 N A:GLY105 4.6 16.8 1.0 CB A:THR101 4.6 14.9 1.0 O3' P:DC8 4.6 22.5 1.0 CA A:SER104 4.6 15.7 1.0 C A:ARG102 4.7 16.9 1.0 CA A:ILE106 4.7 13.8 1.0 CA A:ARG102 4.8 17.1 1.0 O A:HOH653 4.8 40.8 1.0 N A:GLY107 4.8 13.7 1.0 CA A:GLY107 4.8 15.5 1.0 N A:SER104 4.9 15.9 1.0 N A:VAL103 4.9 15.9 1.0 O A:ARG102 5.0 15.4 1.0 C A:SER104 5.0 16.3 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