Sodium in PDB 5j2b: 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: 5j2b 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 (°)	50.710, 79.880, 55.470, 90.00, 107.58, 90.00
R / Rfree (%)	21 / 28.8

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 5j2b). 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: 5j2b:
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:23.5 occ:1.00 O A:THR101 1.9 22.0 1.0 O A:VAL103 2.4 14.5 1.0 O A:HOH666 2.6 37.0 1.0 O A:ILE106 2.7 16.7 1.0 O P:HOH104 2.8 28.3 1.0 OP1 P:DG9 2.8 20.9 1.0 C A:THR101 3.0 20.3 1.0 C A:VAL103 3.2 15.2 1.0 N A:VAL103 3.6 17.8 1.0 C A:ARG102 3.7 20.6 1.0 C A:ILE106 3.8 16.7 1.0 CA A:THR101 3.8 19.4 1.0 N A:SER104 3.8 14.5 1.0 CA A:SER104 3.9 13.8 1.0 N A:ARG102 3.9 20.9 1.0 P P:DG9 4.0 22.8 1.0 N A:ILE106 4.0 16.2 1.0 CA A:VAL103 4.1 16.2 1.0 CA A:ARG102 4.1 21.2 1.0 O A:ARG102 4.1 23.4 1.0 OP2 P:DG9 4.2 25.1 1.0 N A:GLY105 4.2 13.7 1.0 CA A:ILE106 4.4 16.3 1.0 C A:SER104 4.4 12.7 1.0 CB A:ILE106 4.5 16.2 1.0 CB A:THR101 4.5 17.0 1.0 O A:LEU100 4.5 17.4 1.0 O3' P:DC8 4.9 23.8 1.0 N A:GLY107 4.9 15.6 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:Na405 b:41.1 occ:1.00 O A:VAL65 2.4 26.7 1.0 OP1 D:DC3 2.5 23.8 1.0 O A:LYS60 2.7 22.4 1.0 O A:LEU62 2.9 29.4 1.0 C A:VAL65 3.3 25.8 1.0 P D:DC3 3.4 25.5 1.0 OP2 D:DC3 3.4 21.0 1.0 O D:HOH106 3.4 29.0 1.0 N A:VAL65 3.7 26.2 1.0 C A:LYS60 3.8 22.7 1.0 C A:LEU62 3.9 28.1 1.0 N A:GLY64 3.9 28.1 1.0 CA A:VAL65 4.0 26.7 1.0 CA A:PRO63 4.0 28.0 1.0 O3' D:DT2 4.2 23.6 1.0 N A:GLY66 4.3 26.5 1.0 O A:LYS61 4.3 27.8 1.0 N A:PRO63 4.4 28.4 1.0 CA A:LYS60 4.4 21.9 1.0 C A:PRO63 4.4 28.2 1.0 CG A:LYS60 4.4 22.8 1.0 CB A:VAL65 4.5 27.1 1.0 C A:LYS61 4.5 26.2 1.0 CA A:GLY66 4.5 26.5 1.0 C A:GLY64 4.6 27.7 1.0 O5' D:DC3 4.7 29.2 1.0 N A:LYS61 4.8 24.0 1.0 N A:LEU62 4.9 25.7 1.0 CA A:GLY64 4.9 27.9 1.0 CA A:LYS61 5.0 26.1 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