Sodium in PDB 5j2d: Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus, PDB code: 5j2d 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 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.740, 79.940, 55.480, 90.00, 107.63, 90.00
R / Rfree (%)	20.1 / 25.6

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

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C:C Mismatch at the Primer Terminus (pdb code 5j2d). 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 C:C Mismatch at the Primer Terminus, PDB code: 5j2d:
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 C: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 C:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:22.6 occ:1.00 O A:THR101 2.4 19.3 1.0 O P:HOH110 2.4 28.2 1.0 OP1 P:DG9 2.4 19.4 1.0 O A:ILE106 2.6 15.6 1.0 O A:VAL103 2.7 12.9 1.0 O A:HOH728 2.8 36.4 1.0 C A:THR101 3.3 17.4 1.0 C A:ILE106 3.5 15.2 1.0 P P:DG9 3.5 21.3 1.0 C A:VAL103 3.5 15.0 1.0 OP2 P:DG9 3.8 23.1 1.0 N A:ILE106 3.8 16.7 1.0 CA A:THR101 3.8 16.9 1.0 N A:GLY105 4.0 17.1 1.0 CA A:SER104 4.1 16.7 1.0 N A:VAL103 4.1 14.3 1.0 CA A:ILE106 4.2 14.7 1.0 N A:SER104 4.2 15.6 1.0 N A:ARG102 4.3 16.9 1.0 C A:ARG102 4.3 16.1 1.0 C A:SER104 4.4 16.4 1.0 CB A:THR101 4.5 16.2 1.0 N A:GLY107 4.5 14.9 1.0 CA A:VAL103 4.5 14.8 1.0 CB A:ILE106 4.5 14.0 1.0 O3' P:DC8 4.6 20.0 1.0 CA A:ARG102 4.6 17.3 1.0 O5' P:DG9 4.6 24.9 1.0 C A:GLY105 4.6 16.6 1.0 CA A:GLY107 4.7 17.0 1.0 O A:LEU100 4.8 16.3 1.0 O A:ARG102 4.8 16.9 1.0 CA A:GLY105 4.9 17.9 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with C: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 C:C Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:33.9 occ:1.00 O A:VAL65 2.3 24.5 1.0 O A:LEU62 2.4 30.3 1.0 O A:LYS60 2.6 27.5 1.0 OP1 D:DC3 2.7 29.2 1.0 O A:HOH588 2.8 22.0 1.0 C A:VAL65 3.4 24.1 1.0 C A:LEU62 3.5 29.7 1.0 C A:LYS60 3.5 28.3 1.0 O D:HOH107 3.7 29.4 1.0 P D:DC3 3.7 29.7 1.0 N A:VAL65 3.7 23.9 1.0 OP2 D:DC3 3.8 28.6 1.0 CA A:VAL65 4.0 22.9 1.0 N A:GLY64 4.1 27.0 1.0 CA A:PRO63 4.2 29.9 1.0 N A:LEU62 4.2 29.8 1.0 CA A:LYS60 4.2 27.4 1.0 N A:PRO63 4.2 30.5 1.0 C A:LYS61 4.3 30.1 1.0 CB A:VAL65 4.3 22.9 1.0 CG A:LYS60 4.3 29.4 1.0 N A:LYS61 4.4 28.9 1.0 N A:GLY66 4.4 23.5 1.0 CA A:LEU62 4.5 28.9 1.0 C A:PRO63 4.5 28.4 1.0 O3' D:DT2 4.5 29.1 1.0 O A:LYS61 4.5 30.6 1.0 CA A:LYS61 4.6 30.6 1.0 CA A:GLY66 4.7 22.7 1.0 C A:GLY64 4.7 24.6 1.0 O A:ALA59 4.9 22.0 1.0 CB A:LYS60 4.9 27.8 1.0 O5' D:DC3 5.0 33.5 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