Sodium in PDB 5j29: Ternary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus, PDB code: 5j29 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 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.800, 79.830, 55.500, 90.00, 107.59, 90.00
R / Rfree (%)	21.2 / 28.3

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

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A:A Mismatch at the Primer Terminus (pdb code 5j29). 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:A Mismatch at the Primer Terminus, PDB code: 5j29:
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:A 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:A Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:26.6 occ:1.00 OP1 P:DG9 2.2 18.2 1.0 O P:HOH105 2.4 15.9 1.0 O A:ILE106 2.4 14.1 1.0 O A:THR101 2.5 21.8 1.0 O P:HOH115 2.6 34.2 1.0 O A:VAL103 2.8 11.7 1.0 C A:THR101 3.3 20.3 1.0 P P:DG9 3.3 18.3 1.0 C A:ILE106 3.4 16.2 1.0 OP2 P:DG9 3.5 22.2 1.0 C A:VAL103 3.7 13.9 1.0 N A:ILE106 3.7 17.4 1.0 CA A:THR101 3.9 19.5 1.0 N A:GLY105 4.0 16.3 1.0 CA A:ILE106 4.1 16.4 1.0 CA A:SER104 4.2 15.2 1.0 N A:VAL103 4.2 16.4 1.0 N A:ARG102 4.3 19.1 1.0 N A:SER104 4.3 13.3 1.0 C A:ARG102 4.3 18.3 1.0 O3' P:DC8 4.4 17.9 1.0 N A:GLY107 4.5 15.7 1.0 CB A:ILE106 4.5 17.9 1.0 C A:SER104 4.5 15.3 1.0 O5' P:DG9 4.5 22.5 1.0 CB A:THR101 4.6 19.1 1.0 CA A:ARG102 4.6 19.6 1.0 CA A:VAL103 4.6 14.5 1.0 C A:GLY105 4.6 16.6 1.0 CA A:GLY107 4.7 18.7 1.0 O A:LEU100 4.8 18.9 1.0 O A:ARG102 4.8 18.7 1.0 CA A:GLY105 4.9 17.6 1.0 O A:HOH735 5.0 37.9 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with A:A 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:A Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:39.3 occ:1.00 O A:HOH605 2.4 29.9 1.0 O A:LYS60 2.4 30.6 1.0 O A:VAL65 2.4 24.5 1.0 O A:LEU62 2.4 28.2 1.0 OP1 D:DC3 2.8 30.8 1.0 O D:HOH103 3.1 24.0 1.0 C A:LYS60 3.2 30.3 1.0 C A:LEU62 3.4 27.6 1.0 C A:VAL65 3.5 25.9 1.0 N A:VAL65 3.9 22.2 1.0 CA A:LYS60 3.9 30.2 1.0 P D:DC3 3.9 32.3 1.0 C A:LYS61 3.9 28.2 1.0 N A:LEU62 4.0 26.7 1.0 N A:LYS61 4.1 29.4 1.0 OP2 D:DC3 4.1 24.6 1.0 O D:HOH106 4.1 24.4 1.0 CA A:VAL65 4.1 24.7 1.0 CA A:PRO63 4.1 28.6 1.0 N A:PRO63 4.1 28.8 1.0 O A:LYS61 4.2 28.2 1.0 CB A:VAL65 4.2 23.9 1.0 N A:GLY64 4.2 25.5 1.0 CG A:LYS60 4.2 34.8 1.0 CA A:LYS61 4.3 29.4 1.0 CA A:LEU62 4.3 26.4 1.0 O A:ALA59 4.5 25.7 1.0 C A:PRO63 4.5 27.1 1.0 N A:GLY66 4.6 27.6 1.0 CB A:LYS60 4.7 30.8 1.0 O3' D:DT2 4.8 29.7 1.0 C A:GLY64 4.9 24.6 1.0 CA A:GLY66 4.9 29.1 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