Sodium in PDB 5j2j: Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G Mismatch at the Primer Terminus, PDB code: 5j2j 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 (°)	50.820, 80.170, 55.510, 90.00, 107.85, 90.00
R / Rfree (%)	20.1 / 26.6

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G 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 T:G Mismatch at the Primer Terminus (pdb code 5j2j). 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 T:G Mismatch at the Primer Terminus, PDB code: 5j2j:
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 T:G 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 T:G Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:14.7 occ:1.00 O A:THR101 2.4 20.6 1.0 O P:HOH107 2.4 35.1 1.0 OP1 P:DG9 2.5 22.7 1.0 O A:HOH718 2.5 36.0 1.0 O A:VAL103 2.5 14.1 1.0 O A:ILE106 2.5 11.9 1.0 C A:THR101 3.3 17.9 1.0 C A:VAL103 3.4 14.9 1.0 P P:DG9 3.5 17.6 1.0 C A:ILE106 3.5 13.0 1.0 OP2 P:DG9 3.6 20.7 1.0 N A:ILE106 3.8 16.2 1.0 CA A:SER104 3.9 15.2 1.0 N A:GLY105 3.9 12.5 1.0 N A:SER104 4.0 13.3 1.0 O A:HOH662 4.0 23.8 1.0 N A:VAL103 4.0 15.4 1.0 CA A:THR101 4.0 18.8 1.0 CA A:ILE106 4.2 15.1 1.0 C A:ARG102 4.2 16.1 1.0 N A:ARG102 4.3 15.9 1.0 C A:SER104 4.3 14.3 1.0 O3' P:DC8 4.4 17.6 1.0 CA A:VAL103 4.4 14.7 1.0 CA A:ARG102 4.5 16.8 1.0 N A:GLY107 4.5 12.8 1.0 CB A:ILE106 4.6 15.9 1.0 O A:ARG102 4.6 16.6 1.0 C A:GLY105 4.7 15.5 1.0 CB A:THR101 4.7 18.4 1.0 O5' P:DG9 4.7 20.9 1.0 CA A:GLY107 4.8 13.6 1.0 O A:LEU100 4.8 15.9 1.0 CA A:GLY105 4.9 14.6 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:G 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 T:G Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:32.9 occ:1.00 O A:LEU62 2.3 26.6 1.0 O A:LYS60 2.4 24.2 1.0 O A:VAL65 2.4 23.8 1.0 O D:HOH106 2.5 32.9 1.0 OP1 D:DC3 2.5 29.3 1.0 O A:HOH515 2.7 31.3 1.0 C A:LYS60 3.4 25.1 1.0 C A:LEU62 3.4 27.8 1.0 C A:VAL65 3.4 23.3 1.0 O D:HOH111 3.6 35.3 1.0 P D:DC3 3.7 30.4 1.0 N A:VAL65 3.8 23.4 1.0 OP2 D:DC3 3.9 28.9 1.0 CA A:VAL65 4.0 23.8 1.0 C A:LYS61 4.1 27.4 1.0 N A:LEU62 4.1 26.6 1.0 CA A:LYS60 4.1 23.5 1.0 CA A:PRO63 4.1 28.8 1.0 N A:PRO63 4.1 28.6 1.0 CB A:VAL65 4.2 24.7 1.0 N A:GLY64 4.2 26.4 1.0 O A:LYS61 4.3 28.9 1.0 N A:LYS61 4.3 26.7 1.0 CG A:LYS60 4.3 23.9 1.0 CA A:LEU62 4.4 26.4 1.0 N A:GLY66 4.5 23.3 1.0 CA A:LYS61 4.5 27.5 1.0 C A:PRO63 4.5 27.2 1.0 O3' D:DT2 4.6 27.6 1.0 O A:ALA59 4.7 21.8 1.0 CA A:GLY66 4.8 23.7 1.0 C A:GLY64 4.8 24.6 1.0 O5' D:DC3 4.8 32.8 1.0 CB A:LYS60 4.8 22.7 1.0 NZ A:LYS60 4.9 28.0 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