Sodium in PDB 5j2k: Ternary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus

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

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:T Mismatch at the Primer Terminus, PDB code: 5j2k 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 (°)	50.820, 80.170, 55.380, 90.00, 107.86, 90.00
R / Rfree (%)	22 / 28.4

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with T:T 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:T Mismatch at the Primer Terminus (pdb code 5j2k). 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:T Mismatch at the Primer Terminus, PDB code: 5j2k:
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:T 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:T 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 2.2 23.7 1.0 O A:ILE106 2.3 16.2 1.0 OP1 P:DG9 2.4 19.6 1.0 O P:HOH105 2.5 14.9 1.0 O A:VAL103 2.7 16.6 1.0 O A:HOH769 3.0 37.5 1.0 C A:THR101 3.2 20.0 1.0 C A:ILE106 3.3 16.7 1.0 P P:DG9 3.4 20.0 1.0 OP2 P:DG9 3.5 22.8 1.0 N A:ILE106 3.7 18.1 1.0 C A:VAL103 3.7 17.1 1.0 CA A:THR101 3.8 20.2 1.0 O A:HOH750 3.9 44.8 1.0 N A:GLY105 4.0 18.0 1.0 CA A:ILE106 4.0 16.7 1.0 N A:VAL103 4.2 20.2 1.0 CA A:SER104 4.3 16.7 1.0 N A:ARG102 4.3 20.1 1.0 N A:GLY107 4.3 16.9 1.0 O3' P:DC8 4.3 21.0 1.0 N A:SER104 4.4 18.2 1.0 C A:ARG102 4.4 20.8 1.0 CB A:THR101 4.4 19.3 1.0 CB A:ILE106 4.5 16.5 1.0 C A:SER104 4.5 18.4 1.0 CA A:GLY107 4.5 19.7 1.0 C A:GLY105 4.5 18.8 1.0 CA A:VAL103 4.6 18.4 1.0 O5' P:DG9 4.6 23.7 1.0 CA A:ARG102 4.6 20.3 1.0 O A:LEU100 4.8 17.3 1.0 O A:HOH549 4.8 28.2 1.0 CA A:GLY105 4.8 20.1 1.0

Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with T:T 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:T Mismatch at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:34.5 occ:1.00 O A:VAL65 2.1 26.9 1.0 O A:LYS60 2.3 29.3 1.0 O A:LEU62 2.4 29.4 1.0 OP1 D:DC3 2.6 31.9 1.0 O A:HOH592 2.9 28.2 1.0 O D:HOH107 3.0 35.8 1.0 C A:VAL65 3.2 25.7 1.0 C A:LYS60 3.4 29.2 1.0 C A:LEU62 3.5 28.6 1.0 P D:DC3 3.6 31.3 1.0 N A:VAL65 3.6 25.6 1.0 OP2 D:DC3 3.7 27.7 1.0 CA A:VAL65 3.9 25.0 1.0 CA A:PRO63 4.0 29.9 1.0 CB A:VAL65 4.1 25.2 1.0 N A:GLY64 4.1 28.1 1.0 N A:PRO63 4.1 29.1 1.0 CA A:LYS60 4.1 27.0 1.0 N A:LEU62 4.2 28.1 1.0 C A:LYS61 4.3 28.8 1.0 CG A:LYS60 4.3 28.1 1.0 N A:GLY66 4.3 26.3 1.0 C A:PRO63 4.5 29.6 1.0 N A:LYS61 4.5 28.1 1.0 O A:LYS61 4.5 28.0 1.0 CA A:LEU62 4.5 28.4 1.0 O3' D:DT2 4.5 28.9 1.0 CA A:GLY66 4.6 25.5 1.0 CA A:LYS61 4.7 30.0 1.0 C A:GLY64 4.7 27.1 1.0 O A:ALA59 4.8 24.9 1.0 CB A:LYS60 4.8 27.6 1.0 O5' D:DC3 4.9 33.8 1.0 CG1 A:VAL65 5.0 26.0 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