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Sodium in PDB 6nkt: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp, PDB code: 6nkt 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) 31.86 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.330, 79.669, 54.673, 90.00, 106.36, 90.00
R / Rfree (%) 19.9 / 30.3

Other elements in 6nkt:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp (pdb code 6nkt). 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 K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp, PDB code: 6nkt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6nkt

Go back to Sodium Binding Sites List in 6nkt
Sodium binding site 1 out of 2 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp


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 K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:26.5
occ:0.00
 O A:THR101 2.2 31.5 1.0
OP1 P:DG9 2.2 27.6 1.0
O A:ILE106 2.5 28.3 1.0
O A:VAL103 2.5 24.4 1.0
O A:HOH530 2.9 30.4 1.0
C A:VAL103 3.2 24.7 1.0
C A:THR101 3.4 22.6 1.0
CA A:SER104 3.4 22.8 1.0
P P:DG9 3.5 26.8 1.0
C A:ILE106 3.5 24.4 1.0
N A:SER104 3.7 26.2 1.0
N A:GLY105 3.7 24.6 1.0
N A:ILE106 3.7 24.1 1.0
OP2 P:DG9 3.8 31.2 1.0
C A:SER104 3.9 21.6 1.0
C A:ARG102 4.0 30.0 1.0
O A:ARG102 4.0 37.9 1.0
CA A:ILE106 4.2 24.8 1.0
N A:VAL103 4.2 22.0 1.0
CA A:THR101 4.3 26.3 1.0
N A:ARG102 4.3 26.3 1.0
CA A:VAL103 4.3 21.8 1.0
CA A:ARG102 4.4 26.6 1.0
O5' P:DG9 4.4 28.0 1.0
N A:GLY107 4.5 27.7 1.0
C A:GLY105 4.5 22.0 1.0
O3' P:DC8 4.6 26.3 1.0
CA A:GLY105 4.6 23.1 1.0
CB A:SER104 4.7 27.3 1.0
CB A:ILE106 4.7 30.2 1.0
CB A:THR101 4.8 25.2 1.0
O A:SER104 4.9 27.3 1.0
CA A:GLY107 4.9 28.2 1.0

Sodium binding site 2 out of 2 in 6nkt

Go back to Sodium Binding Sites List in 6nkt
Sodium binding site 2 out of 2 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp


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 K289M Variant of Dna Polymerase Beta with Beta-Gamma Difluoro Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:41.4
occ:1.00
 O A:VAL65 2.4 41.4 1.0
O A:LYS60 2.5 42.2 1.0
O A:LEU62 2.7 40.3 1.0
OP1 D:DC3 2.9 42.2 1.0
C A:LYS60 3.6 43.2 1.0
C A:VAL65 3.7 34.2 1.0
OP2 D:DC3 3.7 38.9 1.0
P D:DC3 3.8 41.6 1.0
C A:LEU62 3.9 41.9 1.0
CG A:LYS60 3.9 40.3 1.0
CA A:LYS60 4.2 39.5 1.0
N A:VAL65 4.4 42.6 1.0
N A:LEU62 4.4 41.1 1.0
C A:LYS61 4.5 43.8 1.0
CA A:VAL65 4.5 34.1 1.0
N A:GLY64 4.5 37.0 1.0
NZ A:LYS60 4.5 45.6 1.0
N A:GLY66 4.6 37.3 1.0
CB A:LYS60 4.7 39.4 1.0
CA A:PRO63 4.7 36.2 1.0
CA A:GLY66 4.7 34.2 1.0
N A:LYS61 4.7 45.8 1.0
O3' D:DT2 4.7 38.1 1.0
N A:PRO63 4.7 38.7 1.0
O A:LYS61 4.8 45.9 1.0
CB A:VAL65 4.8 36.0 1.0
CA A:LEU62 4.8 41.0 1.0
CA A:LYS61 4.9 44.3 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.
Page generated: Mon Aug 18 06:15:50 2025

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