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Sodium in PDB 6nkx: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp, PDB code: 6nkx 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) 26.25 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.516, 79.884, 55.200, 90.00, 107.99, 90.00
R / Rfree (%) 18.1 / 23.2

Other elements in 6nkx:

The structure of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp (pdb code 6nkx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp, PDB code: 6nkx:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nkx

Go back to Sodium Binding Sites List in 6nkx
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with 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 "Hot-Spot Sequence" with Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:19.5
occ:1.00
 O A:THR101 2.2 19.9 1.0
O P:HOH205 2.4 21.8 1.0
O A:ILE106 2.4 18.2 1.0
OP1 P:DT9 2.5 21.3 1.0
O A:VAL103 2.5 19.7 1.0
O A:HOH695 2.6 23.6 1.0
C A:THR101 3.3 21.9 1.0
P P:DT9 3.4 19.8 1.0
C A:VAL103 3.5 20.5 1.0
C A:ILE106 3.5 20.8 1.0
OP2 P:DT9 3.6 18.1 1.0
N A:ILE106 3.8 17.3 1.0
CA A:THR101 3.9 22.1 1.0
CA A:SER104 4.1 19.1 1.0
N A:GLY105 4.1 19.0 1.0
N A:SER104 4.1 16.5 1.0
N A:VAL103 4.2 20.5 1.0
CA A:ILE106 4.2 20.9 1.0
C A:ARG102 4.3 21.9 1.0
N A:ARG102 4.3 22.1 1.0
O3' P:DC8 4.4 15.9 1.0
CB A:THR101 4.4 18.3 1.0
C A:SER104 4.4 20.6 1.0
CA A:VAL103 4.5 18.8 1.0
N A:GLY107 4.5 20.5 1.0
CA A:ARG102 4.6 23.1 1.0
CB A:ILE106 4.6 18.0 1.0
O5' P:DT9 4.7 21.9 1.0
C A:GLY105 4.7 22.9 1.0
O A:ARG102 4.7 24.2 1.0
CA A:GLY107 4.7 19.1 1.0
O A:LEU100 4.9 19.8 1.0
O A:HOH652 4.9 30.3 1.0
CA A:GLY105 5.0 18.9 1.0

Sodium binding site 2 out of 3 in 6nkx

Go back to Sodium Binding Sites List in 6nkx
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with 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 "Hot-Spot Sequence" with Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:33.9
occ:1.00
 O A:LYS60 2.4 27.5 1.0
O A:LEU62 2.4 30.1 1.0
O A:HOH593 2.4 39.2 1.0
O D:HOH209 2.4 37.1 1.0
O A:VAL65 2.5 32.1 1.0
OP1 D:DC3 2.7 31.9 1.0
C A:LEU62 3.3 27.6 1.0
C A:LYS60 3.4 34.0 1.0
C A:VAL65 3.6 29.1 1.0
P D:DC3 3.8 32.7 1.0
N A:LEU62 3.9 30.3 1.0
C A:LYS61 3.9 38.5 1.0
N A:VAL65 4.0 31.2 1.0
OP2 D:DC3 4.0 33.3 1.0
N A:PRO63 4.1 35.8 1.0
CA A:PRO63 4.1 30.2 1.0
CA A:LYS60 4.1 27.7 1.0
CA A:LEU62 4.2 30.8 1.0
CA A:VAL65 4.2 28.9 1.0
N A:GLY64 4.3 32.6 1.0
O A:LYS61 4.3 34.8 1.0
N A:LYS61 4.3 33.1 1.0
CA A:LYS61 4.4 31.7 1.0
CG A:LYS60 4.4 36.0 1.0
CB A:VAL65 4.5 27.3 1.0
C A:PRO63 4.5 32.6 1.0
N A:GLY66 4.7 25.1 1.0
O A:ALA59 4.8 30.6 1.0
O3' D:DT2 4.8 31.3 1.0
CB A:LYS60 4.9 36.3 1.0
C A:GLY64 5.0 29.1 1.0
CA A:GLY66 5.0 28.7 1.0

Sodium binding site 3 out of 3 in 6nkx

Go back to Sodium Binding Sites List in 6nkx
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:22.7
occ:1.00
 OD1 A:ASP192 2.2 19.0 1.0
OD2 A:ASP190 2.2 23.0 1.0
OD2 A:ASP256 2.3 25.6 1.0
O1A A:DGT404 2.4 16.9 1.0
CG A:ASP190 2.9 18.9 1.0
OD1 A:ASP190 2.9 21.1 1.0
CG A:ASP192 3.2 19.5 1.0
MG A:MG401 3.4 17.4 1.0
OD2 A:ASP192 3.5 19.2 1.0
CG A:ASP256 3.5 22.8 1.0
PA A:DGT404 3.5 22.9 1.0
C3' P:2DT10 3.6 29.0 1.0
O5' A:DGT404 3.9 19.2 1.0
O2A A:DGT404 4.0 22.3 1.0
CB A:ASP256 4.1 21.0 1.0
C5' A:DGT404 4.1 19.6 1.0
CB A:ASP190 4.2 17.5 1.0
C4' P:2DT10 4.3 29.9 1.0
C5' P:2DT10 4.4 23.2 1.0
O P:HOH210 4.4 32.9 1.0
OD1 A:ASP256 4.5 21.2 1.0
O A:MET191 4.5 18.9 1.0
CB A:ASP192 4.5 18.5 1.0
O1G A:DGT404 4.6 19.1 1.0
C2' P:2DT10 4.8 24.4 1.0
O5' P:2DT10 4.8 24.7 1.0
C A:MET191 4.9 19.4 1.0
O1B A:DGT404 4.9 14.4 1.0
O3A A:DGT404 4.9 23.1 1.0
CA A:ASP192 5.0 20.3 1.0

Reference:

V.K.Batra, S.H.Wilson. PDBX_DESCRIPTOR Ternary Complex Crystal Structure To Be Published.
Page generated: Mon Aug 18 06:16:21 2025

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