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

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

All present enzymatic activity of Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene 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 Beta-Gamma Methylene Dgtp, PDB code: 6nkz 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) 21.33 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.642, 80.043, 55.249, 90.00, 107.92, 90.00
R / Rfree (%) 18.6 / 23.5

Other elements in 6nkz:

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

Magnesium (Mg) 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 Beta-Gamma Methylene Dgtp (pdb code 6nkz). 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 Beta-Gamma Methylene Dgtp, PDB code: 6nkz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nkz

Go back to Sodium Binding Sites List in 6nkz
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 Beta-Gamma Methylene 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 Beta-Gamma Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na101

b:25.3
occ:1.00
 O A:THR101 2.3 24.1 1.0
O A:ILE106 2.4 18.5 1.0
O P:HOH202 2.4 26.1 1.0
O A:VAL103 2.5 22.7 1.0
OP1 P:DT9 2.5 23.4 1.0
O A:HOH715 2.6 25.3 1.0
C A:THR101 3.3 23.4 1.0
C A:VAL103 3.4 24.9 1.0
C A:ILE106 3.5 22.4 1.0
P P:DT9 3.5 23.8 1.0
OP2 P:DT9 3.7 23.3 1.0
N A:ILE106 3.8 21.6 1.0
O A:HOH711 3.9 40.4 1.0
CA A:THR101 3.9 24.8 1.0
CA A:SER104 4.0 24.3 1.0
N A:GLY105 4.0 23.9 1.0
N A:SER104 4.1 21.9 1.0
N A:VAL103 4.1 24.7 1.0
CA A:ILE106 4.2 21.9 1.0
C A:ARG102 4.3 25.2 1.0
N A:ARG102 4.4 25.0 1.0
C A:SER104 4.4 23.9 1.0
CA A:VAL103 4.4 23.1 1.0
CB A:THR101 4.4 25.1 1.0
O3' P:DC8 4.5 20.8 1.0
N A:GLY107 4.5 23.9 1.0
CB A:ILE106 4.6 24.4 1.0
CA A:ARG102 4.6 27.9 1.0
C A:GLY105 4.7 24.3 1.0
O A:ARG102 4.7 27.0 1.0
O A:HOH680 4.7 36.2 1.0
O5' P:DT9 4.8 25.7 1.0
CA A:GLY107 4.8 24.2 1.0
O A:LEU100 4.9 22.3 1.0
CA A:GLY105 4.9 24.6 1.0

Sodium binding site 2 out of 3 in 6nkz

Go back to Sodium Binding Sites List in 6nkz
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 Beta-Gamma Methylene 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 Beta-Gamma Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:34.9
occ:1.00
 O A:LEU62 2.3 37.0 1.0
O A:LYS60 2.4 36.5 1.0
O A:HOH720 2.4 37.8 1.0
O A:VAL65 2.4 35.5 1.0
O D:HOH202 2.6 35.6 1.0
OP1 D:DC3 2.7 31.4 1.0
C A:LEU62 3.3 34.4 1.0
C A:LYS60 3.4 35.9 1.0
C A:VAL65 3.6 32.3 1.0
P D:DC3 3.8 31.5 1.0
N A:LEU62 3.9 35.9 1.0
N A:VAL65 4.0 32.5 1.0
CA A:PRO63 4.0 37.2 1.0
O D:HOH206 4.0 44.4 1.0
N A:PRO63 4.0 37.3 1.0
OP2 D:DC3 4.0 30.2 1.0
CA A:LYS60 4.1 33.4 1.0
C A:LYS61 4.1 39.9 1.0
CA A:VAL65 4.2 29.4 1.0
CG A:LYS60 4.2 34.5 1.0
N A:GLY64 4.2 34.3 1.0
CA A:LEU62 4.3 33.6 1.0
N A:LYS61 4.4 33.5 1.0
CB A:VAL65 4.4 31.6 1.0
O A:LYS61 4.4 36.5 1.0
C A:PRO63 4.4 36.4 1.0
CA A:LYS61 4.5 36.5 1.0
N A:GLY66 4.6 28.8 1.0
CB A:LYS60 4.8 35.9 1.0
O A:ALA59 4.8 33.5 1.0
O3' D:DT2 4.8 34.0 1.0
C A:GLY64 4.9 35.1 1.0
CA A:GLY66 4.9 30.4 1.0

Sodium binding site 3 out of 3 in 6nkz

Go back to Sodium Binding Sites List in 6nkz
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 Beta-Gamma Methylene 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 Beta-Gamma Methylene Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:24.6
occ:1.00
 OD2 A:ASP190 2.1 26.4 1.0
OD1 A:ASP192 2.2 20.7 1.0
OD2 A:ASP256 2.3 29.1 1.0
O1A A:GGH403 2.5 21.9 1.0
O A:HOH587 2.6 33.9 1.0
CG A:ASP190 2.9 24.8 1.0
OD1 A:ASP190 3.0 23.0 1.0
CG A:ASP192 3.2 21.4 1.0
CG A:ASP256 3.4 22.5 1.0
MG A:MG401 3.4 19.3 1.0
OD2 A:ASP192 3.5 21.8 1.0
P1 A:GGH403 3.5 24.0 1.0
C3' P:2DT10 3.6 32.2 1.0
O5' A:GGH403 3.8 22.2 1.0
CB A:ASP256 4.0 24.1 1.0
O2A A:GGH403 4.0 23.4 1.0
C5' A:GGH403 4.1 23.2 1.0
C4' P:2DT10 4.3 31.9 1.0
CB A:ASP190 4.3 22.3 1.0
C5' P:2DT10 4.3 29.3 1.0
OD1 A:ASP256 4.4 23.2 1.0
CB A:ASP192 4.5 22.3 1.0
O1G A:GGH403 4.6 22.8 1.0
O A:HOH624 4.6 27.6 1.0
O5' P:2DT10 4.8 28.1 1.0
O A:MET191 4.8 21.6 1.0
C2' P:2DT10 4.8 27.5 1.0
OP1 P:2DT10 4.9 27.7 1.0
NH2 A:ARG254 4.9 22.8 1.0
O3A A:GGH403 5.0 24.6 1.0
CA A:ASP192 5.0 20.8 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Methylene Dgtp To Be Published.
Page generated: Mon Aug 18 06:16:47 2025

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