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

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

All present enzymatic activity of Ternary Complex Crystal Structure 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 Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp, PDB code: 6nkw 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) 31.16 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.441, 79.186, 55.352, 90.00, 107.60, 90.00
R / Rfree (%) 17.4 / 21.7

Other elements in 6nkw:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp (pdb code 6nkw). 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 Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma-Methylene Dgtp, PDB code: 6nkw:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nkw

Go back to Sodium Binding Sites List in 6nkw
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure 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 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:22.4
occ:1.00
 O A:THR101 2.3 19.6 1.0
O A:ILE106 2.4 18.0 1.0
O P:HOH205 2.5 19.5 1.0
OP1 P:DT9 2.5 19.2 1.0
O A:VAL103 2.5 18.3 1.0
O A:HOH773 2.6 24.9 1.0
C A:THR101 3.4 17.9 1.0
C A:VAL103 3.4 17.5 1.0
C A:ILE106 3.4 18.9 1.0
P P:DT9 3.5 18.6 1.0
OP2 P:DT9 3.6 19.6 1.0
N A:ILE106 3.7 19.6 1.0
CA A:THR101 3.9 20.2 1.0
CA A:SER104 4.0 20.0 1.0
N A:GLY105 4.0 18.0 1.0
N A:SER104 4.1 16.9 1.0
CA A:ILE106 4.1 16.6 1.0
N A:VAL103 4.2 18.2 1.0
C A:ARG102 4.3 22.2 1.0
C A:SER104 4.3 19.5 1.0
O3' P:DC8 4.3 16.4 1.0
CB A:THR101 4.4 21.1 1.0
N A:ARG102 4.4 18.1 1.0
CA A:VAL103 4.4 20.5 1.0
N A:GLY107 4.4 18.0 1.0
CB A:ILE106 4.5 20.1 1.0
C A:GLY105 4.6 19.6 1.0
CA A:ARG102 4.6 22.7 1.0
O A:ARG102 4.7 21.9 1.0
CA A:GLY107 4.7 19.7 1.0
O5' P:DT9 4.7 22.6 1.0
CA A:GLY105 4.8 19.0 1.0
O A:LEU100 4.8 18.8 1.0

Sodium binding site 2 out of 3 in 6nkw

Go back to Sodium Binding Sites List in 6nkw
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure 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 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:30.4
occ:1.00
 O A:VAL65 2.4 26.1 1.0
O A:LEU62 2.4 26.1 1.0
O A:LYS60 2.4 29.3 1.0
O A:HOH767 2.5 34.0 1.0
OP1 D:DC3 2.6 27.8 1.0
O D:HOH206 2.6 33.3 1.0
C A:LEU62 3.4 26.6 1.0
C A:VAL65 3.4 27.7 1.0
C A:LYS60 3.5 27.8 1.0
P D:DC3 3.7 29.7 1.0
N A:VAL65 3.8 23.1 1.0
OP2 D:DC3 3.8 25.9 1.0
CA A:PRO63 4.0 27.4 1.0
N A:LEU62 4.0 24.0 1.0
CA A:VAL65 4.0 24.5 1.0
N A:PRO63 4.1 29.0 1.0
O D:HOH212 4.1 41.0 1.0
C A:LYS61 4.1 29.9 1.0
N A:GLY64 4.1 29.3 1.0
CA A:LYS60 4.3 23.8 1.0
CA A:LEU62 4.3 23.4 1.0
CB A:VAL65 4.3 23.2 1.0
O A:LYS61 4.4 28.6 1.0
CG A:LYS60 4.5 27.5 1.0
N A:GLY66 4.5 26.8 1.0
C A:PRO63 4.5 29.3 1.0
N A:LYS61 4.5 24.6 1.0
O3' D:DT2 4.5 25.8 1.0
CA A:LYS61 4.6 29.2 1.0
C A:GLY64 4.7 25.9 1.0
CA A:GLY66 4.8 29.7 1.0
O A:ALA59 4.9 24.5 1.0
O5' D:DC3 4.9 28.4 1.0
CB A:LYS60 5.0 25.6 1.0

Sodium binding site 3 out of 3 in 6nkw

Go back to Sodium Binding Sites List in 6nkw
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure 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 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:24.4
occ:1.00
 OD1 A:ASP192 2.1 18.5 1.0
OD2 A:ASP256 2.2 22.9 1.0
OD2 A:ASP190 2.2 24.6 1.0
O A:HOH638 2.5 43.5 1.0
O1A A:GGH407 2.7 17.4 1.0
CG A:ASP190 3.0 21.8 1.0
CG A:ASP192 3.2 17.1 1.0
OD1 A:ASP190 3.2 20.8 1.0
CG A:ASP256 3.3 22.8 1.0
C3' P:2DT10 3.5 26.8 1.0
OD2 A:ASP192 3.5 14.9 1.0
MG A:MG401 3.6 16.5 1.0
P1 A:GGH407 3.7 17.7 1.0
CB A:ASP256 3.8 18.0 1.0
O5' A:GGH407 3.9 18.4 1.0
C4' P:2DT10 4.1 26.5 1.0
C5' A:GGH407 4.2 16.7 1.0
C5' P:2DT10 4.2 23.4 1.0
O2A A:GGH407 4.2 19.5 1.0
O A:HOH557 4.2 30.9 1.0
CB A:ASP190 4.3 19.7 1.0
OD1 A:ASP256 4.3 21.1 1.0
CB A:ASP192 4.5 15.6 1.0
O A:MET191 4.6 17.8 1.0
O5' P:2DT10 4.7 24.6 1.0
C2' P:2DT10 4.7 26.8 1.0
O1G A:GGH407 4.8 22.1 1.0
NH2 A:ARG254 4.9 21.7 1.0
N A:ASP256 4.9 17.6 1.0
CA A:ASP192 4.9 16.7 1.0
C A:MET191 4.9 19.5 1.0
OP1 P:2DT10 5.0 24.9 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.
Page generated: Mon Aug 18 06:16:13 2025

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