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

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

All present enzymatic activity of Ternary Complex Crystal Structure 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 Dna Polymerase Beta with "Hot- Spot Sequence" with Dgtp, PDB code: 6nku 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) 23.29 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.630, 79.764, 55.378, 90.00, 107.69, 90.00
R / Rfree (%) 17.4 / 21.1

Other elements in 6nku:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with 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 Dgtp (pdb code 6nku). 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 Dgtp, PDB code: 6nku:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nku

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

b:25.4
occ:1.00
 O A:THR101 2.3 25.9 1.0
O A:ILE106 2.3 22.8 1.0
OP1 P:DT9 2.4 22.6 1.0
O A:VAL103 2.4 21.2 1.0
O P:HOH203 2.5 25.4 1.0
C A:THR101 3.3 23.5 1.0
C A:ILE106 3.4 24.8 1.0
C A:VAL103 3.4 23.3 1.0
P P:DT9 3.5 22.0 1.0
OP2 P:DT9 3.7 20.8 1.0
N A:ILE106 3.8 20.2 1.0
CA A:THR101 3.9 27.4 1.0
O A:HOH752 4.0 45.0 1.0
CA A:SER104 4.0 23.1 1.0
N A:GLY105 4.1 22.4 1.0
CA A:ILE106 4.1 21.2 1.0
N A:SER104 4.1 21.6 1.0
N A:VAL103 4.1 23.9 1.0
C A:ARG102 4.3 25.7 1.0
N A:ARG102 4.4 25.2 1.0
C A:SER104 4.4 21.7 1.0
CA A:VAL103 4.4 21.8 1.0
O3' P:DC8 4.4 22.1 1.0
N A:GLY107 4.4 22.6 1.0
CB A:THR101 4.4 25.1 1.0
CB A:ILE106 4.5 24.6 1.0
CA A:ARG102 4.6 27.7 1.0
C A:GLY105 4.7 22.3 1.0
CA A:GLY107 4.7 22.9 1.0
O A:ARG102 4.7 27.2 1.0
O5' P:DT9 4.7 25.4 1.0
O A:LEU100 4.8 23.2 1.0
CA A:GLY105 4.9 24.8 1.0

Sodium binding site 2 out of 3 in 6nku

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

b:32.7
occ:1.00
 O A:LEU62 2.3 32.4 1.0
O A:VAL65 2.4 31.0 1.0
O A:LYS60 2.4 33.2 1.0
O A:HOH744 2.5 33.8 1.0
OP1 D:DC3 2.6 35.7 1.0
O D:HOH204 2.7 39.6 1.0
C A:LEU62 3.3 33.6 1.0
C A:VAL65 3.4 31.6 1.0
C A:LYS60 3.5 35.9 1.0
P D:DC3 3.7 34.7 1.0
N A:VAL65 3.8 28.7 1.0
OP2 D:DC3 3.9 32.8 1.0
N A:LEU62 4.0 31.3 1.0
CA A:PRO63 4.0 33.3 1.0
CA A:VAL65 4.1 31.0 1.0
N A:PRO63 4.1 35.9 1.0
C A:LYS61 4.1 35.8 1.0
N A:GLY64 4.1 31.7 1.0
CA A:LYS60 4.2 31.1 1.0
CA A:LEU62 4.3 31.1 1.0
CB A:VAL65 4.3 27.8 1.0
CG A:LYS60 4.4 32.6 1.0
C A:PRO63 4.4 31.5 1.0
N A:LYS61 4.4 32.5 1.0
O A:LYS61 4.5 32.7 1.0
N A:GLY66 4.5 29.9 1.0
CA A:LYS61 4.6 32.7 1.0
O3' D:DT2 4.6 36.7 1.0
C A:GLY64 4.8 32.6 1.0
O A:ALA59 4.8 30.0 1.0
CA A:GLY66 4.8 32.2 1.0
O5' D:DC3 4.9 37.5 1.0
CB A:LYS60 5.0 32.1 1.0
NZ A:LYS60 5.0 48.6 1.0

Sodium binding site 3 out of 3 in 6nku

Go back to Sodium Binding Sites List in 6nku
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure 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 Dna Polymerase Beta with "Hot- Spot Sequence" with Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:23.9
occ:1.00
 OD2 A:ASP190 2.2 27.9 1.0
OD1 A:ASP192 2.2 22.2 1.0
OD2 A:ASP256 2.2 25.3 1.0
O1A A:DGT407 2.5 19.1 1.0
CG A:ASP190 2.8 25.3 1.0
OD1 A:ASP190 2.9 22.1 1.0
CG A:ASP192 3.2 20.7 1.0
CG A:ASP256 3.4 24.9 1.0
MG A:MG401 3.5 19.7 1.0
OD2 A:ASP192 3.5 20.9 1.0
PA A:DGT407 3.5 20.9 1.0
C3' P:2DT10 3.6 28.4 1.0
O5' A:DGT407 3.9 24.6 1.0
CB A:ASP256 4.0 23.2 1.0
O2A A:DGT407 4.0 19.4 1.0
C5' A:DGT407 4.2 22.0 1.0
CB A:ASP190 4.2 19.6 1.0
C4' P:2DT10 4.2 31.4 1.0
C5' P:2DT10 4.3 30.3 1.0
O A:HOH601 4.3 33.0 1.0
OD1 A:ASP256 4.4 24.6 1.0
O A:HOH717 4.4 28.0 1.0
CB A:ASP192 4.5 20.4 1.0
O A:MET191 4.6 21.4 1.0
O1G A:DGT407 4.7 18.9 1.0
O5' P:2DT10 4.8 30.4 1.0
C2' P:2DT10 4.8 27.8 1.0
OP1 P:2DT10 4.8 24.9 1.0
NH2 A:ARG254 4.9 24.0 1.0
C A:MET191 4.9 19.9 1.0
O3A A:DGT407 5.0 22.4 1.0
CA A:ASP192 5.0 21.4 1.0
O1B A:DGT407 5.0 18.2 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot-Spot Sequence" with Dgtp To Be Published.
Page generated: Mon Aug 18 06:15:51 2025

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