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

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of 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 Chf Analogue of Dgtp, PDB code: 6nkv 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) 23.73 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.636, 79.707, 55.412, 90.00, 107.63, 90.00
R / Rfree (%) 16.4 / 20.3

Other elements in 6nkv:

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

Fluorine (F) 1 atom
Magnesium (Mg) 2 atoms
Chlorine (Cl) 3 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 Chf Analogue of Dgtp (pdb code 6nkv). 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 Chf Analogue of Dgtp, PDB code: 6nkv:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nkv

Go back to Sodium Binding Sites List in 6nkv
Sodium binding site 1 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf 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 Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:17.4
occ:1.00
 OD1 A:ASP192 2.2 13.4 1.0
OD2 A:ASP190 2.3 17.6 1.0
OD2 A:ASP256 2.3 18.7 1.0
O1A A:GFH408 2.5 11.9 1.0
CG A:ASP190 2.9 16.5 1.0
OD1 A:ASP190 3.1 11.7 1.0
CG A:ASP192 3.2 12.2 1.0
CG A:ASP256 3.4 17.3 1.0
MG A:MG401 3.5 11.8 1.0
C3' P:2DT10 3.5 21.6 1.0
OD2 A:ASP192 3.5 11.6 1.0
PA A:GFH408 3.6 13.6 1.0
O5' A:GFH408 3.9 13.6 1.0
CB A:ASP256 4.1 16.5 1.0
O2A A:GFH408 4.1 14.2 1.0
C4' P:2DT10 4.1 23.4 1.0
C5' P:2DT10 4.2 22.4 1.0
C5' A:GFH408 4.3 13.0 1.0
CB A:ASP190 4.3 14.3 1.0
O A:HOH604 4.4 25.1 1.0
O A:HOH755 4.4 23.3 1.0
OD1 A:ASP256 4.4 15.5 1.0
CB A:ASP192 4.5 11.7 1.0
O1G A:GFH408 4.6 16.0 1.0
O5' P:2DT10 4.7 21.1 1.0
O A:MET191 4.7 11.8 1.0
C2' P:2DT10 4.7 21.0 1.0
OP1 P:2DT10 4.8 19.4 1.0
NH2 A:ARG254 4.8 16.3 1.0
CA A:ASP192 5.0 13.7 1.0

Sodium binding site 2 out of 3 in 6nkv

Go back to Sodium Binding Sites List in 6nkv
Sodium binding site 2 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf 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 Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:17.0
occ:1.00
 O A:THR101 2.3 17.4 1.0
O A:ILE106 2.4 14.4 1.0
O A:VAL103 2.5 12.8 1.0
O A:HOH815 2.5 19.2 1.0
O P:HOH104 2.5 19.8 1.0
OP1 P:DT9 2.6 15.1 1.0
C A:THR101 3.3 17.1 1.0
C A:VAL103 3.4 10.4 1.0
C A:ILE106 3.5 16.8 1.0
P P:DT9 3.6 15.7 1.0
OP2 P:DT9 3.7 14.1 1.0
N A:ILE106 3.8 12.6 1.0
CA A:THR101 3.9 16.6 1.0
O A:HOH759 3.9 47.5 1.0
CA A:SER104 4.0 14.5 1.0
N A:SER104 4.1 14.4 1.0
N A:VAL103 4.1 14.3 1.0
N A:GLY105 4.1 13.5 1.0
CA A:ILE106 4.1 13.6 1.0
C A:ARG102 4.3 17.7 1.0
N A:ARG102 4.3 15.6 1.0
CA A:VAL103 4.4 13.8 1.0
C A:SER104 4.4 14.0 1.0
CB A:THR101 4.4 18.7 1.0
N A:GLY107 4.5 13.4 1.0
CB A:ILE106 4.5 15.5 1.0
O3' P:DC8 4.5 16.4 1.0
CA A:ARG102 4.5 18.8 1.0
O P:HOH125 4.6 41.2 1.0
C A:GLY105 4.7 14.3 1.0
O A:ARG102 4.7 17.9 1.0
CA A:GLY107 4.7 13.7 1.0
O A:HOH797 4.7 35.4 1.0
O A:LEU100 4.8 13.7 1.0
O5' P:DT9 4.8 15.7 1.0
O A:HOH563 4.9 30.4 1.0
CA A:GLY105 5.0 15.5 1.0

Sodium binding site 3 out of 3 in 6nkv

Go back to Sodium Binding Sites List in 6nkv
Sodium binding site 3 out of 3 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with "Hot- Spot Sequence" with Beta-Gamma Chf Analogue of 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 Chf Analogue of Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:22.5
occ:1.00
 O A:LEU62 2.4 20.7 1.0
O A:VAL65 2.4 19.9 1.0
O A:HOH806 2.4 24.7 1.0
O A:LYS60 2.4 23.0 1.0
O D:HOH104 2.6 27.5 1.0
OP1 D:DC3 2.7 23.8 1.0
C A:LEU62 3.3 22.3 1.0
C A:LYS60 3.5 25.9 1.0
C A:VAL65 3.5 21.3 1.0
P D:DC3 3.7 23.6 1.0
OP2 D:DC3 3.8 20.6 1.0
N A:VAL65 3.8 18.2 1.0
N A:LEU62 4.0 20.9 1.0
CA A:PRO63 4.0 25.0 1.0
O D:HOH112 4.1 30.4 1.0
C A:LYS61 4.1 27.5 1.0
N A:PRO63 4.1 26.8 1.0
CA A:VAL65 4.1 18.3 1.0
N A:GLY64 4.2 20.7 1.0
CA A:LYS60 4.2 21.5 1.0
CA A:LEU62 4.3 20.4 1.0
O A:LYS61 4.4 23.2 1.0
CB A:VAL65 4.4 17.4 1.0
N A:LYS61 4.4 23.9 1.0
CG A:LYS60 4.4 28.1 1.0
C A:PRO63 4.5 23.2 1.0
CA A:LYS61 4.5 24.5 1.0
N A:GLY66 4.6 21.8 1.0
O3' D:DT2 4.6 21.3 1.0
C A:GLY64 4.8 21.1 1.0
CA A:GLY66 4.9 23.7 1.0
O A:ALA59 4.9 20.8 1.0
O5' D:DC3 4.9 24.0 1.0
CB A:LYS60 4.9 23.6 1.0

Reference:

V.K.Batra, S.H.Wilson. Ternary Complex Crystal Structure To Be Published.
Page generated: Tue Oct 8 12:17:24 2024

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