Atomistry » Sodium » PDB 6nib-6nxy » 6nkv
Atomistry »
  Sodium »
    PDB 6nib-6nxy »
      6nkv »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy