Atomistry » Sodium » PDB 6nic-6nyp » 6nkz
Atomistry »
  Sodium »
    PDB 6nic-6nyp »
      6nkz »

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

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy