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

Sodium in PDB 6nky: Ternary Complex Crystal Structure of K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp

Enzymatic activity of Ternary Complex Crystal Structure of K289M Variant 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 K289M Variant 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 K289M Variant of Dna Polymerase Beta with "Hot-Spot Sequence" with Beta-Gamma Chf Analogue of Dgtp, PDB code: 6nky 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) 21.98 / 2.09
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.643, 80.158, 55.251, 90.00, 107.89, 90.00
R / Rfree (%) 19.9 / 25.6

Other elements in 6nky:

The structure of Ternary Complex Crystal Structure of K289M Variant 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) 1 atom
Chlorine (Cl) 3 atoms

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 Chf Analogue of Dgtp (pdb code 6nky). 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 Chf Analogue of Dgtp, PDB code: 6nky:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6nky

Go back to Sodium Binding Sites List in 6nky
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 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 K289M Variant 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:31.2
occ:1.00
 OD2 A:ASP190 2.1 34.5 1.0
OD1 A:ASP192 2.2 32.6 1.0
OD2 A:ASP256 2.2 34.5 1.0
O A:HOH537 2.4 41.6 1.0
O1A A:GFH408 2.5 27.9 1.0
CG A:ASP190 3.1 30.6 1.0
CG A:ASP192 3.2 27.5 1.0
C3' P:2DT10 3.4 41.3 1.0
CG A:ASP256 3.4 33.5 1.0
PA A:GFH408 3.5 31.1 1.0
OD1 A:ASP190 3.5 31.4 1.0
OD2 A:ASP192 3.6 26.7 1.0
O5' A:GFH408 3.6 30.9 1.0
MG A:MG401 3.6 26.5 1.0
O2A A:GFH408 3.8 28.7 1.0
C5' A:GFH408 3.9 31.2 1.0
CB A:ASP256 4.0 34.7 1.0
C4' P:2DT10 4.1 41.2 1.0
C5' P:2DT10 4.3 39.8 1.0
OD1 A:ASP256 4.4 33.0 1.0
CB A:ASP190 4.4 29.0 1.0
CB A:ASP192 4.5 30.5 1.0
O5' P:2DT10 4.6 37.9 1.0
O1G A:GFH408 4.6 25.8 1.0
C2' P:2DT10 4.6 37.3 1.0
OP1 P:2DT10 4.7 37.8 1.0
NH2 A:ARG254 4.8 34.9 1.0
O A:MET191 4.9 29.4 1.0
O3A A:GFH408 4.9 30.0 1.0

Sodium binding site 2 out of 3 in 6nky

Go back to Sodium Binding Sites List in 6nky
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 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 K289M Variant 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:29.5
occ:1.00
 O A:THR101 2.3 32.8 1.0
OP1 P:DT9 2.4 29.4 1.0
O A:ILE106 2.4 27.6 1.0
O A:VAL103 2.5 28.9 1.0
O P:HOH101 2.5 31.0 1.0
O A:HOH666 3.2 43.3 1.0
C A:THR101 3.3 35.3 1.0
C A:VAL103 3.4 32.0 1.0
P P:DT9 3.5 33.8 1.0
C A:ILE106 3.5 28.6 1.0
OP2 P:DT9 3.6 28.8 1.0
N A:ILE106 3.8 31.4 1.0
CA A:SER104 3.9 31.8 1.0
O A:HOH662 4.0 42.8 1.0
N A:GLY105 4.0 29.8 1.0
N A:SER104 4.0 29.2 1.0
CA A:THR101 4.1 31.4 1.0
N A:VAL103 4.1 30.0 1.0
CA A:ILE106 4.1 28.8 1.0
C A:ARG102 4.2 29.5 1.0
C A:SER104 4.3 31.8 1.0
N A:ARG102 4.3 29.4 1.0
O3' P:DC8 4.4 29.1 1.0
CA A:VAL103 4.4 30.9 1.0
CA A:ARG102 4.5 33.1 1.0
N A:GLY107 4.5 32.9 1.0
CB A:ILE106 4.5 32.0 1.0
CB A:THR101 4.6 34.8 1.0
O A:ARG102 4.6 32.5 1.0
C A:GLY105 4.6 33.8 1.0
O5' P:DT9 4.7 33.5 1.0
CA A:GLY107 4.8 32.9 1.0
CA A:GLY105 4.9 32.5 1.0
O A:LEU100 4.9 28.2 1.0

Sodium binding site 3 out of 3 in 6nky

Go back to Sodium Binding Sites List in 6nky
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 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 K289M Variant 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:40.4
occ:1.00
 O A:LYS60 2.3 38.4 1.0
O A:LEU62 2.3 41.5 1.0
O A:VAL65 2.4 41.0 1.0
OP1 D:DC3 2.7 42.0 1.0
O D:HOH102 3.1 41.9 1.0
C A:LEU62 3.4 40.8 1.0
C A:LYS60 3.4 41.7 1.0
C A:VAL65 3.5 36.2 1.0
P D:DC3 3.8 42.3 1.0
CA A:PRO63 4.0 42.5 1.0
OP2 D:DC3 4.0 35.9 1.0
N A:VAL65 4.0 36.6 1.0
N A:PRO63 4.0 44.0 1.0
N A:LEU62 4.1 41.6 1.0
C A:LYS61 4.1 44.0 1.0
CA A:LYS60 4.1 40.0 1.0
CA A:VAL65 4.2 38.4 1.0
CG A:LYS60 4.3 37.4 1.0
N A:GLY64 4.3 39.2 1.0
O A:LYS61 4.3 41.1 1.0
CA A:LEU62 4.3 43.0 1.0
N A:LYS61 4.4 42.0 1.0
CB A:VAL65 4.5 39.0 1.0
C A:PRO63 4.5 45.5 1.0
CA A:LYS61 4.6 41.8 1.0
N A:GLY66 4.6 35.5 1.0
O3' D:DT2 4.7 39.4 1.0
CB A:LYS60 4.8 36.3 1.0
CA A:GLY66 4.9 39.1 1.0
O A:ALA59 4.9 39.8 1.0
CD A:LYS60 4.9 42.0 1.0
C A:GLY64 5.0 38.4 1.0
O5' D:DC3 5.0 45.8 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 Chf Analogue of Dgtp To Be Published.
Page generated: Tue Oct 8 12:18:14 2024

Last articles

Mg in 4YWS
Mg in 4YSJ
Mg in 4YS7
Mg in 4YS0
Mg in 4YQH
Mg in 4YQF
Mg in 4YQY
Mg in 4YP9
Mg in 4YPM
Mg in 4YPQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy