Atomistry » Sodium » PDB 5dyn-5emg » 5efd
Atomistry »
  Sodium »
    PDB 5dyn-5emg »
      5efd »

Sodium in PDB 5efd: Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27

Enzymatic activity of Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27

All present enzymatic activity of Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27, PDB code: 5efd was solved by P.Mahanta, A.Bhardwaj, V.S.Reddy, S.Ramakumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.25 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.990, 76.600, 176.490, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.7

Other elements in 5efd:

The structure of Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 (pdb code 5efd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27, PDB code: 5efd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5efd

Go back to Sodium Binding Sites List in 5efd
Sodium binding site 1 out of 2 in the Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:12.7
occ:1.00
 O A:SER18 2.2 15.2 1.0
O A:HOH688 2.2 31.0 1.0
O A:ASP302 2.2 16.9 1.0
O A:LEU305 2.4 13.0 1.0
O A:HOH708 2.4 22.9 1.0
C A:ASP302 3.4 16.6 1.0
C A:SER18 3.4 15.1 1.0
C A:LEU305 3.4 12.4 1.0
CA A:SER306 3.9 11.5 1.0
CA A:ASP302 3.9 16.3 1.0
CB A:ASP302 4.0 16.8 1.0
N A:SER306 4.1 11.6 1.0
N A:LEU305 4.3 13.5 1.0
CA A:SER18 4.3 16.6 1.0
N A:PHE19 4.4 13.4 1.0
CB A:PHE19 4.4 12.4 1.0
CA A:PHE19 4.4 12.7 1.0
O A:HOH712 4.4 35.5 1.0
CA A:LEU305 4.5 12.4 1.0
N A:ALA303 4.5 17.9 1.0
O A:HOH537 4.7 24.0 1.0
C A:SER306 4.7 11.6 1.0
CA A:ALA303 4.8 19.0 1.0
CD2 A:PHE19 4.8 13.2 1.0
C A:ALA303 4.8 18.9 1.0
CB A:SER306 4.9 11.7 1.0
CG A:ASP302 4.9 18.7 1.0
O A:HOH603 4.9 35.0 1.0

Sodium binding site 2 out of 2 in 5efd

Go back to Sodium Binding Sites List in 5efd
Sodium binding site 2 out of 2 in the Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:12.0
occ:1.00
 O B:SER18 2.2 14.9 1.0
O B:ASP302 2.2 15.3 1.0
O B:LEU305 2.4 11.9 1.0
O B:HOH690 2.4 31.3 1.0
O B:HOH705 2.4 22.9 1.0
O B:HOH700 2.5 41.5 1.0
C B:ASP302 3.3 14.9 1.0
C B:SER18 3.4 14.5 1.0
C B:LEU305 3.4 11.2 1.0
CA B:ASP302 3.9 14.9 1.0
CB B:ASP302 4.0 15.4 1.0
CA B:SER306 4.0 10.4 1.0
N B:SER306 4.1 10.5 1.0
CA B:SER18 4.2 15.8 1.0
N B:LEU305 4.3 12.2 1.0
N B:PHE19 4.4 12.7 1.0
O B:HOH516 4.4 23.0 1.0
N B:ALA303 4.4 14.9 1.0
CA B:LEU305 4.5 11.3 1.0
CA B:PHE19 4.5 11.9 1.0
CB B:PHE19 4.5 11.7 1.0
O B:HOH711 4.6 35.6 1.0
CA B:ALA303 4.7 15.2 1.0
C B:ALA303 4.7 15.8 1.0
CD2 B:PHE19 4.8 12.3 1.0
CG B:ASP302 4.8 16.4 1.0
CB B:SER306 4.9 10.2 1.0
C B:SER306 4.9 9.8 1.0

Reference:

P.Mahanta, A.Bhardwaj, V.S.Reddy, S.Ramakumar. Crystal Structure of A Surface Pocket Creating Mutant (W6A) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 To Be Published.
Page generated: Mon Oct 7 20:45:49 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