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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

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