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Sodium in PDB 4qdm: Crystal Structure of N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27

Enzymatic activity of Crystal Structure of N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27

All present enzymatic activity of Crystal Structure of N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27, PDB code: 4qdm 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) 40.19 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.880, 76.580, 176.730, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 19

Other elements in 4qdm:

The structure of Crystal Structure of N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 (pdb code 4qdm). 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 N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27, PDB code: 4qdm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4qdm

Go back to Sodium Binding Sites List in 4qdm
Sodium binding site 1 out of 2 in the Crystal Structure of N-Terminal Mutant (V1L) 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 N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:13.5
occ:1.00
 O A:SER18 2.2 11.8 1.0
O A:ASP302 2.3 14.8 1.0
O A:LEU305 2.3 9.3 1.0
O A:HOH573 2.3 19.3 1.0
O A:HOH631 2.9 37.8 1.0
C A:LEU305 3.4 9.6 1.0
C A:SER18 3.4 11.6 1.0
C A:ASP302 3.4 14.8 1.0
CA A:SER306 3.9 8.8 1.0
CA A:ASP302 4.0 14.1 1.0
CB A:ASP302 4.1 14.2 1.0
N A:SER306 4.1 9.1 1.0
N A:LEU305 4.3 11.2 1.0
CA A:SER18 4.3 12.6 1.0
N A:PHE19 4.3 10.6 1.0
CA A:PHE19 4.4 9.7 1.0
CB A:PHE19 4.4 9.1 1.0
CA A:LEU305 4.4 10.1 1.0
N A:ALA303 4.5 15.0 1.0
O A:HOH543 4.7 20.7 1.0
C A:SER306 4.7 8.6 1.0
CD2 A:PHE19 4.7 9.3 1.0
CA A:ALA303 4.8 16.0 1.0
C A:ALA303 4.8 16.0 1.0
CB A:SER306 4.9 8.8 1.0
CG A:ASP302 4.9 15.5 1.0
CB A:LEU305 5.0 10.2 1.0
O A:SER306 5.0 8.4 1.0

Sodium binding site 2 out of 2 in 4qdm

Go back to Sodium Binding Sites List in 4qdm
Sodium binding site 2 out of 2 in the Crystal Structure of N-Terminal Mutant (V1L) 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 N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:12.9
occ:1.00
 O B:ASP302 2.2 14.3 1.0
O B:SER18 2.3 12.9 1.0
O B:HOH618 2.3 32.5 1.0
O B:HOH558 2.4 24.6 1.0
O B:LEU305 2.4 10.0 1.0
O B:HOH651 2.5 28.1 1.0
C B:ASP302 3.3 13.4 1.0
C B:LEU305 3.5 10.3 1.0
C B:SER18 3.5 13.2 1.0
CA B:ASP302 3.9 12.8 1.0
CB B:ASP302 4.0 13.0 1.0
CA B:SER306 4.0 9.8 1.0
N B:SER306 4.2 10.0 1.0
CA B:SER18 4.3 14.3 1.0
N B:LEU305 4.3 11.3 1.0
N B:ALA303 4.4 13.8 1.0
CA B:LEU305 4.5 10.5 1.0
N B:PHE19 4.5 11.9 1.0
CB B:PHE19 4.5 10.9 1.0
O B:HOH533 4.5 20.0 1.0
CA B:PHE19 4.6 11.4 1.0
O B:HOH598 4.7 30.5 1.0
CA B:ALA303 4.7 14.6 1.0
C B:ALA303 4.7 15.8 1.0
CG B:ASP302 4.8 13.8 1.0
CB B:SER306 4.8 10.5 1.0
CD2 B:PHE19 4.8 10.4 1.0
C B:SER306 4.9 9.3 1.0

Reference:

P.Mahanta, A.Bhardwaj, K.Kumar, V.S.Reddy, S.Ramakumar. Crystal Structure of N-Terminal Mutant (V1L) of An Alkali Thermostable GH10 Xylanase From Bacillus Sp. Ng-27 To Be Published.
Page generated: Mon Oct 7 17:58:13 2024

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