Magnesium 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:

Chlorine (Cl) 1 atom
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5efd

Go back to Magnesium Binding Sites List in 5efd
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401

b:12.4
occ:1.00
OD1 A:ASN292 2.1 16.8 1.0
O A:HOH662 2.1 31.2 1.0
O A:HOH540 2.1 17.4 1.0
O A:ARG351 2.2 13.9 1.0
OD1 A:ASP354 2.2 17.1 1.0
O A:HOH521 2.5 20.7 1.0
O A:HOH625 2.7 26.1 1.0
CG A:ASN292 3.2 16.6 1.0
C A:ARG351 3.3 13.0 1.0
CG A:ASP354 3.3 18.7 1.0
OD2 A:ASP354 3.6 19.6 1.0
CA A:ARG351 4.0 14.2 1.0
CB A:ASN292 4.1 14.4 1.0
ND2 A:ASN292 4.2 18.1 1.0
O A:ASP354 4.2 19.5 1.0
O A:HOH660 4.2 36.5 1.0
N A:ILE352 4.3 12.3 1.0
O A:HOH693 4.3 33.9 1.0
CA A:ILE352 4.3 11.7 1.0
OE2 A:GLU296 4.4 28.5 1.0
CA A:ASN292 4.4 13.1 1.0
C A:ASP354 4.4 20.0 1.0
CB A:ARG351 4.5 16.5 1.0
O A:HOH711 4.5 30.3 1.0
CB A:ASP354 4.6 18.5 1.0
O A:ASN292 4.8 11.4 1.0
N A:ASP354 4.8 15.9 1.0
OXT A:ASP354 4.8 21.8 1.0
CA A:ASP354 4.9 18.3 1.0
C A:ILE352 4.9 11.8 1.0
CG A:GLU296 4.9 19.3 1.0

Magnesium binding site 2 out of 2 in 5efd

Go back to Magnesium Binding Sites List in 5efd
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401

b:13.5
occ:1.00
OD1 B:ASN292 2.0 17.5 1.0
O B:HOH597 2.0 25.4 1.0
O B:HOH517 2.1 20.1 1.0
O B:ARG351 2.1 14.5 1.0
OD1 B:ASP354 2.2 17.0 1.0
O B:HOH593 2.5 21.2 1.0
O B:HOH501 2.7 25.4 1.0
CG B:ASN292 3.2 15.6 1.0
CG B:ASP354 3.2 18.2 1.0
C B:ARG351 3.2 13.3 1.0
OD2 B:ASP354 3.6 19.5 1.0
CA B:ARG351 4.0 14.0 1.0
CB B:ASN292 4.1 13.9 1.0
OE2 B:GLU296 4.1 25.6 1.0
ND2 B:ASN292 4.1 18.0 1.0
O B:ASP354 4.2 18.0 1.0
N B:ILE352 4.2 12.0 1.0
CA B:ILE352 4.3 11.5 1.0
CA B:ASN292 4.3 12.7 1.0
O B:HOH538 4.3 22.5 1.0
C B:ASP354 4.3 18.7 1.0
CB B:ASP354 4.5 18.1 1.0
CB B:ARG351 4.6 16.2 1.0
O B:ASN292 4.6 12.3 1.0
CG B:GLU296 4.7 18.9 1.0
OXT B:ASP354 4.7 20.1 1.0
CA B:ASP354 4.7 17.4 1.0
N B:ASP354 4.8 14.9 1.0
C B:ILE352 4.9 11.5 1.0
CD B:GLU296 4.9 22.8 1.0
C B:ASN292 4.9 12.8 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 Dec 14 20:15:10 2020

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