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Magnesium 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:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 2 in 4qdm

Go back to Magnesium Binding Sites List in 4qdm
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401

b:5.6
occ:1.00
 OD1 A:ASN292 2.2 14.2 1.0
O A:HOH535 2.2 24.8 1.0
O A:ARG351 2.2 11.0 1.0
O A:HOH682 2.3 11.7 1.0
OD1 A:ASP354 2.3 11.0 1.0
O A:HOH514 2.4 14.3 1.0
O A:HOH695 2.5 25.8 1.0
CG A:ASN292 3.3 14.1 1.0
C A:ARG351 3.3 10.4 1.0
CG A:ASP354 3.4 12.2 1.0
OD2 A:ASP354 3.7 12.4 1.0
CA A:ARG351 4.0 11.4 1.0
O A:HOH710 4.1 34.4 1.0
CB A:ASN292 4.2 12.9 1.0
ND2 A:ASN292 4.3 15.9 1.0
O A:ASP354 4.3 12.6 1.0
N A:ILE352 4.3 9.5 1.0
O A:HOH619 4.3 30.9 1.0
CA A:ILE352 4.4 9.2 1.0
CA A:ASN292 4.4 11.6 1.0
OE2 A:GLU296 4.5 30.1 1.0
C A:ASP354 4.5 13.2 1.0
CB A:ARG351 4.6 13.2 1.0
O A:ASN292 4.7 10.2 1.0
CB A:ASP354 4.7 12.3 1.0
OXT A:ASP354 4.8 13.5 1.0
N A:ASP354 4.9 11.6 1.0
CA A:ASP354 5.0 12.3 1.0
CG A:GLU296 5.0 19.2 1.0

Magnesium binding site 2 out of 2 in 4qdm

Go back to Magnesium Binding Sites List in 4qdm
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg401

b:8.0
occ:1.00
 O B:HOH701 2.0 20.3 1.0
OD1 B:ASN292 2.1 15.9 1.0
O B:ARG351 2.1 11.8 1.0
OD1 B:ASP354 2.2 14.4 1.0
O B:HOH529 2.4 18.0 1.0
O B:HOH542 2.5 16.2 1.0
O B:HOH708 2.5 24.0 1.0
CG B:ASP354 3.2 15.6 1.0
C B:ARG351 3.2 11.9 1.0
CG B:ASN292 3.3 15.4 1.0
OD2 B:ASP354 3.6 15.2 1.0
CA B:ARG351 4.0 12.8 1.0
O B:HOH642 4.1 29.5 1.0
CB B:ASN292 4.2 13.4 1.0
N B:ILE352 4.2 10.8 1.0
ND2 B:ASN292 4.3 17.9 1.0
OE2 B:GLU296 4.3 24.9 1.0
O B:ASP354 4.3 17.1 1.0
CA B:ASN292 4.3 12.0 1.0
C B:ASP354 4.4 17.5 1.0
CA B:ILE352 4.4 10.1 1.0
OXT B:ASP354 4.5 19.6 1.0
CB B:ASP354 4.5 15.9 1.0
CB B:ARG351 4.5 15.0 1.0
O B:ASN292 4.6 10.9 1.0
CG B:GLU296 4.8 16.5 1.0
CA B:ASP354 4.8 15.7 1.0
N B:ASP354 4.8 13.5 1.0
C B:ASN292 4.9 11.5 1.0
CD B:GLU296 5.0 19.6 1.0
C B:ILE352 5.0 10.2 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 Aug 11 22:20:29 2025

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