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Magnesium in PDB 4w87: Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide

Enzymatic activity of Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide

All present enzymatic activity of Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide:
3.2.1.151;

Protein crystallography data

The structure of Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide, PDB code: 4w87 was solved by C.R.Santos, R.L.Cordeiro, D.W.S.Wong, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.14 / 2.15
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 96.504, 96.504, 95.857, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide (pdb code 4w87). 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 XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide, PDB code: 4w87:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4w87

Go back to Magnesium Binding Sites List in 4w87
Magnesium binding site 1 out of 2 in the Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide


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 XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:43.2
occ:1.00
 O A:HOH663 1.8 43.0 1.0
O B:HOH652 1.9 35.3 1.0
O B:HOH653 2.0 36.7 1.0
O A:HOH664 2.2 28.4 1.0
O A:HOH662 2.2 29.6 1.0
O A:HOH665 2.2 35.4 1.0
OD1 B:ASP270 3.5 38.7 1.0
OD2 B:ASP270 3.6 40.9 1.0
O B:HOH673 3.9 21.4 1.0
CG B:ASP270 4.0 38.1 1.0
OD1 A:ASN278 4.0 33.0 1.0
O A:GLY277 4.3 27.1 1.0
OD1 A:ASP281 4.4 29.7 1.0
OD2 A:ASP281 4.6 36.6 1.0
CG A:ASP281 4.9 31.1 1.0
C A:GLY277 4.9 28.3 1.0
CB B:ALA274 4.9 23.1 1.0
CA A:ASN278 4.9 31.5 1.0

Magnesium binding site 2 out of 2 in 4w87

Go back to Magnesium Binding Sites List in 4w87
Magnesium binding site 2 out of 2 in the Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide


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 XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:38.2
occ:1.00
 O B:HOH655 1.8 36.2 1.0
O A:HOH673 1.9 31.3 1.0
O A:HOH672 1.9 24.6 1.0
O B:HOH656 2.1 40.3 1.0
O B:HOH654 2.1 26.8 1.0
O B:HOH657 2.3 24.4 1.0
OD1 A:ASP270 3.5 40.0 1.0
O A:HOH649 3.9 26.1 1.0
OD2 A:ASP270 4.0 38.3 1.0
OD1 B:ASN278 4.0 35.5 1.0
OD1 B:ASP281 4.1 30.8 1.0
CG A:ASP270 4.1 39.0 1.0
OD2 B:ASP281 4.2 38.8 1.0
O B:GLY277 4.3 25.8 1.0
CG B:ASP281 4.5 33.8 1.0
O B:HOH750 4.7 32.6 1.0
CA B:ASN278 4.8 28.6 1.0
C B:GLY277 4.9 27.8 1.0

Reference:

C.R.Santos, R.L.Cordeiro, D.W.Wong, M.T.Murakami. Structural Basis For Xyloglucan Specificity and Alpha-D-Xylp(16)-D-Glcp Recognition at the -1 Subsite Within the GH5 Family. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25714929
DOI: 10.1021/ACS.BIOCHEM.5B00011
Page generated: Tue Aug 12 01:10:52 2025

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