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Magnesium in PDB 4w88: Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Ruminal Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide and Tris

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

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

Protein crystallography data

The structure of Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Ruminal Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide and Tris, PDB code: 4w88 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) 43.56 / 1.58
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 97.658, 97.658, 95.985, 90.00, 90.00, 120.00
R / Rfree (%) 12.5 / 16.2

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 Ruminal Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide and Tris (pdb code 4w88). 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 Ruminal Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide and Tris, PDB code: 4w88:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4w88

Go back to Magnesium Binding Sites List in 4w88
Magnesium binding site 1 out of 2 in the Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Ruminal Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide and Tris


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 Ruminal Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide and Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg506

b:29.0
occ:1.00
 O A:HOH822 2.0 28.2 1.0
O A:HOH823 2.0 30.8 1.0
O B:HOH765 2.0 25.0 1.0
O B:HOH835 2.1 21.6 1.0
O B:HOH820 2.1 32.4 1.0
O B:HOH834 2.2 30.7 1.0
OD1 B:ASN278 3.8 29.0 1.0
OD2 A:ASP270 4.0 30.5 1.0
O A:HOH696 4.1 21.9 1.0
OD1 A:ASP270 4.2 33.7 1.0
OD1 B:ASP281 4.2 19.9 1.0
OD2 B:ASP281 4.4 30.9 1.0
O B:GLY277 4.4 18.9 1.0
CG A:ASP270 4.5 26.8 1.0
CA B:ASN278 4.5 18.8 1.0
O B:HOH672 4.5 49.0 1.0
CG B:ASP281 4.6 22.8 1.0
O B:HOH811 4.7 33.2 1.0
C B:GLY277 4.7 19.5 1.0
CG B:ASN278 4.8 26.9 1.0
N B:ASN278 4.9 18.6 1.0

Magnesium binding site 2 out of 2 in 4w88

Go back to Magnesium Binding Sites List in 4w88
Magnesium binding site 2 out of 2 in the Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Ruminal Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide and Tris


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 Ruminal Metagenomic Library, in Complex with A Xyloglucan Oligosaccharide and Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:28.6
occ:1.00
 O B:HOH836 1.9 28.8 1.0
O B:HOH837 2.0 31.6 1.0
O A:HOH824 2.1 22.1 1.0
O A:HOH772 2.1 28.7 1.0
O A:HOH825 2.1 32.9 1.0
O A:HOH826 2.2 30.5 1.0
OD1 A:ASN278 3.9 29.6 1.0
OD2 B:ASP270 4.0 32.4 1.0
OD1 B:ASP270 4.1 31.6 1.0
O B:HOH689 4.1 21.6 1.0
OD1 A:ASP281 4.2 21.5 1.0
OD2 A:ASP281 4.3 30.1 1.0
O A:GLY277 4.3 17.6 1.0
CG B:ASP270 4.4 26.1 1.0
CA A:ASN278 4.5 18.6 1.0
O A:HOH670 4.6 47.2 1.0
CG A:ASP281 4.6 25.9 1.0
O A:HOH815 4.6 33.8 1.0
C A:GLY277 4.8 18.0 1.0
CG A:ASN278 4.8 25.6 1.0
N A:ASN278 4.8 19.6 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 20 13:08:28 2024

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