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Magnesium in PDB 4w86: Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Ruminal Metagenomic Library, in Complex with Glucose 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 Glucose 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 Glucose 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 Glucose and Tris, PDB code: 4w86 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) 48.52 / 2.64
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 96.950, 96.950, 95.785, 90.00, 90.00, 120.00
R / Rfree (%) 21.5 / 23.6

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 Glucose and Tris (pdb code 4w86). 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 Glucose and Tris, PDB code: 4w86:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4w86

Go back to Magnesium Binding Sites List in 4w86
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 Glucose 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 Glucose and Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:67.4
occ:1.00
 O A:HOH606 1.9 60.9 1.0
O B:HOH620 2.0 61.0 1.0
O B:HOH601 2.0 67.4 1.0
O A:HOH604 2.3 50.7 1.0
O A:HOH618 2.4 61.9 1.0
O A:HOH603 2.6 46.2 1.0
OD1 A:ASN278 3.7 59.0 1.0
OD1 B:ASP270 3.8 65.0 1.0
OD2 B:ASP270 4.1 65.9 1.0
OD1 A:ASP281 4.3 62.1 1.0
O B:HOH628 4.4 64.7 1.0
CG B:ASP270 4.4 65.0 1.0
O A:GLY277 4.4 57.7 1.0
OD2 A:ASP281 4.6 64.2 1.0
CA A:ASN278 4.6 58.2 1.0
CG A:ASN278 4.8 58.2 1.0
CG A:ASP281 4.8 62.1 1.0
C A:GLY277 5.0 58.1 1.0

Magnesium binding site 2 out of 2 in 4w86

Go back to Magnesium Binding Sites List in 4w86
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 Glucose 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 Glucose and Tris within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:77.9
occ:1.00
 O B:HOH607 2.0 56.3 1.0
O A:HOH601 2.0 58.4 1.0
O B:HOH624 2.1 55.3 1.0
O B:HOH603 2.2 56.5 1.0
O B:HOH625 2.3 69.9 1.0
O B:HOH606 2.3 57.3 1.0
OD1 B:ASN278 3.5 59.3 1.0
OD1 B:ASP281 4.1 63.1 1.0
O B:GLY277 4.1 56.9 1.0
OD2 A:ASP270 4.2 65.1 1.0
OD1 A:ASP270 4.3 65.1 1.0
CA B:ASN278 4.3 58.2 1.0
CG B:ASN278 4.6 58.6 1.0
OD2 B:ASP281 4.6 63.2 1.0
CG A:ASP270 4.7 64.8 1.0
C B:GLY277 4.7 58.2 1.0
CG B:ASP281 4.7 62.1 1.0
N B:ASN278 4.8 58.4 1.0
CB B:ASN278 4.9 58.7 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 13:08:27 2024

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