Atomistry » Magnesium » PDB 4w5q-4wfn » 4w84
Atomistry »
  Magnesium »
    PDB 4w5q-4wfn »
      4w84 »

Magnesium in PDB 4w84: Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Ruminal Metagenomic Library, in the Native Form

Enzymatic activity of Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Ruminal Metagenomic Library, in the Native Form

All present enzymatic activity of Crystal Structure of XEG5A, A GH5 Xyloglucan-Specific Endo-Beta-1,4- Glucanase From Ruminal Metagenomic Library, in the Native Form:
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 the Native Form, PDB code: 4w84 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) 31.61 / 1.79
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 97.241, 97.241, 95.678, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 20.2

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 the Native Form (pdb code 4w84). 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 the Native Form, PDB code: 4w84:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4w84

Go back to Magnesium Binding Sites List in 4w84
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 the Native Form


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 the Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:33.4
occ:1.00
 O B:HOH775 2.1 33.9 1.0
O A:HOH613 2.1 26.4 1.0
O A:HOH602 2.1 33.8 1.0
O A:HOH655 2.1 35.8 1.0
O A:HOH777 2.1 30.7 1.0
O B:HOH602 2.1 35.9 1.0
OD1 A:ASN278 3.7 33.1 1.0
OD2 B:ASP270 4.0 35.3 1.0
OD1 B:ASP270 4.0 37.2 1.0
O B:HOH691 4.1 25.5 1.0
OD2 A:ASP281 4.2 35.0 1.0
O A:GLY277 4.2 24.1 1.0
OD1 A:ASP281 4.3 27.0 1.0
CG B:ASP270 4.4 35.4 1.0
CA A:ASN278 4.4 25.0 1.0
CG A:ASP281 4.6 29.8 1.0
C A:GLY277 4.7 24.7 1.0
CG A:ASN278 4.7 31.4 1.0
N A:ASN278 4.8 24.8 1.0
O A:HOH760 4.8 37.4 1.0

Magnesium binding site 2 out of 2 in 4w84

Go back to Magnesium Binding Sites List in 4w84
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 the Native Form


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 the Native Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:33.9
occ:1.00
 O A:HOH778 2.1 33.1 1.0
O B:HOH779 2.1 37.5 1.0
O B:HOH601 2.1 31.5 1.0
O A:HOH779 2.1 35.1 1.0
O B:HOH777 2.1 27.7 1.0
O B:HOH778 2.1 30.2 1.0
OD1 B:ASN278 3.8 32.1 1.0
OD2 A:ASP270 4.0 35.4 1.0
OD1 A:ASP270 4.0 35.3 1.0
O A:HOH709 4.1 25.4 1.0
O B:GLY277 4.2 24.9 1.0
OD1 B:ASP281 4.3 27.2 1.0
OD2 B:ASP281 4.3 36.1 1.0
CG A:ASP270 4.4 34.4 1.0
CA B:ASN278 4.5 24.8 1.0
CG B:ASP281 4.7 29.9 1.0
O B:HOH800 4.7 35.1 1.0
C B:GLY277 4.7 25.0 1.0
CG B:ASN278 4.8 31.0 1.0
N B:ASN278 4.8 23.5 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 01:10:29 2025

Last articles

Mg in 6LU1
Mg in 6LT4
Mg in 6LY7
Mg in 6LY6
Mg in 6LY3
Mg in 6LX1
Mg in 6LTW
Mg in 6LVW
Mg in 6LUH
Mg in 6LTS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy