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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 20 13:08:09 2024

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