Magnesium in PDB 9l3o: Crystal Structure of Endo-Processive Xyloglucanase XEG5A From Aspergillus Oryzae with Xxlg

The structure of Crystal Structure of Endo-Processive Xyloglucanase XEG5A From Aspergillus Oryzae with Xxlg, PDB code: 9l3o was solved by Y.Nakamichi, N.Shimada, M.Watanabe, T.Fujii, T.Matsuzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.84 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.706, 105.896, 82.946, 90, 91.6, 90
R / Rfree (%)	20.4 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Endo-Processive Xyloglucanase XEG5A From Aspergillus Oryzae with Xxlg (pdb code 9l3o). 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 Endo-Processive Xyloglucanase XEG5A From Aspergillus Oryzae with Xxlg, PDB code: 9l3o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Endo-Processive Xyloglucanase XEG5A From Aspergillus Oryzae with Xxlg


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 Endo-Processive Xyloglucanase XEG5A From Aspergillus Oryzae with Xxlg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg609 b:51.6 occ:1.00 O A:HOH903 1.9 32.6 1.0 O A:HOH725 2.2 52.8 1.0 O A:HOH812 2.5 33.3 1.0 O A:HOH921 2.8 53.0 1.0 O4 E:BGC4 3.0 47.9 1.0 O1 A:PG4601 3.1 59.0 1.0 C1 A:PG4601 3.8 50.0 1.0 OE1 A:GLU285 3.9 32.8 1.0 C2 A:PG4601 4.0 54.0 1.0 C4 E:BGC4 4.0 58.8 1.0 O3 E:BGC4 4.1 55.2 1.0 O1 A:PEG608 4.1 53.0 1.0 OE2 A:GLU285 4.3 31.2 1.0 CZ2 A:TRP319 4.4 31.9 1.0 NE2 A:HIS125 4.4 34.0 1.0 O A:HOH770 4.5 32.7 1.0 CD A:GLU285 4.5 32.6 1.0 CE1 A:HIS126 4.5 34.8 1.0 CH2 A:TRP319 4.6 32.6 1.0 CE2 A:TRP319 4.6 40.0 1.0 O A:HOH897 4.6 41.9 1.0 C3 E:BGC4 4.6 61.5 1.0 OE2 A:GLU173 4.7 35.8 1.0 OE1 A:GLU173 4.8 34.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Endo-Processive Xyloglucanase XEG5A From Aspergillus Oryzae with Xxlg


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 Endo-Processive Xyloglucanase XEG5A From Aspergillus Oryzae with Xxlg within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:51.2 occ:1.00 O B:HOH870 2.2 32.7 1.0 O B:HOH919 2.4 49.2 1.0 O B:HOH805 2.5 37.2 1.0 O B:HOH776 2.7 43.0 1.0 O4 I:BGC4 2.7 46.1 1.0 O1 B:PEG607 2.8 55.3 1.0 O3 I:BGC4 3.4 52.7 1.0 C4 I:BGC4 3.7 55.2 1.0 C1 B:PEG607 3.9 46.4 1.0 O4 B:PEG606 3.9 55.2 1.0 CE1 B:HIS126 4.0 31.3 1.0 C3 I:BGC4 4.1 54.1 1.0 OE1 B:GLU173 4.2 37.5 1.0 O B:HOH815 4.2 42.4 1.0 OE1 B:GLU285 4.4 31.9 1.0 NE2 B:HIS125 4.4 32.8 1.0 O2 B:PEG607 4.5 59.1 1.0 OE2 B:GLU173 4.6 37.4 1.0 CD B:GLU173 4.6 38.0 1.0 C2 B:PEG607 4.8 56.2 1.0 ND2 B:ASN172 4.8 36.8 1.0 O B:HOH773 4.8 32.5 1.0 NE2 B:HIS126 4.9 39.1 1.0 OE2 B:GLU285 4.9 32.7 1.0 O4 B:PEG607 4.9 57.3 1.0 ND1 B:HIS126 5.0 41.6 1.0

Y.Nakamichi, N.Shimada, M.Watanabe, T.Fujii, K.Yaoi, T.Matsuzawa. Structural Insights Into Substrate Recognition of Tri-Modular Xyloglucanase From Aspergillus Oryzae. J.Struct.Biol. V. 217 08213 2025.
ISSN: ESSN 1095-8657
PubMed: 40414580
DOI: 10.1016/J.JSB.2025.108213