Zinc in PDB 8qy3: Xylanase From Bacillus Circulans Mutant E78Q/F125A Bound to Xylotriose

The structure of Xylanase From Bacillus Circulans Mutant E78Q/F125A Bound to Xylotriose, PDB code: 8qy3 was solved by A.Chikunova, M.Saberi, M.Ubbink, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.18 / 1.24
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.838, 80.838, 131.543, 90, 90, 90
R / Rfree (%)	19.5 / 23

The binding sites of Zinc atom in the Xylanase From Bacillus Circulans Mutant E78Q/F125A Bound to Xylotriose (pdb code 8qy3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Xylanase From Bacillus Circulans Mutant E78Q/F125A Bound to Xylotriose, PDB code: 8qy3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Xylanase From Bacillus Circulans Mutant E78Q/F125A Bound to Xylotriose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Xylanase From Bacillus Circulans Mutant E78Q/F125A Bound to Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:18.4 occ:1.00 NE2 A:HIS156 1.9 15.8 1.0 O8 A:BTB203 2.1 17.1 1.0 O4 A:BTB203 2.2 18.9 1.0 O6 A:BTB203 2.2 16.9 1.0 N A:BTB203 2.2 19.7 1.0 O1 A:BTB203 2.2 17.2 1.0 C2 A:BTB203 2.8 19.7 1.0 CE1 A:HIS156 2.9 19.8 1.0 C5 A:BTB203 2.9 19.8 1.0 CD2 A:HIS156 3.0 16.4 1.0 C4 A:BTB203 3.0 21.1 1.0 C6 A:BTB203 3.0 18.1 1.0 C1 A:BTB203 3.0 20.8 1.0 C8 A:BTB203 3.0 18.2 1.0 C7 A:BTB203 3.1 18.3 1.0 O A:THR97 3.9 17.4 1.0 O A:HOH430 4.0 32.2 1.0 ND1 A:HIS156 4.1 21.6 1.0 CG A:HIS156 4.1 17.3 1.0 OG A:SER155 4.3 27.5 1.0 C3 A:BTB203 4.3 23.1 1.0 N A:THR97 4.8 16.8 1.0

Zinc binding site 2 out of 2 in the Xylanase From Bacillus Circulans Mutant E78Q/F125A Bound to Xylotriose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Xylanase From Bacillus Circulans Mutant E78Q/F125A Bound to Xylotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:29.3 occ:0.50 OD2 A:ASP119 1.9 35.2 1.0 OD2 A:ASP121 2.0 28.1 1.0 CG A:ASP119 2.6 31.6 1.0 OD1 A:ASP119 2.7 29.1 1.0 CG A:ASP121 3.0 31.8 1.0 CB A:ASP121 3.5 28.1 1.0 O A:HOH396 3.9 28.4 1.0 OD1 A:ASP121 4.0 36.3 1.0 CB A:ASP119 4.1 31.1 1.0 OG A:SER117 4.6 26.6 1.0 CA A:ASP121 4.8 27.7 1.0 N A:ASP121 4.8 32.2 1.0 O A:HOH312 4.9 47.2 1.0

M.Saberi, A.Chikunova, M.Ubbink. Bimodal Substrate Binding in the Active Site of the Glycosidase Bcx Febs J. 2024.
ISSN: ISSN 1742-464X
DOI: 10.1111/FEBS.17251