Zinc in PDB 7y9p: Xylitol Dehydrogenase S96C/S99C/Y102C Mutant(Thermostabilized Form) From Pichia Stipitis

The structure of Xylitol Dehydrogenase S96C/S99C/Y102C Mutant(Thermostabilized Form) From Pichia Stipitis, PDB code: 7y9p was solved by K.Yoshiwara, Y.Watanabe, S.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.35 / 2.80
Space group	P 6 2 2
Cell size a, b, c (Å), α, β, γ (°)	158.272, 158.272, 65.497, 90, 90, 120
R / Rfree (%)	22.3 / 27.4

The binding sites of Zinc atom in the Xylitol Dehydrogenase S96C/S99C/Y102C Mutant(Thermostabilized Form) From Pichia Stipitis (pdb code 7y9p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Xylitol Dehydrogenase S96C/S99C/Y102C Mutant(Thermostabilized Form) From Pichia Stipitis, PDB code: 7y9p:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Xylitol Dehydrogenase S96C/S99C/Y102C Mutant(Thermostabilized Form) From Pichia Stipitis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Xylitol Dehydrogenase S96C/S99C/Y102C Mutant(Thermostabilized Form) From Pichia Stipitis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:114.1 occ:1.00 OE2 A:GLU67 2.2 72.5 1.0 NE2 A:HIS66 2.3 64.7 1.0 SG A:CYS41 2.3 89.0 1.0 O A:HOH510 2.6 51.8 1.0 CE1 A:HIS66 3.1 70.6 1.0 CB A:CYS41 3.3 82.3 1.0 CD A:GLU67 3.4 65.8 1.0 CD2 A:HIS66 3.4 69.1 1.0 OE1 A:GLU159 3.6 61.8 1.0 O A:HOH513 3.9 49.3 1.0 CG A:GLU67 3.9 61.6 1.0 ND1 A:HIS66 4.3 64.9 1.0 CD A:GLU159 4.3 59.2 1.0 OE2 A:GLU159 4.4 57.5 1.0 OG A:SER43 4.4 93.7 1.0 OE1 A:GLU67 4.4 67.6 1.0 CG A:HIS66 4.5 62.1 1.0 CA A:CYS41 4.7 81.3 1.0 N A:CYS41 5.0 72.7 1.0 CB A:SER43 5.0 81.3 1.0

Zinc binding site 2 out of 2 in the Xylitol Dehydrogenase S96C/S99C/Y102C Mutant(Thermostabilized Form) From Pichia Stipitis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Xylitol Dehydrogenase S96C/S99C/Y102C Mutant(Thermostabilized Form) From Pichia Stipitis within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:61.8 occ:1.00 SG A:CYS110 2.3 47.3 1.0 SG A:CYS99 2.3 52.3 1.0 SG A:CYS96 2.3 48.8 1.0 SG A:CYS102 2.3 49.7 1.0 CB A:CYS99 3.2 48.2 1.0 CB A:CYS110 3.2 47.9 1.0 CB A:CYS96 3.4 47.6 1.0 CB A:CYS102 3.5 45.4 1.0 N A:CYS96 3.6 46.8 1.0 N A:CYS99 3.7 48.8 1.0 N A:ARG97 3.9 50.5 1.0 CA A:CYS110 3.9 53.1 1.0 CA A:CYS96 3.9 44.3 1.0 CA A:CYS99 4.0 47.7 1.0 N A:CYS102 4.2 50.8 1.0 C A:CYS96 4.3 53.4 1.0 ND1 A:HIS112 4.3 59.6 1.0 CA A:CYS102 4.4 48.2 1.0 N A:PHE98 4.5 53.4 1.0 CD A:PRO111 4.6 54.9 1.0 CB A:PRO95 4.6 53.5 1.0 C A:CYS99 4.6 47.3 1.0 C A:PRO95 4.7 50.2 1.0 C A:CYS110 4.7 53.8 1.0 O A:CYS99 4.8 48.5 1.0 CA A:ARG97 4.8 50.7 1.0 C A:PHE98 4.9 49.8 1.0 N A:PRO111 4.9 55.3 1.0

K.Yoshiwara, S.Watanabe, Y.Watanabe. Molecular Evolutionary Insight of Structural Zinc Atom in Yeast Xylitol Dehydrogenases and Its Application in Bioethanol Production By Lignocellulosic Biomass. Sci Rep V. 13 1920 2023.
ISSN: ESSN 2045-2322
PubMed: 36732376
DOI: 10.1038/S41598-023-29195-7