Calcium in PDB 7d88: Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna

All present enzymatic activity of Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna:
3.2.1.8;

The structure of Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna, PDB code: 7d88 was solved by W.Xie, Q.Yu, C.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.33 / 2.34
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.842, 109.842, 85.57, 90, 90, 90
R / Rfree (%)	21.4 / 24.8

The binding sites of Calcium atom in the Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna (pdb code 7d88). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna, PDB code: 7d88:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:54.4 occ:1.00 N A:ILE222 3.2 54.6 1.0 N A:GLY251 3.2 42.5 1.0 N A:VAL221 3.3 52.8 1.0 CG1 A:ILE222 3.5 47.4 1.0 N A:SER223 3.5 54.3 1.0 N A:ASN220 3.5 49.0 1.0 OG A:SER223 3.6 59.0 1.0 N A:GLN250 3.7 45.5 1.0 CA A:GLY251 3.8 40.2 1.0 CA A:VAL221 4.0 54.7 1.0 CA A:TYR219 4.0 48.0 1.0 C A:TYR219 4.0 51.7 1.0 C A:VAL221 4.0 60.5 1.0 CA A:ILE222 4.1 52.8 1.0 C A:ASN220 4.1 55.6 1.0 CB A:SER223 4.2 52.7 1.0 CB A:VAL221 4.2 53.9 1.0 CA A:ASN220 4.2 54.8 1.0 C A:ILE222 4.2 54.1 1.0 C A:GLN250 4.2 46.6 1.0 O A:ASP218 4.3 49.6 1.0 CB A:ILE222 4.3 57.5 1.0 CA A:GLN250 4.4 43.5 1.0 C A:VAL249 4.4 43.0 1.0 CA A:SER223 4.5 51.0 1.0 CB A:VAL249 4.5 51.1 1.0 N A:HIS252 4.5 41.7 1.0 CB A:GLN250 4.6 40.9 1.0 CD1 A:ILE222 4.6 47.3 1.0 C A:GLY251 4.7 44.6 1.0 CA A:VAL249 4.7 43.2 1.0 CB A:TYR219 4.8 45.9 1.0 O A:TYR219 4.9 49.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Novel Thermostable GH10 Xylanase Xyna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:67.9 occ:1.00 CE A:LYS115 3.1 52.6 1.0 CG A:GLU98 3.3 48.6 1.0 NZ A:LYS115 3.5 46.9 1.0 CA A:GLU98 3.7 44.1 1.0 CB A:GLU98 3.8 48.5 1.0 CB A:ALA103 3.9 38.2 1.0 CD A:LYS115 4.3 50.5 1.0 N A:GLU98 4.4 41.0 1.0 CB A:LYS115 4.5 46.4 1.0 CG A:LYS115 4.5 43.2 1.0 OD1 A:ASP74 4.5 47.2 1.0 CD A:GLU98 4.6 50.0 1.0 C A:ASN97 4.7 44.7 1.0 O A:ASN97 4.7 38.1 1.0 C A:GLU98 4.8 45.1 1.0 O A:GLU98 4.9 39.9 1.0 CB A:ASN97 4.9 44.6 1.0 O A:HOH625 4.9 39.6 1.0 CA A:ALA103 5.0 38.7 1.0

W.Xie, Q.Yu, R.Zhang, Y.Liu, R.Cao, S.Wang, R.Zhan, Z.Liu, K.Wang, C.Wang. Insights Into the Catalytic Mechanism of A Novel Xyna and Structure-Based Engineering For Improving Bifunctional Activities. Biochemistry V. 60 2071 2021.
ISSN: ISSN 0006-2960
PubMed: 34156819
DOI: 10.1021/ACS.BIOCHEM.1C00134