Calcium in PDB 7d89: Crystal Structure of An Inactivated Double Mutant (E182AE280A) of A Novel Thermostable GH10 Xylanase Xyna

All present enzymatic activity of Crystal Structure of An Inactivated Double Mutant (E182AE280A) of A Novel Thermostable GH10 Xylanase Xyna:
3.2.1.8;

The structure of Crystal Structure of An Inactivated Double Mutant (E182AE280A) of A Novel Thermostable GH10 Xylanase Xyna, PDB code: 7d89 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)	49.28 / 2.89
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	110.193, 110.193, 84.983, 90, 90, 90
R / Rfree (%)	23.2 / 27.9

The binding sites of Calcium atom in the Crystal Structure of An Inactivated Double Mutant (E182AE280A) of A Novel Thermostable GH10 Xylanase Xyna (pdb code 7d89). 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 An Inactivated Double Mutant (E182AE280A) of A Novel Thermostable GH10 Xylanase Xyna, PDB code: 7d89:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of An Inactivated Double Mutant (E182AE280A) 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 An Inactivated Double Mutant (E182AE280A) of A Novel Thermostable GH10 Xylanase Xyna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:70.0 occ:1.00 CE A:LYS115 3.1 43.0 1.0 NZ A:LYS115 3.3 40.0 1.0 CA A:GLU98 3.6 42.8 1.0 CG A:GLU98 3.6 55.3 1.0 CB A:ALA103 3.8 45.5 1.0 CB A:GLU98 3.9 49.3 1.0 N A:GLU98 4.3 50.1 1.0 CD A:LYS115 4.3 39.1 1.0 OD2 A:ASP74 4.4 52.8 1.0 C A:ASN97 4.6 50.0 1.0 CG A:LYS115 4.6 40.5 1.0 CB A:LYS115 4.6 43.2 1.0 C A:GLU98 4.7 47.0 1.0 O A:ASN97 4.7 42.2 1.0 CD A:GLU98 4.7 52.7 1.0 CB A:ASN97 4.7 53.1 1.0 O A:GLU98 4.8 47.6 1.0 OD1 A:ASP74 5.0 53.9 1.0 CA A:ALA103 5.0 43.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of An Inactivated Double Mutant (E182AE280A) 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 An Inactivated Double Mutant (E182AE280A) of A Novel Thermostable GH10 Xylanase Xyna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:63.0 occ:1.00 N A:VAL221 3.1 56.8 1.0 N A:ASN220 3.3 54.9 1.0 N A:ILE222 3.3 63.5 1.0 CG2 A:VAL221 3.3 65.0 1.0 N A:GLY251 3.4 50.0 1.0 OG A:SER223 3.7 60.7 1.0 N A:SER223 3.7 61.8 1.0 C A:TYR219 3.8 56.4 1.0 CG1 A:ILE222 3.8 53.5 1.0 CA A:TYR219 3.8 53.4 1.0 CA A:VAL221 3.9 59.2 1.0 C A:ASN220 3.9 61.3 1.0 CA A:ASN220 4.0 60.0 1.0 N A:GLN250 4.0 52.7 1.0 CA A:GLY251 4.0 54.3 1.0 C A:VAL221 4.0 61.3 1.0 CB A:VAL221 4.1 60.8 1.0 O A:ASP218 4.2 50.9 1.0 CA A:ILE222 4.2 57.6 1.0 CB A:SER223 4.4 59.1 1.0 C A:GLN250 4.5 47.4 1.0 C A:ILE222 4.5 58.9 1.0 N A:HIS252 4.5 55.3 1.0 CB A:ILE222 4.5 54.0 1.0 CA A:GLN250 4.6 49.6 1.0 C A:VAL249 4.7 51.0 1.0 CA A:SER223 4.7 62.0 1.0 O A:TYR219 4.7 54.9 1.0 CB A:TYR219 4.7 46.9 1.0 CG1 A:VAL221 4.7 54.5 1.0 CB A:GLN250 4.7 48.0 1.0 CB A:VAL249 4.8 51.8 1.0 C A:GLY251 4.8 56.9 1.0 CD1 A:ILE222 4.8 48.9 1.0 N A:TYR219 4.8 52.6 1.0 CA A:VAL249 4.9 50.3 1.0 C A:ASP218 4.9 52.8 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