Calcium in PDB 2y6k: Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase

All present enzymatic activity of Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase:
3.2.1.8;

The structure of Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase, PDB code: 2y6k was solved by L.Von Schantz, M.Hakansson, D.T.Logan, B.Walse, J.Osterlin, E.Nordberg-Karlsson, M.Ohlin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.670, 50.350, 62.480, 90.00, 90.00, 90.00
R / Rfree (%)	12.3 / 18.3

The binding sites of Calcium atom in the Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase (pdb code 2y6k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase, PDB code: 2y6k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1167 b:14.2 occ:1.00 O A:LYS55 2.3 12.6 1.0 OE1 A:GLU52 2.3 17.6 1.0 O A:GLU52 2.3 17.2 1.0 O A:GLY9 2.4 12.7 1.0 OD1 A:ASP160 2.4 13.6 1.0 OE2 A:GLU11 2.4 15.0 1.0 OD2 A:ASP160 2.7 14.0 1.0 CG A:ASP160 2.9 12.6 1.0 C A:GLU52 3.3 18.0 1.0 C A:GLY9 3.3 12.9 1.0 C A:LYS55 3.4 11.8 1.0 CD A:GLU52 3.5 20.2 1.0 CD A:GLU11 3.5 18.0 1.0 CA A:GLY9 3.6 12.5 1.0 N A:LYS55 3.8 16.7 1.0 CB A:GLU52 3.9 22.8 1.0 CA A:GLU52 4.0 18.6 1.0 CG A:GLU11 4.1 16.3 1.0 CA A:LYS55 4.1 14.4 1.0 CG A:GLU52 4.3 23.6 1.0 N A:GLY53 4.3 18.7 1.0 CB A:ASP160 4.3 12.7 1.0 N A:GLU52 4.4 17.1 1.0 CA A:GLY53 4.4 17.2 1.0 OE2 A:GLU52 4.5 29.4 1.0 N A:VAL56 4.5 11.8 1.0 OE1 A:GLU11 4.6 20.1 1.0 N A:ASN54 4.6 18.9 1.0 CB A:LYS55 4.6 17.5 1.0 N A:PHE10 4.6 12.1 1.0 C A:GLY53 4.6 17.5 1.0 CB A:ALA50 4.7 23.6 1.0 CA A:VAL56 4.8 11.4 1.0 N A:GLY161 4.9 10.9 1.0 N A:GLU11 4.9 14.1 1.0

Calcium binding site 2 out of 2 in the Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xylotetraose Bound to X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1168 b:14.5 occ:0.30 O A:HOH2046 2.2 40.0 1.0 O A:HOH2054 2.3 22.7 1.0 OD1 A:ASP29 2.3 14.4 0.3 O A:ALA22 2.4 18.8 1.0 O A:TRP28 2.4 12.3 1.0 O A:HOH2121 2.6 28.8 1.0 C A:TRP28 3.4 11.1 1.0 CG A:ASP29 3.5 15.4 0.3 C A:ALA22 3.6 15.2 1.0 N A:ASP29 4.0 11.0 1.0 CA A:ASP29 4.0 11.0 0.7 CA A:ASP29 4.0 10.8 0.3 CA A:GLU23 4.0 21.7 0.5 CA A:GLU23 4.0 21.7 0.5 O A:HOH2047 4.1 39.5 1.0 O A:HOH2055 4.1 13.8 1.0 CB A:ASP29 4.1 14.1 0.7 CD1 A:LEU76 4.2 22.6 0.5 O A:VAL25 4.3 13.5 1.0 N A:GLU23 4.3 18.4 1.0 N A:TRP28 4.3 11.0 1.0 CB A:ASP29 4.3 14.7 0.3 OD2 A:ASP29 4.3 23.0 0.3 CA A:TRP28 4.5 11.3 1.0 O A:HOH2060 4.6 30.1 1.0 CG A:GLU23 4.6 28.2 0.5 CA A:ALA22 4.7 16.0 1.0 CG A:GLU23 4.8 28.1 0.5 CB A:GLU23 4.9 24.6 0.5 CG A:ASP29 4.9 18.9 0.7 CB A:GLU23 4.9 24.7 0.5 CD2 A:LEU76 4.9 25.4 0.5 C A:GLU23 4.9 19.1 1.0

L.Von Schantz, M.Hakansson, D.T.Logan, B.Walse, J.Osterlin, E.Nordberg-Karlsson, M.Ohlin. Structural Basis For Carbohydrate-Binding Specificity--A Comparative Assessment of Two Engineered Carbohydrate-Binding Modules. Glycobiology V. 22 948 2012.
ISSN: ESSN 1460-2423
PubMed: 22434778
DOI: 10.1093/GLYCOB/CWS063