Calcium in PDB 2y6l: Xylopentaose Binding X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase

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

The structure of Xylopentaose Binding X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase, PDB code: 2y6l 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 / 1.28
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.900, 49.480, 62.490, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 18.3

The binding sites of Calcium atom in the Xylopentaose Binding X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase (pdb code 2y6l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Xylopentaose Binding X-2 Engineered Mutated CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase, PDB code: 2y6l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Xylopentaose Binding 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 Xylopentaose Binding 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:12.6 occ:1.00 O A:GLU52 2.3 15.5 1.0 O A:LYS55 2.3 11.4 1.0 OE1 A:GLU52 2.3 16.4 1.0 O A:GLY9 2.3 11.9 1.0 OD1 A:ASP160 2.4 11.1 1.0 OE2 A:GLU11 2.4 16.9 1.0 OD2 A:ASP160 2.6 12.3 1.0 CG A:ASP160 2.8 11.1 1.0 C A:GLU52 3.2 15.2 1.0 C A:GLY9 3.3 11.1 1.0 C A:LYS55 3.4 10.6 1.0 CD A:GLU11 3.5 15.9 1.0 CD A:GLU52 3.5 20.3 1.0 CA A:GLY9 3.5 12.1 1.0 CB A:GLU52 3.9 18.2 1.0 N A:LYS55 3.9 13.5 1.0 CG A:GLU11 4.0 14.5 1.0 CA A:GLU52 4.0 17.1 1.0 CA A:LYS55 4.2 12.4 1.0 N A:GLY53 4.2 16.8 1.0 N A:GLU52 4.3 16.5 1.0 CG A:GLU52 4.3 20.6 1.0 CB A:ASP160 4.3 11.0 1.0 CA A:GLY53 4.4 17.3 1.0 OE2 A:GLU52 4.5 30.5 1.0 N A:VAL56 4.5 10.4 1.0 N A:PHE10 4.5 10.8 1.0 OE1 A:GLU11 4.6 17.2 1.0 CB A:ALA50 4.6 17.2 1.0 C A:GLY53 4.6 17.0 1.0 N A:ASN54 4.6 16.4 1.0 CB A:LYS55 4.7 14.8 1.0 CA A:VAL56 4.8 9.6 1.0 N A:GLY161 4.9 9.9 1.0 N A:GLU11 5.0 11.5 1.0 N A:GLY9 5.0 11.4 1.0

Calcium binding site 2 out of 2 in the Xylopentaose Binding 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 Xylopentaose Binding 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:Ca1169 b:20.3 occ:0.70 O A:ALA22 2.3 16.2 1.0 OD1 A:ASP29 2.3 17.2 0.7 O A:HOH2050 2.3 26.9 1.0 O A:HOH2055 2.3 17.3 1.0 O A:TRP28 2.4 11.2 1.0 O A:HOH2114 2.5 22.1 1.0 C A:TRP28 3.3 9.1 1.0 C A:ALA22 3.5 14.1 1.0 CG A:ASP29 3.5 15.7 0.7 OE1 A:GLU23 3.7 49.9 1.0 N A:ASP29 3.9 9.4 1.0 CA A:ASP29 4.0 9.7 0.3 CA A:ASP29 4.0 9.8 0.7 CB A:ASP29 4.0 12.1 0.3 O A:HOH2048 4.0 12.3 1.0 CA A:GLU23 4.1 17.2 1.0 N A:GLU23 4.3 14.5 1.0 O A:VAL25 4.3 10.7 1.0 CB A:ASP29 4.3 12.2 0.7 N A:TRP28 4.4 9.2 1.0 OD2 A:ASP29 4.4 24.7 0.7 CA A:TRP28 4.5 9.2 1.0 CA A:ALA22 4.5 15.0 1.0 CD A:GLU23 4.7 38.3 1.0 CG A:ASP29 4.8 14.1 0.3 O A:HOH2059 4.8 21.6 1.0 OD1 A:ASP29 4.9 16.9 0.3 O A:HOH2051 4.9 41.2 1.0 C A:GLU23 5.0 15.9 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