Calcium in PDB 2y6h: X-2 L110F CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase

All present enzymatic activity of X-2 L110F CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase:
3.2.1.8;

The structure of X-2 L110F CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase, PDB code: 2y6h 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 / 1.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.510, 50.350, 62.740, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 17

The binding sites of Calcium atom in the X-2 L110F CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase (pdb code 2y6h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the X-2 L110F CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase, PDB code: 2y6h:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the X-2 L110F 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 X-2 L110F 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:1.00 O A:LYS55 2.3 18.4 1.0 OE1 A:GLU52 2.3 25.6 1.0 O A:GLU52 2.3 23.7 1.0 OE2 A:GLU11 2.4 22.5 1.0 OD1 A:ASP160 2.4 17.3 1.0 O A:GLY9 2.4 18.4 1.0 OD2 A:ASP160 2.6 18.7 1.0 CG A:ASP160 2.8 16.7 1.0 C A:GLU52 3.3 25.6 1.0 C A:GLY9 3.4 17.2 1.0 CD A:GLU11 3.4 23.0 1.0 C A:LYS55 3.5 17.8 1.0 CD A:GLU52 3.5 31.5 1.0 CA A:GLY9 3.6 18.9 1.0 CB A:GLU52 3.8 28.7 1.0 CG A:GLU11 3.9 24.4 1.0 N A:LYS55 3.9 19.6 1.0 CA A:GLU52 4.0 27.7 1.0 CA A:LYS55 4.2 19.9 1.0 N A:GLY53 4.2 28.0 1.0 N A:GLU52 4.3 26.8 1.0 CA A:GLY53 4.3 28.3 1.0 CG A:GLU52 4.3 32.7 1.0 CB A:ASP160 4.3 16.6 1.0 OE2 A:GLU52 4.5 43.3 1.0 N A:VAL56 4.5 16.5 1.0 OE1 A:GLU11 4.5 26.0 1.0 C A:GLY53 4.5 26.1 1.0 CB A:LYS55 4.6 21.9 1.0 N A:PHE10 4.6 16.1 1.0 N A:ASN54 4.6 24.9 1.0 CB A:ALA50 4.7 22.8 1.0 CA A:VAL56 4.8 14.9 1.0 N A:GLY161 4.9 15.7 1.0 N A:GLU11 4.9 19.0 1.0

Calcium binding site 2 out of 2 in the X-2 L110F 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 X-2 L110F CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1170 b:20.9 occ:0.50 O A:HOH2059 2.1 31.3 1.0 O A:HOH2049 2.2 31.2 0.5 OD1 A:ASP29 2.2 26.4 0.5 O A:HOH2137 2.4 30.2 1.0 O A:ALA22 2.5 20.8 1.0 O A:TRP28 2.7 16.1 1.0 CG A:ASP29 3.3 21.0 0.5 C A:TRP28 3.6 13.5 1.0 C A:ALA22 3.7 18.3 1.0 CA A:GLU23 4.0 23.0 0.5 CA A:GLU23 4.0 23.1 0.5 OD2 A:ASP29 4.1 34.4 0.5 O A:HOH2051 4.1 38.4 1.0 CA A:ASP29 4.1 13.0 0.5 N A:ASP29 4.2 13.3 1.0 CA A:ASP29 4.2 13.4 0.5 O A:HOH2067 4.3 57.6 1.0 CB A:ASP29 4.3 17.2 0.5 CB A:ASP29 4.3 15.5 0.5 CG A:GLU23 4.3 28.5 0.5 N A:GLU23 4.4 20.7 1.0 O A:HOH2058 4.4 17.4 1.0 O A:VAL25 4.4 17.3 1.0 N A:TRP28 4.5 13.8 1.0 O A:HOH2062 4.5 32.4 1.0 CA A:TRP28 4.7 13.5 1.0 CB A:GLU23 4.7 26.4 0.5 CG A:GLU23 4.7 30.3 0.5 CB A:GLU23 4.8 25.8 0.5 O A:LEU76 4.8 15.2 1.0 CA A:ALA22 4.8 18.5 1.0 C A:GLU23 5.0 21.7 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