Calcium in PDB 2y64: Xylopentaose Binding Mutated (X-2 L110F) CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase

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

The structure of Xylopentaose Binding Mutated (X-2 L110F) CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase, PDB code: 2y64 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 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.460, 50.680, 62.550, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 20

The binding sites of Calcium atom in the Xylopentaose Binding Mutated (X-2 L110F) CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase (pdb code 2y64). 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 Mutated (X-2 L110F) CBM4-2 Carbohydrate Binding Module From A Thermostable Rhodothermus Marinus Xylanase, PDB code: 2y64:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Xylopentaose Binding Mutated (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 Xylopentaose Binding Mutated (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:Ca1168 b:16.1 occ:1.00 OE1 A:GLU52 2.3 19.6 1.0 O A:GLU52 2.3 18.0 1.0 O A:LYS55 2.3 16.1 1.0 OE2 A:GLU11 2.4 18.2 1.0 OD1 A:ASP160 2.4 16.0 1.0 O A:GLY9 2.4 15.4 1.0 OD2 A:ASP160 2.6 15.1 1.0 CG A:ASP160 2.8 14.9 1.0 C A:GLU52 3.3 18.7 1.0 C A:GLY9 3.3 15.1 1.0 CD A:GLU11 3.4 19.3 1.0 C A:LYS55 3.5 16.4 1.0 CD A:GLU52 3.5 21.6 1.0 CA A:GLY9 3.6 16.5 1.0 CB A:GLU52 3.9 20.3 1.0 N A:LYS55 3.9 18.9 1.0 CG A:GLU11 3.9 20.1 1.0 CA A:GLU52 4.0 19.3 1.0 CA A:LYS55 4.1 18.6 1.0 N A:GLY53 4.2 20.3 1.0 CG A:GLU52 4.2 21.8 1.0 CB A:ASP160 4.3 14.8 1.0 CA A:GLY53 4.3 19.3 1.0 OE2 A:GLU52 4.4 26.8 1.0 N A:GLU52 4.4 20.6 1.0 OE1 A:GLU11 4.5 21.2 1.0 N A:VAL56 4.6 16.5 1.0 N A:ASN54 4.6 18.0 1.0 N A:PHE10 4.6 14.0 1.0 C A:GLY53 4.6 18.2 1.0 CB A:LYS55 4.6 21.0 1.0 CB A:ALA50 4.8 24.0 1.0 N A:GLU11 4.8 17.5 1.0 CA A:VAL56 4.8 15.4 1.0 N A:GLY161 4.9 15.2 1.0

Calcium binding site 2 out of 2 in the Xylopentaose Binding Mutated (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 Xylopentaose Binding Mutated (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:19.8 occ:0.70 O A:HOH2047 2.3 23.8 1.0 OD1 A:ASP29 2.3 18.6 0.7 O A:HOH2052 2.3 26.6 0.5 O A:HOH2038 2.3 22.4 0.5 O A:HOH2109 2.4 26.7 1.0 O A:ALA22 2.4 21.8 1.0 O A:TRP28 2.5 16.1 1.0 C A:TRP28 3.4 14.8 1.0 CG A:ASP29 3.6 18.3 0.7 C A:ALA22 3.7 19.9 1.0 N A:ASP29 4.0 16.1 1.0 CA A:ASP29 4.1 16.4 0.3 CA A:ASP29 4.1 16.4 0.7 CA A:GLU23 4.1 22.7 1.0 O A:HOH2055 4.2 44.5 1.0 O A:HOH2036 4.3 16.3 1.0 CB A:ASP29 4.3 17.8 0.3 N A:GLU23 4.4 21.5 1.0 N A:TRP28 4.4 13.5 1.0 OD2 A:ASP29 4.4 25.3 0.7 CB A:ASP29 4.4 17.9 0.7 O A:VAL25 4.5 16.8 1.0 CD1 A:LEU76 4.5 19.7 0.3 O A:HOH2051 4.5 29.3 1.0 CA A:TRP28 4.5 13.5 1.0 O A:HOH2042 4.6 40.8 1.0 CG A:GLU23 4.7 30.3 1.0 CA A:ALA22 4.7 19.6 1.0 CB A:GLU23 4.9 24.8 1.0 CG A:ASP29 4.9 18.3 0.3 O A:LEU76 4.9 16.8 1.0 OD2 A:ASP29 5.0 25.1 0.3 CG A:LEU76 5.0 18.9 0.3

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