Calcium in PDB 1dyo: Xylan-Binding Domain From Cbm 22, Formally X6B Domain

The structure of Xylan-Binding Domain From Cbm 22, Formally X6B Domain, PDB code: 1dyo was solved by G.J.Davies, S.J.Charnock, H.J.Gilbert, C.M.G.A.Fontes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.10
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.490, 89.490, 207.690, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 25

The binding sites of Calcium atom in the Xylan-Binding Domain From Cbm 22, Formally X6B Domain (pdb code 1dyo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Xylan-Binding Domain From Cbm 22, Formally X6B Domain, PDB code: 1dyo:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Xylan-Binding Domain From Cbm 22, Formally X6B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xylan-Binding Domain From Cbm 22, Formally X6B Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:48.3 occ:1.00 O A:THR14 2.5 42.5 1.0 O A:GLU42 2.6 44.1 1.0 O A:LYS39 2.7 42.4 1.0 OE2 A:GLU16 2.9 54.7 1.0 OD1 A:ASP149 2.9 39.4 1.0 OD2 A:ASP149 3.0 38.8 1.0 CG A:ASP149 3.3 39.1 1.0 C A:LYS39 3.6 43.9 1.0 C A:THR14 3.7 45.2 1.0 C A:GLU42 3.7 46.9 1.0 CD A:GLU16 4.0 58.3 1.0 N A:GLU42 4.1 47.6 1.0 N A:LYS39 4.3 42.9 1.0 CA A:GLU42 4.4 48.2 1.0 O A:HOH2043 4.4 44.0 1.0 N A:GLY40 4.4 45.5 1.0 CA A:GLY40 4.4 44.8 1.0 CA A:THR14 4.4 43.7 1.0 CA A:LYS39 4.4 44.0 1.0 N A:PHE15 4.5 44.5 1.0 CB A:PHE15 4.6 43.8 1.0 C A:GLY40 4.6 45.7 1.0 CB A:ALA37 4.6 42.6 1.0 CG A:GLU16 4.6 54.4 1.0 CB A:GLU42 4.6 51.2 1.0 N A:SER41 4.7 46.9 1.0 C A:PHE15 4.7 47.3 1.0 CA A:PHE15 4.7 46.2 1.0 N A:SER43 4.7 44.9 1.0 CA A:SER43 4.8 44.1 1.0 CB A:LYS39 4.8 45.9 1.0 OE2 A:GLU150 4.8 43.2 1.0 N A:GLU16 4.8 49.9 1.0 CB A:ASP149 4.8 38.7 1.0 OE1 A:GLU16 4.8 61.9 1.0 CG2 A:THR14 4.9 40.0 1.0

Calcium binding site 2 out of 2 in the Xylan-Binding Domain From Cbm 22, Formally X6B Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xylan-Binding Domain From Cbm 22, Formally X6B Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca300 b:50.0 occ:1.00 O B:THR14 2.6 39.7 1.0 O B:GLU42 2.6 44.3 1.0 OE2 B:GLU16 2.6 46.6 1.0 O B:HOH2147 2.7 40.7 1.0 OD1 B:ASP149 2.7 43.0 1.0 OD2 B:ASP149 2.7 41.1 1.0 O B:LYS39 2.7 46.4 1.0 CG B:ASP149 3.1 41.9 1.0 CD B:GLU16 3.6 47.9 1.0 C B:THR14 3.7 41.5 1.0 C B:LYS39 3.7 46.1 1.0 C B:GLU42 3.7 46.8 1.0 CG B:GLU16 4.0 47.9 1.0 N B:GLU42 4.1 45.9 1.0 CA B:THR14 4.2 42.1 1.0 CB B:THR14 4.4 43.5 1.0 N B:LYS39 4.5 44.9 1.0 CA B:GLU42 4.5 46.9 1.0 N B:GLY40 4.5 46.2 1.0 CA B:GLY40 4.5 47.0 1.0 CA B:LYS39 4.5 46.7 1.0 OE2 B:GLU150 4.6 44.2 1.0 CB B:ALA37 4.6 39.8 1.0 CB B:ASP149 4.6 40.5 1.0 O B:HOH2064 4.6 49.7 1.0 OE1 B:GLU16 4.6 50.0 1.0 N B:SER43 4.7 43.9 1.0 C B:PHE15 4.7 43.1 1.0 CB B:PHE15 4.7 39.1 1.0 N B:PHE15 4.7 39.8 1.0 C B:GLY40 4.8 47.3 1.0 N B:GLU16 4.8 45.3 1.0 CA B:SER43 4.8 40.0 1.0 CB B:LYS39 4.8 46.7 1.0 N B:SER41 4.8 49.2 1.0 CA B:PHE15 4.9 41.2 1.0

S.J.Charnock, D.N.Bolam, J.P.Turkenburg, H.J.Gilbert, L.M.A.Ferreira, G.J.Davies, C.M.G.A.Fontes. The X6 Thermostabilising Domains of Xylanases Are Carbohydrate Binding Modules: Structure and Biochemistry of the Clostridium Thermocellum X6B Domain Biochemistry V. 39 5013 2000.
ISSN: ISSN 0006-2960
PubMed: 10819965
DOI: 10.1021/BI992821Q