Calcium in PDB 2yik: Catalytic Domain of Clostridium Thermocellum Celt

All present enzymatic activity of Catalytic Domain of Clostridium Thermocellum Celt:
3.2.1.4;

The structure of Catalytic Domain of Clostridium Thermocellum Celt, PDB code: 2yik was solved by J.-Y.Tsai, M.M.Kesavulu, C.-D.Hsiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.38 / 2.10
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.860, 96.860, 159.920, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 19.9

The structure of Catalytic Domain of Clostridium Thermocellum Celt also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Calcium atom in the Catalytic Domain of Clostridium Thermocellum Celt (pdb code 2yik). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Catalytic Domain of Clostridium Thermocellum Celt, PDB code: 2yik:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Catalytic Domain of Clostridium Thermocellum Celt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catalytic Domain of Clostridium Thermocellum Celt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1332 b:29.2 occ:1.00 O A:ASP337 2.4 29.3 1.0 O A:SER340 2.5 28.1 1.0 ND2 A:ASN333 2.5 22.0 1.0 OD2 A:ASP337 2.6 30.0 1.0 O A:HOH2243 2.6 24.6 1.0 OE1 A:GLU344 2.7 27.0 1.0 OE2 A:GLU344 2.7 25.7 1.0 CD A:GLU344 3.0 27.0 1.0 CG A:ASP337 3.3 31.1 1.0 CG A:ASN333 3.4 24.8 1.0 C A:ASP337 3.5 30.1 1.0 OD1 A:ASN333 3.5 25.1 1.0 C A:SER340 3.6 30.0 1.0 CB A:ASP337 3.7 29.3 1.0 OD1 A:ASP337 4.2 30.0 1.0 CA A:ASP337 4.2 29.4 1.0 CA A:GLN341 4.3 28.1 1.0 N A:SER340 4.4 34.7 1.0 N A:GLN341 4.4 28.9 1.0 O A:LYS338 4.4 34.2 1.0 N A:LYS338 4.5 32.3 1.0 CG A:GLU344 4.5 25.9 1.0 CB A:PHE343 4.6 25.6 1.0 CA A:SER340 4.6 32.0 1.0 C A:LYS338 4.6 35.7 1.0 O A:HOH2253 4.6 35.2 1.0 OE1 A:GLN341 4.6 29.3 1.0 C A:GLN341 4.7 27.4 1.0 N A:PHE343 4.7 26.4 1.0 CA A:LYS338 4.7 34.8 1.0 N A:ASN342 4.8 27.0 1.0 O A:HOH2242 4.8 21.8 1.0 CB A:ASN333 4.8 24.9 1.0 N A:GLU344 4.8 24.7 1.0 OG A:SER340 4.8 34.9 1.0 O A:ASN333 4.8 24.0 1.0

Calcium binding site 2 out of 3 in the Catalytic Domain of Clostridium Thermocellum Celt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catalytic Domain of Clostridium Thermocellum Celt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1333 b:30.7 occ:1.00 O A:LYS277 2.5 28.3 1.0 OD1 A:ASP280 2.6 23.1 1.0 O A:HOH2203 2.6 19.3 1.0 OD2 A:ASP281 2.6 25.5 1.0 O A:HOH2209 2.6 19.5 1.0 OD2 A:ASP280 2.7 24.3 1.0 CG A:ASP280 3.0 23.7 1.0 CG A:ASP281 3.4 26.3 1.0 CE A:LYS277 3.5 37.8 1.0 C A:LYS277 3.6 27.6 1.0 OD1 A:ASP281 3.6 22.5 1.0 O A:ASN319 3.9 22.6 1.0 N A:LYS277 4.2 26.5 1.0 CD A:LYS277 4.2 39.4 1.0 CG A:LYS277 4.2 34.2 1.0 C A:ASN319 4.2 23.3 1.0 CA A:LYS277 4.3 27.6 1.0 N A:ASP281 4.5 24.0 1.0 OG A:SER275 4.5 20.7 1.0 N A:TRP278 4.5 26.0 1.0 CB A:ASP280 4.5 23.1 1.0 N A:ASP320 4.6 22.1 1.0 CA A:TRP278 4.6 24.2 1.0 CB A:ASP281 4.7 24.6 1.0 NZ A:LYS277 4.7 35.6 1.0 CA A:ASP320 4.7 22.9 1.0 OD1 A:ASN319 4.8 27.3 1.0 CA A:ASN319 4.8 23.5 1.0 CB A:ASP217 4.8 24.3 1.0 O A:TRP318 4.9 22.8 1.0 CB A:LYS277 4.9 30.5 1.0

Calcium binding site 3 out of 3 in the Catalytic Domain of Clostridium Thermocellum Celt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catalytic Domain of Clostridium Thermocellum Celt within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1531 b:32.2 occ:1.00 O A:LYS107 2.4 29.5 1.0 OD1 A:ASP105 2.5 32.9 1.0 OD1 A:ASP101 2.6 28.1 1.0 OD1 A:ASP103 2.6 38.8 1.0 OD2 A:ASP103 2.9 41.2 1.0 CG A:ASP103 3.1 36.0 1.0 CG A:ASP105 3.3 34.1 1.0 C A:LYS107 3.5 30.5 1.0 OD2 A:ASP105 3.6 36.6 1.0 CG A:ASP101 3.7 28.1 1.0 N A:LYS107 4.0 30.1 1.0 O A:HOH2039 4.1 42.8 1.0 CA A:LYS107 4.3 30.7 1.0 N A:ASP105 4.4 32.3 1.0 CB A:ASP105 4.5 32.6 1.0 OD2 A:ASP101 4.5 31.2 1.0 O A:HOH2069 4.5 39.9 1.0 N A:VAL108 4.5 30.8 1.0 CB A:ASP101 4.6 27.9 1.0 CA A:ASP101 4.6 26.2 1.0 CB A:ASP103 4.6 34.4 1.0 CA A:VAL108 4.6 29.4 1.0 CB A:LYS107 4.7 32.5 1.0 N A:GLY106 4.8 31.5 1.0 CA A:ASP105 4.8 31.9 1.0 C A:ASP105 5.0 31.8 1.0 N A:GLY104 5.0 32.3 1.0 C A:ASP101 5.0 27.4 1.0

M.M.Kesavulu, J.-Y.Tsai, H.-L.Lee, P.-H.Liang, C.-D.Hsiao. Structure of the Catalytic Domain of the Clostridium Thermocellum Cellulase Celt Acta Crystallogr.,Sect.D V. 68 310 2012.
ISSN: ISSN 0907-4449
PubMed: 22349233
DOI: 10.1107/S0907444912001990