Calcium in PDB 7cpk: Xylanase R From Bacillus Sp. Tar-1

All present enzymatic activity of Xylanase R From Bacillus Sp. Tar-1:
3.2.1.8;

The structure of Xylanase R From Bacillus Sp. Tar-1, PDB code: 7cpk was solved by K.Kuwata, M.Suzuki, T.Takita, K.Nakatani, T.Li, Y.Katano, K.Kojima, K.Mizutani, B.Mikami, R.Yatsunami, S.Nakamura, K.Yasukawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.87 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.920, 56.240, 126.650, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 19

The structure of Xylanase R From Bacillus Sp. Tar-1 also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Calcium atom in the Xylanase R From Bacillus Sp. Tar-1 (pdb code 7cpk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Xylanase R From Bacillus Sp. Tar-1, PDB code: 7cpk:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Xylanase R From Bacillus Sp. Tar-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xylanase R From Bacillus Sp. Tar-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:15.4 occ:1.00 O A:ARG348 2.3 16.8 1.0 O A:HOH571 2.3 16.2 1.0 O A:HOH581 2.4 16.7 1.0 OD1 A:ASP289 2.4 18.3 1.0 OD1 A:ASP351 2.4 16.2 1.0 O A:HOH645 2.4 14.8 1.0 O A:HOH545 2.6 18.0 1.0 CG A:ASP351 3.4 16.0 1.0 C A:ARG348 3.5 16.0 1.0 CG A:ASP289 3.5 16.6 1.0 OD2 A:ASP351 3.7 18.1 1.0 OE1 A:GLU293 4.2 16.1 1.0 O A:HOH599 4.2 18.6 1.0 OE2 A:GLU353 4.3 14.8 1.0 CB A:ASP289 4.3 15.5 1.0 CA A:ARG348 4.3 15.4 1.0 OD2 A:ASP289 4.3 16.1 1.0 CA A:ILE349 4.3 14.1 1.0 N A:ILE349 4.4 16.0 1.0 O A:ASP351 4.4 17.9 1.0 CA A:ASP289 4.4 15.8 1.0 CB A:GLU353 4.5 16.0 1.0 NI A:NI406 4.6 15.6 1.0 O A:ASP289 4.6 14.4 1.0 CD A:GLU293 4.7 16.2 1.0 CG A:GLU293 4.8 14.5 1.0 O A:GLU353 4.8 16.2 1.0 CB A:ASP351 4.8 16.3 1.0 C A:ASP351 4.8 15.5 1.0 CB A:ARG348 4.8 13.9 1.0 N A:GLU353 4.8 15.9 1.0 N A:ASP351 4.9 15.4 1.0 C A:ASP289 4.9 14.1 1.0 CD A:GLU353 5.0 15.5 1.0 C A:ILE349 5.0 16.0 1.0

Calcium binding site 2 out of 3 in the Xylanase R From Bacillus Sp. Tar-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xylanase R From Bacillus Sp. Tar-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:17.1 occ:0.61 O A:ALA299 2.2 19.0 1.0 O A:GLN19 2.3 19.1 1.0 O A:HOH746 2.4 29.9 1.0 O A:ILE302 2.4 18.5 1.0 O A:HOH750 2.4 26.7 1.0 O A:HOH753 2.6 57.5 1.0 C A:ALA299 3.4 14.6 1.0 C A:ILE302 3.4 14.6 1.0 C A:GLN19 3.5 17.3 1.0 CA A:SER303 4.0 15.7 1.0 CA A:ALA299 4.2 16.8 1.0 N A:SER303 4.2 15.2 1.0 N A:ILE302 4.3 15.3 1.0 CA A:PHE20 4.3 16.6 1.0 N A:PHE20 4.4 16.4 1.0 N A:ALA300 4.4 17.6 1.0 CB A:PHE20 4.4 16.6 1.0 CA A:GLN19 4.4 17.5 1.0 CB A:ALA299 4.4 19.8 1.0 CA A:ILE302 4.4 13.6 1.0 CA A:ALA300 4.5 19.1 1.0 O A:HOH572 4.5 27.4 1.0 C A:ALA300 4.6 21.7 1.0 O A:ALA300 4.7 24.1 1.0 O A:HOH754 4.7 31.6 1.0 C A:SER303 4.8 15.6 1.0 CD2 A:PHE20 4.8 17.0 1.0 O A:SER303 4.9 14.7 1.0 CB A:ILE302 5.0 12.9 1.0

Calcium binding site 3 out of 3 in the Xylanase R From Bacillus Sp. Tar-1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xylanase R From Bacillus Sp. Tar-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:20.8 occ:0.53 OH A:TYR273 2.3 27.2 1.0 O A:ASP312 2.4 18.2 1.0 OD1 A:ASP318 2.4 24.2 1.0 O A:ASP331 2.5 21.6 1.0 OD2 A:ASP318 2.5 25.4 1.0 CG A:ASP318 2.8 23.4 1.0 CG2 A:THR315 3.4 21.4 1.0 CZ A:TYR273 3.4 25.8 1.0 C A:ASP312 3.6 17.1 1.0 C A:ASP331 3.6 21.3 1.0 CE1 A:TYR273 3.7 26.4 1.0 N A:ASP331 3.9 20.9 1.0 O A:HOH521 3.9 42.5 1.0 CB A:ASP318 4.3 23.1 1.0 CA A:ASP312 4.3 17.7 1.0 CB A:ASP312 4.4 16.5 1.0 CA A:ASP331 4.4 20.6 1.0 CB A:ILE330 4.5 24.9 1.0 N A:ASN313 4.6 18.1 1.0 N A:ALA332 4.6 19.1 1.0 CA A:ASN313 4.6 19.0 1.0 CE2 A:TYR273 4.7 26.8 1.0 C A:ASN313 4.8 21.1 1.0 CG2 A:ILE330 4.8 26.9 1.0 O A:HOH542 4.8 23.9 1.0 CA A:ALA332 4.9 16.6 1.0 CB A:THR315 4.9 19.6 1.0 C A:ILE330 4.9 22.6 1.0 CA A:ILE330 4.9 23.1 1.0 CD A:PRO333 4.9 18.5 1.0 N A:HIS314 5.0 19.1 1.0 N A:THR315 5.0 18.9 1.0

M.Suzuki, T.Takita, K.Kuwata, K.Nakatani, T.Li, Y.Katano, K.Kojima, K.Mizutani, B.Mikami, R.Yatsunami, S.Nakamura, K.Yasukawa. Insight Into the Mechanism of Thermostabilization of Bacillus Sp. Strain Tar-1 Xylanase By the Mutation of SER92 to Glu To Be Published.