Calcium in PDB 7cpl: 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: 7cpl 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)	35.93 / 1.52
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.085, 53.897, 127.413, 90.00, 90.00, 90.00
R / Rfree (%)	13.4 / 17.2

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 7cpl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Xylanase R From Bacillus Sp. Tar-1, PDB code: 7cpl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 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:Ca408 b:18.1 occ:1.00 O A:ARG348 2.3 20.4 1.0 OD1 A:ASP289 2.3 19.8 1.0 O A:HOH598 2.4 20.0 1.0 O A:HOH550 2.4 17.4 1.0 OD1 A:ASP351 2.5 20.4 1.0 O A:HOH617 2.5 17.6 1.0 O A:HOH535 2.6 17.2 1.0 CG A:ASP351 3.4 18.9 1.0 C A:ARG348 3.4 18.4 1.0 CG A:ASP289 3.4 17.9 1.0 OD2 A:ASP351 3.7 20.8 1.0 OE1 A:GLU293 4.1 18.9 1.0 OE1 A:GLU353 4.2 20.3 1.0 O A:HOH603 4.3 20.9 1.0 OD2 A:ASP289 4.3 19.4 1.0 CB A:ASP289 4.3 18.9 1.0 CA A:ARG348 4.3 19.8 1.0 CA A:ILE349 4.3 17.5 1.0 N A:ILE349 4.3 17.4 1.0 CA A:ASP289 4.4 17.4 1.0 O A:ASP351 4.4 18.4 1.0 NI A:NI412 4.5 17.7 1.0 CB A:GLU353 4.5 19.1 1.0 O A:ASP289 4.6 17.5 1.0 CD A:GLU293 4.7 18.9 1.0 CG A:GLU293 4.8 18.5 1.0 CB A:ARG348 4.8 19.3 1.0 CB A:ASP351 4.8 17.3 1.0 O A:GLU353 4.8 20.2 1.0 C A:ASP351 4.8 17.5 1.0 N A:ASP351 4.9 19.7 1.0 N A:GLU353 4.9 19.8 1.0 C A:ILE349 4.9 16.6 1.0 C A:ASP289 5.0 17.8 1.0 CD A:GLU353 5.0 19.9 1.0

Calcium binding site 2 out of 4 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:Ca409 b:18.9 occ:0.55 O A:GLN19 2.3 20.9 1.0 O A:ALA299 2.3 21.0 1.0 O A:HOH752 2.3 29.8 1.0 O A:ILE302 2.4 19.8 1.0 O A:HOH760 2.4 31.1 1.0 O A:HOH757 2.4 59.5 1.0 C A:ALA299 3.4 20.1 1.0 C A:ILE302 3.4 16.9 1.0 C A:GLN19 3.5 19.5 1.0 CA A:SER303 4.1 15.5 1.0 O A:HOH772 4.1 39.5 1.0 N A:SER303 4.2 16.6 1.0 CA A:ALA299 4.2 20.1 1.0 N A:ILE302 4.3 19.2 1.0 CA A:PHE20 4.4 16.7 1.0 N A:PHE20 4.4 16.8 1.0 O A:HOH816 4.4 42.1 1.0 N A:ALA300 4.4 21.4 1.0 CA A:GLN19 4.4 19.2 1.0 CB A:PHE20 4.4 18.3 1.0 CB A:ALA299 4.4 21.1 1.0 CA A:ILE302 4.4 16.8 1.0 O A:HOH648 4.4 34.0 1.0 CA A:ALA300 4.5 22.4 1.0 C A:ALA300 4.6 23.5 1.0 C A:SER303 4.8 15.4 1.0 O A:ALA300 4.8 26.3 1.0 CD2 A:PHE20 4.8 19.1 1.0 O A:SER303 4.9 16.8 1.0

Calcium binding site 3 out of 4 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:Ca410 b:22.8 occ:0.57 OH A:TYR273 2.3 25.2 1.0 O A:ASP312 2.3 20.3 1.0 O A:ASP331 2.4 23.4 1.0 OD1 A:ASP318 2.4 27.2 1.0 OD2 A:ASP318 2.6 28.3 1.0 CG A:ASP318 2.8 25.6 1.0 CZ A:TYR273 3.3 26.2 1.0 CG2 A:THR315 3.4 21.6 1.0 CE1 A:TYR273 3.5 26.5 1.0 C A:ASP312 3.5 20.5 1.0 C A:ASP331 3.6 22.9 1.0 N A:ASP331 3.8 23.0 1.0 O A:HOH698 4.0 46.5 1.0 CA A:ASP312 4.3 19.2 1.0 CA A:ASP331 4.3 23.3 1.0 CB A:ASP312 4.3 20.0 1.0 CB A:ASP318 4.4 24.8 1.0 CB A:ILE330 4.4 25.0 1.0 N A:ASN313 4.5 19.4 1.0 CE2 A:TYR273 4.6 28.6 1.0 N A:ALA332 4.6 20.7 1.0 CA A:ASN313 4.6 20.4 1.0 CG2 A:ILE330 4.6 26.1 1.0 C A:ASN313 4.8 20.2 1.0 C5 A:MPD407 4.8 72.9 1.0 CA A:ALA332 4.8 21.3 1.0 C A:ILE330 4.8 24.9 1.0 CA A:ILE330 4.9 23.6 1.0 CD1 A:TYR273 4.9 27.9 1.0 CB A:THR315 4.9 18.6 1.0 O A:HOH560 4.9 27.4 1.0 CD A:PRO333 5.0 19.1 1.0 N A:HIS314 5.0 19.8 1.0

Calcium binding site 4 out of 4 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 4 of Xylanase R From Bacillus Sp. Tar-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca411 b:80.7 occ:1.00 OD2 A:ASP275 2.4 40.1 1.0 O A:HOH773 2.5 59.0 1.0 OD1 A:ASP275 2.6 42.6 1.0 CG A:ASP275 2.9 39.2 1.0 O A:HOH767 3.0 48.2 1.0 OG A:SER272 4.2 43.4 1.0 CB A:ASP275 4.3 35.8 1.0 O A:HOH583 4.6 35.6 1.0 O A:HOH567 4.8 34.5 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.