Nickel 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:

Calcium

(Ca)

3 atoms

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

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Xylanase R From Bacillus Sp. Tar-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni406 b:15.6 occ:1.00 OD2 A:ASP289 2.0 16.1 1.0 OE1 A:GLU293 2.0 16.1 1.0 OE2 A:GLU353 2.0 14.8 1.0 NE2 A:HIS357 2.0 17.6 1.0 CD A:GLU293 2.8 16.2 1.0 CG A:ASP289 2.8 16.6 1.0 CD A:GLU353 2.8 15.5 1.0 OE2 A:GLU293 2.9 20.4 1.0 OD1 A:ASP289 2.9 18.3 1.0 CE1 A:HIS357 2.9 21.1 1.0 OE1 A:GLU353 3.0 16.0 1.0 CD2 A:HIS357 3.1 18.0 1.0 O A:HOH571 3.7 16.2 1.0 O A:HOH545 3.8 18.0 1.0 ND1 A:HIS357 4.1 20.7 1.0 CG A:GLU293 4.2 14.5 1.0 CG A:HIS357 4.2 19.4 1.0 CB A:ASP289 4.2 15.5 1.0 CG A:GLU353 4.3 15.2 1.0 NH2 A:ARG348 4.4 20.4 1.0 CA A:CA403 4.6 15.4 1.0 CE1 A:HIS355 4.8 22.2 1.0 CB A:GLU353 4.8 16.0 1.0 C A:ASP289 4.9 14.1 1.0 O A:ASP289 5.0 14.4 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Xylanase R From Bacillus Sp. Tar-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni407 b:17.1 occ:1.00 OD2 A:ASP21 2.0 20.3 1.0 OE2 A:GLU82 2.0 17.9 1.0 CG A:ASP21 2.7 19.4 1.0 OD1 A:ASP21 2.7 20.1 1.0 CD A:GLU82 3.0 18.0 1.0 CG A:GLU82 3.4 14.6 1.0 OE1 A:GLU82 4.1 21.1 1.0 CB A:ASP21 4.1 15.9 1.0 CB A:GLU82 4.3 12.7 1.0 O A:HOH597 4.3 27.1 1.0 O A:HOH637 5.0 24.3 1.0 O A:ASN44 5.0 14.4 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.