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

Enzymatic activity of Xylanase R From Bacillus Sp. Tar-1

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

Protein crystallography data

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

Other elements in 7cpk:

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

Calcium (Ca) 3 atoms

Nickel Binding Sites:

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 7cpk

Go back to Nickel Binding Sites List in 7cpk
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 7cpk

Go back to Nickel Binding Sites List in 7cpk
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

Reference:

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.
Page generated: Wed Dec 16 01:59:33 2020

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