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Nickel in PDB 2dro: Crystal Structure of Reducing-End-Xylose Releasing Exo-Oligoxylanase D263C Mutant

Enzymatic activity of Crystal Structure of Reducing-End-Xylose Releasing Exo-Oligoxylanase D263C Mutant

All present enzymatic activity of Crystal Structure of Reducing-End-Xylose Releasing Exo-Oligoxylanase D263C Mutant:
3.2.1.156;

Protein crystallography data

The structure of Crystal Structure of Reducing-End-Xylose Releasing Exo-Oligoxylanase D263C Mutant, PDB code: 2dro was solved by S.Fushinobu, M.Hidaka, Y.Honda, T.Wakagi, H.Shoun, M.Kitaoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.07 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.242, 86.369, 87.653, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 18.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Reducing-End-Xylose Releasing Exo-Oligoxylanase D263C Mutant (pdb code 2dro). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Reducing-End-Xylose Releasing Exo-Oligoxylanase D263C Mutant, PDB code: 2dro:

Nickel binding site 1 out of 1 in 2dro

Go back to Nickel Binding Sites List in 2dro
Nickel binding site 1 out of 1 in the Crystal Structure of Reducing-End-Xylose Releasing Exo-Oligoxylanase D263C Mutant


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Reducing-End-Xylose Releasing Exo-Oligoxylanase D263C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1400

b:13.9
occ:1.00
OE2 A:GLU27 1.9 17.8 1.0
OE1 A:GLU30 2.0 15.7 1.0
CD A:GLU27 2.7 16.2 1.0
OE1 A:GLU27 2.8 15.9 1.0
CD A:GLU30 2.9 13.1 1.0
OE2 A:GLU30 3.1 15.4 1.0
CG A:GLU27 4.2 15.4 1.0
CG A:GLU30 4.3 14.4 1.0
O A:HOH1566 4.4 30.7 1.0
O A:HOH1467 4.4 20.3 1.0
CB A:GLU30 4.6 13.4 1.0
CA A:GLU27 4.9 14.6 1.0

Reference:

M.Hidaka, S.Fushinobu, Y.Honda, T.Wakagi, H.Shoun, M.Kitaoka. Structural Explanation For the Acquisition of Glycosynthase Activity J.Biochem. 2009.
ISSN: ISSN 0021-924X
PubMed: 19819900
DOI: 10.1093/JB/MVP159
Page generated: Wed Dec 16 01:17:39 2020

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