Nickel in PDB 2xvk: Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with 5-Fluoro-Alpha-D-Xylopyranosyl Fluoride

The structure of Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with 5-Fluoro-Alpha-D-Xylopyranosyl Fluoride, PDB code: 2xvk was solved by J.Larsbrink, A.Izumi, F.Ibatullin, A.Nakhai, H.J.Gilbert, G.J.Davies, H.Brumer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.985 / 2.50
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	156.524, 156.524, 227.762, 90.00, 90.00, 120.00
R / Rfree (%)	19.49 / 23.97

The structure of Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with 5-Fluoro-Alpha-D-Xylopyranosyl Fluoride also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Nickel atom in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with 5-Fluoro-Alpha-D-Xylopyranosyl Fluoride (pdb code 2xvk). 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 Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with 5-Fluoro-Alpha-D-Xylopyranosyl Fluoride, PDB code: 2xvk:

Nickel binding site 1 out of 1 in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with 5-Fluoro-Alpha-D-Xylopyranosyl Fluoride


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 Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with 5-Fluoro-Alpha-D-Xylopyranosyl Fluoride within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1993 b:45.8 occ:1.00 NE2 A:HIS882 2.2 43.1 1.0 CL A:CL1990 2.3 67.5 1.0 CL A:CL1991 2.3 60.4 1.0 CL A:CL1992 2.4 58.8 1.0 CL A:CL1989 2.4 60.1 1.0 CD2 A:HIS882 3.0 39.7 1.0 CE1 A:HIS882 3.3 42.5 1.0 OE1 A:GLU885 3.8 51.4 1.0 OD1 A:ASN503 3.8 63.9 1.0 CG A:ASN503 4.2 59.4 1.0 CG A:HIS882 4.2 44.4 1.0 ND1 A:HIS882 4.3 47.9 1.0 CB A:ASN503 4.5 51.9 1.0 CD A:GLU885 4.5 54.2 1.0 CB A:GLU885 4.9 43.4 1.0 ND2 A:ASN503 4.9 54.5 1.0 CB A:GLN881 5.0 49.0 1.0

J.Larsbrink, A.Izumi, F.Ibatullin, A.Nakhai, H.J.Gilbert, G.J.Davies, H.Brumer. Structural and Enzymatic Characterisation of A Glycoside Hydrolase Family 31 Alpha-Xylosidase From Cellvibrio Japonicus Involved in Xyloglucan Saccharification. Biochem.J. V. 436 567 2011.
ISSN: ISSN 0264-6021
PubMed: 21426303
DOI: 10.1042/BJ20110299