Nickel in PDB 2xvg: Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus

The structure of Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus, PDB code: 2xvg 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)	49.885 / 2.60
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	156.193, 156.193, 227.759, 90.00, 90.00, 120.00
R / Rfree (%)	20.38 / 25.9

The structure of Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Nickel atom in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus (pdb code 2xvg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus, PDB code: 2xvg:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1998 b:44.7 occ:1.00 NE2 A:HIS882 2.0 48.2 1.0 CL A:CL1991 2.2 64.9 1.0 CL A:CL1993 2.3 69.5 1.0 CL A:CL1990 2.3 56.9 1.0 CL A:CL1992 2.3 56.5 1.0 CD2 A:HIS882 2.8 37.3 1.0 CE1 A:HIS882 3.1 49.4 1.0 OD1 A:ASN503 3.7 64.2 1.0 OE1 A:GLU885 3.8 43.2 1.0 CG A:ASN503 4.0 60.1 1.0 CG A:HIS882 4.0 42.0 1.0 ND1 A:HIS882 4.1 55.9 1.0 CB A:ASN503 4.3 50.2 1.0 CD A:GLU885 4.5 49.4 1.0 CB A:GLU885 4.7 42.8 1.0 ND2 A:ASN503 4.8 58.1 1.0 CB A:GLN881 5.0 57.1 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1999 b:66.5 occ:1.00 ND1 A:HIS500 2.2 69.5 1.0 O A:HOH2016 2.2 53.8 1.0 O A:HOH2040 2.5 40.1 1.0 O A:HOH2015 2.7 40.5 1.0 CE1 A:HIS500 3.1 66.2 1.0 CG A:HIS500 3.3 61.9 1.0 CB A:HIS500 3.6 58.3 1.0 O A:HOH2041 3.8 56.3 1.0 OD1 A:ASP497 4.0 70.9 1.0 NE2 A:HIS500 4.2 57.9 1.0 CD2 A:HIS500 4.3 55.0 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