Nickel in PDB 2xvl: Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh)

The structure of Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh), PDB code: 2xvl 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)	54.548 / 2.30
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	157.653, 157.653, 226.688, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 18.53

The structure of Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh) also contains other interesting chemical elements:

Chlorine

(Cl)

7 atoms

The binding sites of Nickel atom in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh) (pdb code 2xvl). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh), PDB code: 2xvl:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh)


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 Pentaerythritol Propoxylate (5 4 Po Oh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1989 b:19.6 occ:1.00 NE2 A:HIS882 2.3 10.2 1.0 CL A:CL2000 2.4 40.6 1.0 CL A:CL1996 2.4 43.9 1.0 CL A:CL1997 2.5 39.3 1.0 CL A:CL1998 2.5 41.2 1.0 CL A:CL1999 2.6 45.0 1.0 CD2 A:HIS882 3.0 9.5 1.0 CE1 A:HIS882 3.4 11.8 1.0 OE1 A:GLU885 3.9 14.8 1.0 ND2 A:ASN503 3.9 13.8 1.0 CG A:ASN503 4.2 21.2 1.0 CG A:HIS882 4.3 16.8 1.0 ND1 A:HIS882 4.4 22.3 1.0 CB A:ASN503 4.4 13.9 1.0 CD A:GLU885 4.5 14.7 1.0 CB A:GLU885 4.7 15.8 1.0 OD1 A:ASN503 4.8 25.6 1.0 CG A:GLU885 4.9 16.0 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh)


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 in Complex with Pentaerythritol Propoxylate (5 4 Po Oh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1990 b:34.8 occ:1.00 ND1 A:HIS500 2.3 18.0 1.0 O A:HOH2048 2.4 26.8 1.0 O A:HOH2325 2.5 26.5 1.0 O A:HOH2121 2.5 31.9 1.0 O A:HOH2119 2.6 30.2 1.0 CL A:CL2002 2.6 63.0 1.0 CE1 A:HIS500 3.2 11.0 1.0 CG A:HIS500 3.3 16.4 1.0 CB A:HIS500 3.6 12.4 1.0 O A:HOH2326 4.1 25.3 1.0 NE2 A:HIS500 4.3 21.2 1.0 CD2 A:HIS500 4.4 20.5 1.0 OD1 A:ASP497 4.5 21.9 1.0 O A:HOH2328 4.8 30.9 1.0 CG1 A:VAL496 4.9 11.0 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with Pentaerythritol Propoxylate (5 4 Po Oh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1991 b:64.8 occ:1.00 NE2 A:HIS700 2.4 66.6 1.0 O A:HOH2489 2.7 37.6 1.0 O A:HOH2058 2.8 46.1 1.0 O A:HOH2177 2.8 44.2 1.0 O A:HOH2176 2.8 45.8 1.0 CD2 A:HIS700 3.1 58.6 1.0 CE1 A:HIS700 3.5 64.5 1.0 O A:HOH2493 3.7 36.3 1.0 O A:HOH2182 3.9 42.7 1.0 CG A:HIS700 4.3 54.9 1.0 ND1 A:HIS700 4.5 61.1 1.0 CB A:ASP696 4.5 32.6 1.0 OD2 A:ASP696 5.0 56.2 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