Chlorine 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
Nickel	(Ni)	1 atom

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Alpha-Xylosidase (GH31) From Cellvibrio Japonicus in Complex with 5-Fluoro-Alpha-D-Xylopyranosyl Fluoride, PDB code: 2xvk:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl1989 b:60.1 occ:1.00 NI A:NI1993 2.4 45.8 1.0 CL A:CL1991 2.7 60.4 1.0 OD1 A:ASN503 3.4 63.9 1.0 CL A:CL1990 3.5 67.5 1.0 CL A:CL1992 3.9 58.8 1.0 NE2 A:HIS882 4.0 43.1 1.0 CD2 A:HIS882 4.2 39.7 1.0 CG A:ASN503 4.3 59.4 1.0 NE A:ARG458 4.4 36.1 1.0 CD A:ARG458 4.5 33.2 1.0 CB A:ASN503 4.8 51.9 1.0 CZ A:ARG458 5.0 44.1 1.0

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl binding site number 2 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:Cl1990 b:67.5 occ:1.00 NI A:NI1993 2.3 45.8 1.0 OD1 A:ASN503 3.1 63.9 1.0 CL A:CL1992 3.1 58.8 1.0 CG A:ASN503 3.3 59.4 1.0 ND2 A:ASN503 3.4 54.5 1.0 CL A:CL1989 3.5 60.1 1.0 NE2 A:HIS882 3.5 43.1 1.0 CE1 A:HIS882 3.9 42.5 1.0 CB A:ASN503 4.2 51.9 1.0 CL A:CL1991 4.3 60.4 1.0 CD2 A:HIS882 4.7 39.7 1.0

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl1991 b:60.4 occ:1.00 NI A:NI1993 2.3 45.8 1.0 CL A:CL1992 2.5 58.8 1.0 CL A:CL1989 2.7 60.1 1.0 OE1 A:GLU885 3.0 51.4 1.0 CG A:GLN881 3.6 52.5 1.0 CD A:GLU885 3.7 54.2 1.0 CB A:GLN881 3.8 49.0 1.0 NE2 A:HIS882 3.9 43.1 1.0 OE2 A:GLU885 4.0 55.8 1.0 CD2 A:HIS882 4.1 39.7 1.0 CL A:CL1990 4.3 67.5 1.0 O A:HOH2056 4.7 48.2 1.0 CG A:GLU885 4.9 46.9 1.0 CD A:GLN881 4.9 56.7 1.0 N A:GLN881 5.0 45.6 1.0 CA A:GLN881 5.0 42.0 1.0

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl1992 b:58.8 occ:1.00 NI A:NI1993 2.4 45.8 1.0 CL A:CL1991 2.5 60.4 1.0 CL A:CL1990 3.1 67.5 1.0 OE1 A:GLU885 3.5 51.4 1.0 CD A:GLU885 3.6 54.2 1.0 CL A:CL1989 3.9 60.1 1.0 OE2 A:GLU885 3.9 55.8 1.0 NE2 A:HIS882 4.0 43.1 1.0 CG A:GLU885 4.1 46.9 1.0 CB A:GLU885 4.5 43.4 1.0 CE1 A:HIS882 4.8 42.5 1.0 CD2 A:HIS882 4.8 39.7 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