Calcium in PDB 1jxn: Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose

The structure of Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose, PDB code: 1jxn was solved by G.F.Audette, D.J.H.Olson, A.R.S.Ross, J.W.Quail, L.T.J.Delbaere, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.810, 69.000, 119.020, 90.00, 106.76, 90.00
R / Rfree (%)	20.2 / 28.9

The structure of Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose (pdb code 1jxn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose, PDB code: 1jxn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca246 b:16.7 occ:1.00 O A:HOH518 2.2 14.7 1.0 OD1 A:ASP127 2.3 13.4 1.0 OD1 A:ASP137 2.3 28.6 1.0 OD2 A:ASP127 2.3 12.7 1.0 O A:HOH517 2.4 13.1 1.0 OD1 A:ASN134 2.4 27.7 1.0 O A:ILE129 2.5 25.6 1.0 CG A:ASP127 2.6 13.8 1.0 CG A:ASN134 3.3 26.3 1.0 CG A:ASP137 3.4 24.6 1.0 C A:ILE129 3.6 27.0 1.0 CB A:ASN134 3.7 23.9 1.0 OD2 A:ASP137 4.1 26.4 1.0 MN A:MN245 4.1 22.8 1.0 CB A:ASP127 4.1 12.5 1.0 O A:HOH515 4.2 9.6 1.0 NE1 A:TRP136 4.4 13.7 1.0 CG2 A:ILE129 4.4 22.2 1.0 CA A:GLY130 4.4 28.1 1.0 N A:GLY130 4.5 28.8 1.0 CB A:ASP137 4.5 21.1 1.0 N A:ILE129 4.5 26.2 1.0 O A:GLY105 4.6 20.5 1.0 CA A:ILE129 4.6 25.9 1.0 ND2 A:ASN134 4.6 24.2 1.0 OD2 A:ASP87 4.7 21.4 1.0 CZ A:PHE107 4.7 24.6 1.0 CA A:GLY105 4.7 19.1 1.0 O A:ASP87 4.8 16.9 1.0 CE1 A:HIS142 4.9 16.1 1.0 CE1 A:PHE107 4.9 23.3 1.0 CA A:ASP127 5.0 19.2 1.0 CE2 A:TRP136 5.0 12.9 1.0 CZ2 A:TRP136 5.0 14.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca246 b:18.0 occ:1.00 O B:ILE129 2.1 28.3 1.0 O B:HOH641 2.4 25.1 1.0 OD2 B:ASP127 2.4 21.9 1.0 O B:HOH618 2.4 13.3 1.0 OD1 B:ASP127 2.5 22.1 1.0 OD1 B:ASN134 2.8 26.4 1.0 CG B:ASP127 2.8 21.0 1.0 OD1 B:ASP137 3.1 23.3 1.0 C B:ILE129 3.4 27.4 1.0 CG B:ASP137 3.4 25.8 1.0 OD2 B:ASP137 3.4 25.7 1.0 CG B:ASN134 3.8 24.0 1.0 CG2 B:ILE129 4.0 20.0 1.0 CB B:ASN134 4.2 25.8 1.0 N B:GLY130 4.2 29.5 1.0 NE1 B:TRP136 4.3 17.9 1.0 CA B:GLY130 4.3 31.0 1.0 CB B:ASP127 4.3 15.8 1.0 CA B:ILE129 4.3 24.4 1.0 N B:ILE129 4.4 24.2 1.0 O B:HOH620 4.4 11.2 1.0 CB B:ASP137 4.5 24.9 1.0 MN B:MN245 4.5 20.4 1.0 OD2 B:ASP87 4.6 24.0 1.0 O B:ASP87 4.7 23.6 1.0 O B:GLY105 4.7 23.0 1.0 CZ B:PHE107 4.7 19.3 1.0 CB B:ILE129 4.8 21.9 1.0 CE2 B:TRP136 4.9 19.2 1.0 CA B:GLY105 4.9 22.5 1.0 ND2 B:ASN134 5.0 18.4 1.0 CZ2 B:TRP136 5.0 20.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca246 b:21.5 occ:1.00 OD1 C:ASN134 2.2 19.0 1.0 O C:HOH916 2.3 9.9 1.0 OD1 C:ASP127 2.3 18.9 1.0 O C:ILE129 2.3 25.1 1.0 OD2 C:ASP127 2.3 19.0 1.0 O C:HOH917 2.4 12.7 1.0 CG C:ASP127 2.6 20.6 1.0 OD1 C:ASP137 2.8 24.5 1.0 CG C:ASP137 3.2 24.2 1.0 CG C:ASN134 3.3 18.7 1.0 OD2 C:ASP137 3.3 23.5 1.0 C C:ILE129 3.5 25.5 1.0 CB C:ASN134 3.7 17.5 1.0 CG2 C:ILE129 3.8 23.1 1.0 O C:HOH918 3.8 10.8 1.0 CB C:ASP127 4.1 18.1 1.0 MN C:MN245 4.3 19.1 1.0 CB C:ASP137 4.3 22.4 1.0 CA C:ILE129 4.3 24.7 1.0 N C:ILE129 4.4 23.9 1.0 N C:GLY130 4.5 26.9 1.0 ND2 C:ASN134 4.5 17.8 1.0 NE1 C:TRP136 4.5 26.0 1.0 CA C:GLY130 4.6 27.1 1.0 CE1 C:HIS142 4.6 16.3 1.0 CB C:ILE129 4.6 24.2 1.0 CZ C:PHE107 4.8 23.0 1.0 O C:ASP87 4.8 21.1 1.0 CZ2 C:TRP136 4.8 25.5 1.0 OD2 C:ASP87 4.9 26.3 1.0 NE2 C:HIS142 4.9 14.9 1.0 CE2 C:TRP136 4.9 25.8 1.0 O C:GLY105 4.9 18.9 1.0 CA C:ASP127 5.0 20.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Lectin I From Ulex Europaeus in Complex with the Methyl Glycoside of Alpha-L-Fucose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca246 b:19.9 occ:1.00 OD1 D:ASP127 2.2 10.4 1.0 O D:HOH821 2.2 13.5 1.0 OD2 D:ASP127 2.3 9.1 1.0 O D:HOH820 2.4 19.6 1.0 O D:ILE129 2.5 20.3 1.0 OD1 D:ASN134 2.5 11.0 1.0 CG D:ASP127 2.5 8.7 1.0 OD2 D:ASP137 2.5 31.2 1.0 CG D:ASN134 3.6 12.3 1.0 CG D:ASP137 3.6 28.0 1.0 C D:ILE129 3.6 20.9 1.0 CB D:ASN134 4.0 14.3 1.0 CG2 D:ILE129 4.0 17.3 1.0 CB D:ASP127 4.0 4.9 1.0 OD1 D:ASP137 4.2 30.5 1.0 O D:HOH822 4.3 16.2 1.0 CE1 D:HIS142 4.4 13.6 1.0 MN D:MN245 4.4 20.9 1.0 N D:ILE129 4.4 16.4 1.0 CZ D:PHE107 4.5 15.6 1.0 O D:GLY105 4.5 14.7 1.0 CA D:ILE129 4.5 19.0 1.0 N D:GLY130 4.6 20.9 1.0 NE1 D:TRP136 4.6 18.2 1.0 CA D:GLY130 4.6 19.5 1.0 CB D:ASP137 4.7 23.5 1.0 OD2 D:ASP87 4.7 23.6 1.0 NE2 D:HIS142 4.7 14.2 1.0 ND2 D:ASN134 4.7 6.0 1.0 CA D:ASP127 4.8 8.8 1.0 O D:ASP87 4.8 19.8 1.0 CA D:GLY105 4.9 13.1 1.0 CB D:ILE129 4.9 19.6 1.0 CZ2 D:TRP136 5.0 18.2 1.0

G.F.Audette, D.J.H.Olson, A.R.S.Ross, J.W.Quail, L.T.J.Delbaere. Examination of the Structural Basis For O(H) Blood Group Specificity By Ulex Europaeus Lectin I Can.J.Chem. V. 80 1010 2002.
ISSN: ISSN 0008-4042
DOI: 10.1139/V02-134