Calcium in PDB 1oxc: Lecb (Pa-Lii) in Complex with Fucose

The structure of Lecb (Pa-Lii) in Complex with Fucose, PDB code: 1oxc was solved by R.Loris, D.Tielker, K.-E.Jaeger, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.088, 73.058, 99.889, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 18.5

The binding sites of Calcium atom in the Lecb (Pa-Lii) in Complex with Fucose (pdb code 1oxc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Lecb (Pa-Lii) in Complex with Fucose, PDB code: 1oxc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Lecb (Pa-Lii) in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lecb (Pa-Lii) in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca116 b:6.4 occ:1.00 OD1 A:ASP99 2.4 8.6 1.0 OD1 A:ASP101 2.4 7.8 1.0 OE2 A:GLU95 2.4 7.2 1.0 OD2 A:ASP104 2.4 7.1 1.0 O2 A:FUL115 2.5 7.3 0.5 O2 A:FUC1115 2.5 7.3 0.5 OE1 A:GLU95 2.5 6.8 1.0 O3 A:FUL115 2.6 6.6 0.5 O3 A:FUC1115 2.6 6.6 0.5 OD1 A:ASP104 2.6 7.0 1.0 CD A:GLU95 2.8 6.7 1.0 CG A:ASP104 2.9 6.3 1.0 C2 A:FUL115 3.2 7.3 0.5 C2 A:FUC1115 3.2 7.3 0.5 C3 A:FUL115 3.3 6.9 0.5 C3 A:FUC1115 3.3 6.9 0.5 CG A:ASP99 3.4 8.5 1.0 CG A:ASP101 3.4 6.7 1.0 OD2 A:ASP99 3.7 8.8 1.0 CA A:CA117 3.7 6.2 1.0 OD2 A:ASP101 3.9 6.6 1.0 N A:ASP101 4.1 6.9 1.0 O A:HOH155 4.1 12.1 1.0 OD1 A:ASP96 4.2 7.8 1.0 CG A:GLU95 4.3 6.8 1.0 CB A:ASP104 4.4 6.7 1.0 N A:TYR102 4.5 6.8 1.0 N A:ASN100 4.5 8.0 1.0 N A:ASP96 4.5 6.7 1.0 N A:GLY97 4.5 8.8 1.0 CB A:ASP101 4.6 7.0 1.0 C1 A:FUL115 4.6 10.2 0.5 C1 A:FUC1115 4.6 10.2 0.5 C4 A:FUL115 4.7 7.4 0.5 C4 A:FUC1115 4.7 7.4 0.5 CA A:GLU95 4.7 5.7 1.0 OD1 A:ASN103 4.7 6.3 1.0 CB A:ASP99 4.7 9.2 1.0 CA A:ASP101 4.8 6.8 1.0 O4 A:FUL115 4.8 7.5 0.5 O4 A:FUC1115 4.8 7.5 0.5 N A:ASP99 4.8 9.2 1.0 CB A:GLU95 4.9 6.8 1.0 CG A:ASP96 4.9 7.1 1.0 N A:ASP104 4.9 6.4 1.0 CA A:ASN100 5.0 7.8 1.0

Calcium binding site 2 out of 8 in the Lecb (Pa-Lii) in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lecb (Pa-Lii) in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca117 b:6.2 occ:1.00 OD1 A:ASN103 2.3 6.3 1.0 O A:ASN21 2.4 6.1 1.0 OD2 A:ASP101 2.4 6.6 1.0 OD1 A:ASP104 2.4 7.0 1.0 O B:GLY114 2.5 7.0 1.0 O3 A:FUL115 2.5 6.6 0.5 O3 A:FUC1115 2.5 6.6 0.5 O4 A:FUL115 2.5 7.5 0.5 O4 A:FUC1115 2.5 7.5 0.5 CG A:ASP101 3.1 6.7 1.0 OD1 A:ASP101 3.1 7.8 1.0 C3 A:FUL115 3.4 6.9 0.5 C3 A:FUC1115 3.4 6.9 0.5 CG A:ASN103 3.4 6.3 1.0 C B:GLY114 3.4 7.7 1.0 C4 A:FUL115 3.4 7.4 0.5 C4 A:FUC1115 3.4 7.4 0.5 C A:ASN21 3.6 5.9 1.0 OXT B:GLY114 3.6 8.8 1.0 CG A:ASP104 3.6 6.3 1.0 C2 A:FUL115 3.6 7.3 0.5 C2 A:FUC1115 3.6 7.3 0.5 CA A:CA116 3.7 6.4 1.0 ND2 A:ASN103 3.8 6.5 1.0 N A:ASP104 4.1 6.4 1.0 CB A:ASN21 4.1 6.3 1.0 CA A:ASP104 4.2 6.3 1.0 O2 A:FUL115 4.4 7.3 0.5 O2 A:FUC1115 4.4 7.3 0.5 C A:ASN103 4.4 5.5 1.0 CA A:SER22 4.4 6.5 1.0 N A:SER22 4.4 6.1 1.0 O A:HOH166 4.5 14.6 1.0 CB A:ASP104 4.5 6.7 1.0 OD2 A:ASP104 4.5 7.1 1.0 CA A:ASN21 4.5 6.1 1.0 OD2 A:ASP99 4.5 8.8 1.0 CB A:SER22 4.6 6.5 1.0 CB A:ASP101 4.6 7.0 1.0 CB A:ASN103 4.7 6.1 1.0 C5 A:FUL115 4.8 7.7 0.5 C5 A:FUC1115 4.8 7.7 0.5 CA B:GLY114 4.8 7.9 1.0 O A:ASN103 4.8 6.1 1.0 N A:ASN103 4.8 6.0 1.0 C1 A:FUL115 4.9 10.2 0.5 C1 A:FUC1115 4.9 10.2 0.5 CA A:ASN103 4.9 5.8 1.0 O5 A:FUL115 4.9 8.1 0.5 O5 A:FUC1115 4.9 8.1 0.5

Calcium binding site 3 out of 8 in the Lecb (Pa-Lii) in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lecb (Pa-Lii) in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca116 b:5.9 occ:1.00 OD1 B:ASP99 2.3 7.7 1.0 OD1 B:ASP101 2.3 6.4 1.0 OE2 B:GLU95 2.4 6.0 1.0 OD2 B:ASP104 2.4 6.2 1.0 OE1 B:GLU95 2.5 6.9 1.0 O2 B:FUC115 2.5 7.5 1.0 O3 B:FUC115 2.5 7.4 1.0 OD1 B:ASP104 2.6 5.3 1.0 CD B:GLU95 2.7 6.1 1.0 CG B:ASP104 2.9 5.4 1.0 C2 B:FUC115 3.2 7.1 1.0 C3 B:FUC115 3.3 6.4 1.0 CG B:ASP99 3.4 6.8 1.0 CG B:ASP101 3.4 6.1 1.0 OD2 B:ASP99 3.7 7.1 1.0 CA B:CA117 3.7 5.8 1.0 OD2 B:ASP101 3.9 6.0 1.0 N B:ASP101 4.1 8.7 1.0 OD1 B:ASP96 4.1 8.2 1.0 CG B:GLU95 4.2 6.9 1.0 O B:HOH179 4.2 16.5 1.0 N B:TYR102 4.4 6.2 1.0 CB B:ASP104 4.4 5.4 1.0 N B:ASP96 4.5 6.5 1.0 N B:GLY97 4.6 7.4 1.0 CB B:ASP101 4.6 6.9 1.0 N B:ASN100 4.7 9.8 1.0 C4 B:FUC115 4.7 7.3 1.0 OD1 B:ASN103 4.7 5.5 1.0 CB B:ASP99 4.7 8.7 1.0 CA B:GLU95 4.7 6.4 1.0 CA B:ASP101 4.7 6.6 1.0 N B:ASP99 4.8 7.8 1.0 C1 B:FUC115 4.8 8.0 1.0 O4 B:FUC115 4.8 6.8 1.0 CB B:GLU95 4.9 7.2 1.0 CG B:ASP96 4.9 7.6 1.0 C B:ASP101 5.0 6.2 1.0 N B:ASP104 5.0 6.0 1.0 C B:ASP99 5.0 9.3 1.0

Calcium binding site 4 out of 8 in the Lecb (Pa-Lii) in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lecb (Pa-Lii) in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca117 b:5.8 occ:1.00 OD1 B:ASN103 2.3 5.5 1.0 O B:ASN21 2.4 6.1 1.0 OD2 B:ASP101 2.4 6.0 1.0 OD1 B:ASP104 2.4 5.3 1.0 O A:GLY114 2.4 6.3 1.0 O3 B:FUC115 2.5 7.4 1.0 O4 B:FUC115 2.5 6.8 1.0 CG B:ASP101 3.1 6.1 1.0 OD1 B:ASP101 3.1 6.4 1.0 C3 B:FUC115 3.3 6.4 1.0 CG B:ASN103 3.4 5.4 1.0 C A:GLY114 3.4 6.5 1.0 C4 B:FUC115 3.4 7.3 1.0 C B:ASN21 3.6 5.3 1.0 CG B:ASP104 3.6 5.4 1.0 C2 B:FUC115 3.6 7.1 1.0 OXT A:GLY114 3.6 8.7 1.0 CA B:CA116 3.7 5.9 1.0 ND2 B:ASN103 3.7 5.6 1.0 N B:ASP104 4.1 6.0 1.0 CB B:ASN21 4.1 5.6 1.0 CA B:ASP104 4.2 5.9 1.0 CA B:SER22 4.4 5.8 1.0 O2 B:FUC115 4.4 7.5 1.0 N B:SER22 4.4 5.5 1.0 C B:ASN103 4.4 5.7 1.0 OD2 B:ASP104 4.5 6.2 1.0 CB B:ASP104 4.5 5.4 1.0 CA B:ASN21 4.5 5.0 1.0 CB B:ASP101 4.5 6.9 1.0 OD2 B:ASP99 4.6 7.1 1.0 CB B:SER22 4.6 5.6 1.0 O A:HOH133 4.6 8.6 1.0 CB B:ASN103 4.7 5.8 1.0 C5 B:FUC115 4.7 8.6 1.0 CA A:GLY114 4.8 7.2 1.0 O B:ASN103 4.8 5.7 1.0 N B:ASN103 4.9 5.1 1.0 O5 B:FUC115 4.9 7.6 1.0 CA B:ASN103 5.0 5.4 1.0

Calcium binding site 5 out of 8 in the Lecb (Pa-Lii) in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Lecb (Pa-Lii) in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca116 b:5.9 occ:1.00 OD1 C:ASP101 2.4 6.6 1.0 OD1 C:ASP99 2.4 8.0 1.0 OE2 C:GLU95 2.4 6.4 1.0 OD2 C:ASP104 2.4 6.1 1.0 OE1 C:GLU95 2.5 7.2 1.0 O2 C:FUC115 2.5 7.4 1.0 O3 C:FUC115 2.5 6.4 1.0 OD1 C:ASP104 2.7 6.0 1.0 CD C:GLU95 2.8 7.1 1.0 CG C:ASP104 2.9 5.8 1.0 C2 C:FUC115 3.2 6.9 1.0 C3 C:FUC115 3.3 7.0 1.0 CG C:ASP101 3.4 6.4 1.0 CG C:ASP99 3.4 7.9 1.0 OD2 C:ASP99 3.7 8.3 1.0 CA C:CA117 3.7 5.9 1.0 OD2 C:ASP101 3.9 6.4 1.0 N C:ASP101 4.1 7.5 1.0 OD1 C:ASP96 4.2 7.8 1.0 CG C:GLU95 4.2 6.6 1.0 CB C:ASP104 4.4 5.2 1.0 N C:TYR102 4.4 5.4 1.0 N C:GLY97 4.5 7.2 1.0 N C:ASP96 4.5 5.7 1.0 N C:ASN100 4.5 7.8 1.0 CB C:ASP101 4.5 6.8 1.0 CA C:GLU95 4.7 5.8 1.0 C4 C:FUC115 4.7 6.7 1.0 OD1 C:ASN103 4.7 6.6 1.0 CA C:ASP101 4.7 6.6 1.0 CB C:ASP99 4.7 8.9 1.0 C1 C:FUC115 4.8 8.2 1.0 N C:ASP99 4.8 8.5 1.0 O4 C:FUC115 4.8 6.4 1.0 CB C:GLU95 4.9 6.8 1.0 CA C:GLY97 5.0 8.2 1.0 N C:ASP104 5.0 6.0 1.0 C C:ASP101 5.0 5.9 1.0 CG C:ASP96 5.0 7.0 1.0 C C:ASP99 5.0 7.7 1.0

Calcium binding site 6 out of 8 in the Lecb (Pa-Lii) in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Lecb (Pa-Lii) in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca117 b:5.9 occ:1.00 OD1 C:ASN103 2.3 6.6 1.0 OD2 C:ASP101 2.4 6.4 1.0 O C:ASN21 2.4 6.0 1.0 OD1 C:ASP104 2.4 6.0 1.0 O D:GLY114 2.4 6.7 1.0 O4 C:FUC115 2.5 6.4 1.0 O3 C:FUC115 2.5 6.4 1.0 CG C:ASP101 3.1 6.4 1.0 OD1 C:ASP101 3.1 6.6 1.0 C3 C:FUC115 3.3 7.0 1.0 CG C:ASN103 3.4 6.2 1.0 C D:GLY114 3.4 7.0 1.0 C4 C:FUC115 3.4 6.7 1.0 C C:ASN21 3.6 5.4 1.0 CG C:ASP104 3.6 5.8 1.0 OXT D:GLY114 3.6 7.7 1.0 C2 C:FUC115 3.7 6.9 1.0 CA C:CA116 3.7 5.9 1.0 ND2 C:ASN103 3.7 6.2 1.0 CB C:ASN21 4.1 5.8 1.0 N C:ASP104 4.1 6.0 1.0 CA C:ASP104 4.2 5.7 1.0 C C:ASN103 4.4 5.3 1.0 O2 C:FUC115 4.4 7.4 1.0 CA C:SER22 4.4 6.1 1.0 N C:SER22 4.4 5.8 1.0 OD2 C:ASP104 4.5 6.1 1.0 CB C:ASP104 4.5 5.2 1.0 CA C:ASN21 4.5 5.8 1.0 OD2 C:ASP99 4.5 8.3 1.0 CB C:ASP101 4.5 6.8 1.0 O D:HOH170 4.5 16.6 1.0 CB C:SER22 4.6 6.0 1.0 CB C:ASN103 4.7 5.5 1.0 C5 C:FUC115 4.7 7.7 1.0 CA D:GLY114 4.8 6.7 1.0 O C:ASN103 4.8 5.8 1.0 N C:ASN103 4.9 5.4 1.0 O5 C:FUC115 4.9 7.9 1.0 CA C:ASN103 4.9 5.3 1.0

Calcium binding site 7 out of 8 in the Lecb (Pa-Lii) in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Lecb (Pa-Lii) in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca116 b:7.1 occ:1.00 OD1 D:ASP99 2.4 10.2 1.0 OD2 D:ASP101 2.4 8.3 1.0 OE2 D:GLU95 2.4 7.6 1.0 OD2 D:ASP104 2.5 6.5 1.0 OE1 D:GLU95 2.5 7.5 1.0 O2 D:FUL115 2.5 8.1 0.5 O2 D:FUC1115 2.5 8.1 0.5 O3 D:FUL115 2.6 8.4 0.5 O3 D:FUC1115 2.6 8.4 0.5 OD1 D:ASP104 2.6 6.5 1.0 CD D:GLU95 2.8 7.7 1.0 CG D:ASP104 2.9 6.1 1.0 C2 D:FUL115 3.2 8.6 0.5 C2 D:FUC1115 3.2 8.6 0.5 C3 D:FUL115 3.4 8.5 0.5 C3 D:FUC1115 3.4 8.5 0.5 CG D:ASP101 3.4 7.6 1.0 CG D:ASP99 3.4 10.0 1.0 OD2 D:ASP99 3.7 9.8 1.0 CA D:CA117 3.7 7.0 1.0 OD1 D:ASP101 3.9 8.0 1.0 N D:ASP101 4.0 9.9 1.0 O D:HOH154 4.1 14.3 1.0 CG D:GLU95 4.3 7.8 1.0 OD1 D:ASP96 4.3 8.4 1.0 CB D:ASP104 4.4 6.1 1.0 N D:TYR102 4.4 7.8 1.0 N D:GLY97 4.5 8.2 1.0 N D:ASN100 4.5 10.5 1.0 CB D:ASP101 4.5 8.1 1.0 N D:ASP96 4.6 6.9 1.0 C4 D:FUL115 4.7 8.2 0.5 C4 D:FUC1115 4.7 8.2 0.5 OD1 D:ASN103 4.7 7.4 1.0 CA D:ASP101 4.7 8.9 1.0 CB D:ASP99 4.7 10.0 1.0 CA D:GLU95 4.7 6.5 1.0 N D:ASP99 4.8 10.9 1.0 C1 D:FUL115 4.8 9.7 0.5 C1 D:FUC1115 4.8 9.7 0.5 O4 D:FUL115 4.8 8.5 0.5 O4 D:FUC1115 4.8 8.5 0.5 CB D:GLU95 4.9 7.1 1.0 CA D:GLY97 4.9 9.4 1.0 N D:ASP104 4.9 6.4 1.0 C D:ASP99 5.0 10.3 1.0 C D:ASP101 5.0 8.6 1.0 CG D:ASP96 5.0 7.5 1.0 CA D:ASN100 5.0 11.4 1.0 C D:ASN100 5.0 10.3 1.0

Calcium binding site 8 out of 8 in the Lecb (Pa-Lii) in Complex with Fucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Lecb (Pa-Lii) in Complex with Fucose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca117 b:7.0 occ:1.00 OD1 D:ASN103 2.3 7.4 1.0 O D:ASN21 2.4 6.2 1.0 OD1 D:ASP101 2.4 8.0 1.0 OD1 D:ASP104 2.4 6.5 1.0 O C:GLY114 2.5 8.3 1.0 O4 D:FUL115 2.5 8.5 0.5 O4 D:FUC1115 2.5 8.5 0.5 O3 D:FUL115 2.5 8.4 0.5 O3 D:FUC1115 2.5 8.4 0.5 CG D:ASP101 3.1 7.6 1.0 OD2 D:ASP101 3.1 8.3 1.0 C3 D:FUL115 3.4 8.5 0.5 C3 D:FUC1115 3.4 8.5 0.5 CG D:ASN103 3.4 6.4 1.0 C C:GLY114 3.4 9.8 1.0 C4 D:FUL115 3.4 8.2 0.5 C4 D:FUC1115 3.4 8.2 0.5 C D:ASN21 3.6 6.0 1.0 CG D:ASP104 3.6 6.1 1.0 C2 D:FUL115 3.6 8.6 0.5 C2 D:FUC1115 3.6 8.6 0.5 OXT C:GLY114 3.7 12.3 1.0 CA D:CA116 3.7 7.1 1.0 ND2 D:ASN103 3.8 7.1 1.0 N D:ASP104 4.1 6.4 1.0 CA D:ASP104 4.2 5.6 1.0 CB D:ASN21 4.2 5.9 1.0 CA D:SER22 4.3 6.8 1.0 C D:ASN103 4.4 5.8 1.0 N D:SER22 4.4 7.0 1.0 O D:HOH150 4.4 12.0 1.0 O2 D:FUL115 4.4 8.1 0.5 O2 D:FUC1115 4.4 8.1 0.5 CB D:ASP104 4.5 6.1 1.0 OD2 D:ASP104 4.5 6.5 1.0 CB D:SER22 4.5 6.4 1.0 OD2 D:ASP99 4.5 9.8 1.0 CA D:ASN21 4.5 5.9 1.0 CB D:ASP101 4.6 8.1 1.0 CB D:ASN103 4.7 6.2 1.0 O D:ASN103 4.7 5.5 1.0 C5 D:FUL115 4.8 9.7 0.5 C5 D:FUC1115 4.8 9.7 0.5 CA C:GLY114 4.8 8.6 1.0 N D:ASN103 4.9 5.9 1.0 CA D:ASN103 4.9 5.7 1.0 O5 D:FUL115 5.0 8.7 0.5 O5 D:FUC1115 5.0 8.7 0.5

R.Loris, D.Tielker, K.-E.Jaeger, L.Wyns. Structural Basis of Carbohydrate Recognition By the Lectin Lecb From Pseudomonas Aeruginosa J.Mol.Biol. V. 331 861 2003.
ISSN: ISSN 0022-2836
PubMed: 12909014
DOI: 10.1016/S0022-2836(03)00754-X