Calcium in PDB 6y0v: Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution

The structure of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution, PDB code: 6y0v was solved by S.Baeriswyl, A.Stocker, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.06 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.14, 104.88, 52.996, 90, 93.38, 90
R / Rfree (%)	17.9 / 23.3

The binding sites of Calcium atom in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution (pdb code 6y0v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution, PDB code: 6y0v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:26.9 occ:1.00 O A:ASN21 2.3 20.4 1.0 OD1 A:ASN103 2.3 22.4 1.0 OD2 A:ASP104 2.4 22.5 1.0 OD2 A:ASP101 2.4 24.3 1.0 O C:GLY114 2.5 21.8 1.0 O3 E:ZDC101 2.5 24.2 1.0 O2 E:ZDC101 2.6 22.4 1.0 OD1 A:ASP101 3.1 24.3 1.0 CG A:ASP101 3.1 23.4 1.0 CG A:ASN103 3.4 23.1 1.0 C3 E:ZDC101 3.5 25.2 1.0 C A:ASN21 3.5 21.2 1.0 C C:GLY114 3.5 21.9 1.0 C2 E:ZDC101 3.6 24.7 1.0 CG A:ASP104 3.6 22.6 1.0 OXT C:GLY114 3.7 22.6 1.0 CA A:CA302 3.7 23.4 1.0 C4 E:ZDC101 3.8 26.8 1.0 ND2 A:ASN103 3.8 24.1 1.0 CB A:ASN21 4.0 19.7 1.0 CA A:ASP104 4.1 20.4 1.0 N A:ASP104 4.2 19.7 1.0 N A:SER22 4.4 21.0 1.0 CA A:ASN21 4.4 21.3 1.0 CA A:SER22 4.4 23.2 1.0 CB A:ASP104 4.4 21.9 1.0 C A:ASN103 4.4 21.0 1.0 OD1 A:ASP104 4.5 23.1 1.0 O4 E:ZDC101 4.5 26.2 1.0 OD2 A:ASP99 4.6 33.0 1.0 CB A:ASP101 4.6 22.7 1.0 CB A:SER22 4.6 23.1 1.0 CB A:ASN103 4.7 22.8 1.0 O A:ASN103 4.8 20.7 1.0 O C:HOH440 4.8 30.1 1.0 CA C:GLY114 4.8 21.7 1.0 N A:ASN103 4.8 22.2 1.0 C1 E:ZDC101 4.9 26.5 1.0 CA A:ASN103 4.9 21.7 1.0 O5 E:ZDC101 4.9 27.3 1.0

Calcium binding site 2 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:23.4 occ:1.00 OE2 A:GLU95 2.3 23.7 1.0 OD1 A:ASP101 2.3 24.3 1.0 OE1 A:GLU95 2.4 25.9 1.0 OD1 A:ASP99 2.4 33.2 1.0 OD1 A:ASP104 2.4 23.1 1.0 O3 E:ZDC101 2.6 24.2 1.0 OD2 A:ASP104 2.6 22.5 1.0 O4 E:ZDC101 2.6 26.2 1.0 CD A:GLU95 2.6 25.0 1.0 CG A:ASP104 2.9 22.6 1.0 CG A:ASP99 3.4 33.6 1.0 CG A:ASP101 3.4 23.4 1.0 C4 E:ZDC101 3.4 26.8 1.0 C3 E:ZDC101 3.5 25.2 1.0 OD2 A:ASP99 3.7 33.0 1.0 CA A:CA301 3.7 26.9 1.0 O E:HOH203 3.9 33.3 1.0 OD2 A:ASP101 3.9 24.3 1.0 N A:ASP101 4.0 24.4 1.0 CG A:GLU95 4.1 24.2 1.0 OD1 A:ASP96 4.2 27.5 1.0 N A:ASN100 4.3 27.1 1.0 N A:TYR102 4.4 24.5 1.0 CB A:ASP104 4.4 21.9 1.0 N A:ASP96 4.5 25.9 1.0 CB A:ASP101 4.6 22.7 1.0 CA A:GLU95 4.6 24.7 1.0 N A:GLY97 4.6 28.7 1.0 CA A:ASP101 4.7 23.7 1.0 CB A:ASP99 4.8 33.4 1.0 CB A:GLU95 4.8 24.4 1.0 OD1 A:ASN103 4.8 22.4 1.0 C2 E:ZDC101 4.8 24.7 1.0 N A:ASP99 4.8 32.1 1.0 C5 E:ZDC101 4.9 29.1 1.0 C A:ASP101 4.9 23.8 1.0 C A:ASP99 4.9 28.9 1.0 CG A:ASP96 5.0 28.3 1.0 CA A:ASN100 5.0 26.7 1.0 O2 E:ZDC101 5.0 22.4 1.0 C A:ASN100 5.0 25.3 1.0 CA A:GLY97 5.0 29.8 1.0

Calcium binding site 3 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:22.1 occ:1.00 OD1 B:ASN103 2.3 20.2 1.0 O B:ASN21 2.3 18.0 1.0 O3 B:ZDC303 2.4 24.1 1.0 OD2 B:ASP101 2.4 16.7 1.0 OD2 B:ASP104 2.4 19.2 1.0 O2 B:ZDC303 2.4 21.4 1.0 O D:GLY114 2.5 25.4 1.0 OD1 B:ASP101 3.0 14.5 1.0 CG B:ASP101 3.1 16.0 1.0 C3 B:ZDC303 3.3 24.1 1.0 C2 B:ZDC303 3.4 23.3 1.0 CG B:ASN103 3.4 18.8 1.0 C D:GLY114 3.5 22.9 1.0 C B:ASN21 3.5 19.6 1.0 CG B:ASP104 3.7 19.1 1.0 OXT D:GLY114 3.7 21.5 1.0 C4 B:ZDC303 3.7 24.1 1.0 CA B:CA302 3.7 20.2 1.0 ND2 B:ASN103 3.9 17.2 1.0 CB B:ASN21 4.1 17.2 1.0 CA B:ASP104 4.2 15.9 1.0 N B:ASP104 4.2 15.7 1.0 N B:SER22 4.4 20.8 1.0 CA B:SER22 4.4 22.0 1.0 O4 B:ZDC303 4.4 22.7 1.0 OD2 B:ASP99 4.4 27.2 1.0 C B:ASN103 4.4 16.6 1.0 CA B:ASN21 4.5 19.3 1.0 CB B:ASP104 4.5 17.4 1.0 CB B:ASP101 4.5 16.9 1.0 OD1 B:ASP104 4.5 20.9 1.0 CB B:SER22 4.5 21.5 1.0 CB B:ASN103 4.7 18.7 1.0 C1 B:ZDC303 4.7 24.1 1.0 O B:ASN103 4.8 15.3 1.0 CA D:GLY114 4.9 21.8 1.0 N B:ASN103 4.9 18.8 1.0 CA B:ASN103 4.9 17.7 1.0

Calcium binding site 4 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:20.2 occ:1.00 OD1 B:ASP101 2.3 14.5 1.0 OD1 B:ASP99 2.4 23.9 1.0 OD1 B:ASP104 2.4 20.9 1.0 OE2 B:GLU95 2.5 23.4 1.0 OE1 B:GLU95 2.5 22.6 1.0 O4 B:ZDC303 2.5 22.7 1.0 O3 B:ZDC303 2.5 24.1 1.0 OD2 B:ASP104 2.6 19.2 1.0 CD B:GLU95 2.8 22.6 1.0 CG B:ASP104 2.9 19.1 1.0 C4 B:ZDC303 3.3 24.1 1.0 CG B:ASP99 3.4 25.2 1.0 CG B:ASP101 3.4 16.0 1.0 C3 B:ZDC303 3.4 24.1 1.0 OD2 B:ASP99 3.6 27.2 1.0 CA B:CA301 3.7 22.1 1.0 OD2 B:ASP101 3.9 16.7 1.0 N B:ASP101 4.0 19.0 1.0 OD2 B:ASP96 4.0 30.6 1.0 O B:HOH449 4.1 25.8 1.0 CG B:GLU95 4.3 22.0 1.0 N B:ASN100 4.4 23.9 1.0 CB B:ASP104 4.4 17.4 1.0 N B:TYR102 4.4 20.0 1.0 N B:GLY97 4.5 24.2 1.0 N B:ASP96 4.5 21.1 1.0 CB B:ASP101 4.5 16.9 1.0 CA B:ASP101 4.7 18.0 1.0 CA B:GLU95 4.7 20.4 1.0 CB B:ASP99 4.7 24.6 1.0 C2 B:ZDC303 4.7 23.3 1.0 C5 B:ZDC303 4.8 26.1 1.0 OD1 B:ASN103 4.8 20.2 1.0 N B:ASP99 4.8 26.5 1.0 O2 B:ZDC303 4.8 21.4 1.0 CG B:ASP96 4.9 30.2 1.0 CB B:GLU95 4.9 21.1 1.0 C B:ASP101 4.9 19.4 1.0 C B:ASP99 4.9 24.4 1.0 CA B:GLY97 5.0 25.0 1.0 C B:ASN100 5.0 21.8 1.0 CA B:ASN100 5.0 23.9 1.0

Calcium binding site 5 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:20.5 occ:1.00 OD1 C:ASP101 2.3 18.6 1.0 OE2 C:GLU95 2.4 18.1 1.0 OE1 C:GLU95 2.5 17.0 1.0 OD1 C:ASP99 2.5 23.5 1.0 OD2 C:ASP104 2.5 17.7 1.0 O3 G:ZDC101 2.5 20.4 1.0 O4 G:ZDC101 2.5 20.4 1.0 OD1 C:ASP104 2.7 17.7 1.0 CD C:GLU95 2.7 17.9 1.0 CG C:ASP104 2.9 17.5 1.0 C4 G:ZDC101 3.3 21.4 1.0 C3 G:ZDC101 3.4 20.8 1.0 CG C:ASP101 3.4 19.4 1.0 CG C:ASP99 3.5 23.3 1.0 CA C:CA302 3.7 21.4 1.0 OD2 C:ASP99 3.7 21.6 1.0 OD2 C:ASP101 4.0 20.0 1.0 N C:ASP101 4.0 20.1 1.0 OD1 C:ASP96 4.1 17.6 1.0 O C:HOH431 4.2 27.5 1.0 CG C:GLU95 4.2 17.8 1.0 N C:ASN100 4.3 23.8 1.0 N C:TYR102 4.4 18.1 1.0 CB C:ASP104 4.4 17.4 1.0 N C:ASP96 4.5 18.4 1.0 N C:GLY97 4.6 20.4 1.0 CB C:ASP101 4.6 19.1 1.0 CA C:GLU95 4.7 18.8 1.0 CA C:ASP101 4.7 19.4 1.0 C2 G:ZDC101 4.7 20.1 1.0 C5 G:ZDC101 4.8 22.7 1.0 CB C:ASP99 4.8 23.6 1.0 OD1 C:ASN103 4.8 19.0 1.0 N C:ASP99 4.8 25.0 1.0 CB C:GLU95 4.9 18.7 1.0 CA C:ASN100 4.9 23.7 1.0 CG C:ASP96 4.9 18.3 1.0 C C:ASP99 4.9 23.7 1.0 O2 G:ZDC101 4.9 19.7 1.0 C C:ASP101 4.9 18.8 1.0 C C:ASN100 5.0 22.1 1.0

Calcium binding site 6 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:21.4 occ:1.00 O3 G:ZDC101 2.3 20.4 1.0 OD1 C:ASP104 2.4 17.7 1.0 OD2 C:ASP101 2.4 20.0 1.0 O C:ASN21 2.4 19.4 1.0 OD1 C:ASN103 2.4 19.0 1.0 O A:GLY114 2.5 22.4 1.0 O2 G:ZDC101 2.5 19.7 1.0 OD1 C:ASP101 3.0 18.6 1.0 CG C:ASP101 3.1 19.4 1.0 C3 G:ZDC101 3.3 20.8 1.0 C2 G:ZDC101 3.4 20.1 1.0 C A:GLY114 3.4 20.8 1.0 CG C:ASN103 3.5 18.7 1.0 C C:ASN21 3.6 19.5 1.0 OXT A:GLY114 3.6 19.8 1.0 CG C:ASP104 3.6 17.5 1.0 C4 G:ZDC101 3.7 21.4 1.0 CA C:CA301 3.7 20.5 1.0 ND2 C:ASN103 4.0 20.3 1.0 CB C:ASN21 4.2 17.8 1.0 CA C:ASP104 4.2 17.2 1.0 N C:ASP104 4.2 16.8 1.0 O4 G:ZDC101 4.3 20.4 1.0 CA C:SER22 4.4 21.6 1.0 N C:SER22 4.4 20.7 1.0 OD2 C:ASP104 4.4 17.7 1.0 CB C:ASP104 4.5 17.4 1.0 CB C:ASP101 4.5 19.1 1.0 C C:ASN103 4.5 16.2 1.0 CA C:ASN21 4.5 19.1 1.0 OD2 C:ASP99 4.5 21.6 1.0 CB C:SER22 4.6 21.8 1.0 O C:HOH432 4.7 44.6 1.0 C1 G:ZDC101 4.7 19.4 1.0 CA A:GLY114 4.8 18.7 1.0 CB C:ASN103 4.8 17.4 1.0 O C:ASN103 4.8 15.4 1.0 N C:ASN103 4.9 15.8 1.0 O5 G:ZDC101 5.0 21.1 1.0 C5 G:ZDC101 5.0 22.7 1.0

Calcium binding site 7 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:23.5 occ:1.00 OD1 D:ASP101 2.3 19.2 1.0 OD1 D:ASP99 2.4 29.1 1.0 O3 H:ZDC101 2.5 22.6 1.0 OE2 D:GLU95 2.5 21.5 1.0 OD2 D:ASP104 2.5 20.2 1.0 OE1 D:GLU95 2.5 21.9 1.0 O4 H:ZDC101 2.5 21.9 1.0 OD1 D:ASP104 2.5 18.0 1.0 CD D:GLU95 2.8 21.7 1.0 CG D:ASP104 2.9 19.0 1.0 CG D:ASP99 3.3 28.5 1.0 C4 H:ZDC101 3.3 23.8 1.0 CG D:ASP101 3.4 19.6 1.0 C3 H:ZDC101 3.4 23.6 1.0 OD2 D:ASP99 3.6 28.2 1.0 CA D:CA302 3.6 25.9 1.0 OD2 D:ASP101 3.9 20.5 1.0 N D:ASP101 4.1 20.4 1.0 OD1 D:ASP96 4.1 28.1 1.0 CG D:GLU95 4.3 20.6 1.0 N D:ASN100 4.4 25.0 1.0 N D:TYR102 4.4 18.8 1.0 CB D:ASP104 4.4 18.2 1.0 O D:HOH435 4.4 38.6 1.0 CB D:ASP101 4.6 18.8 1.0 N D:ASP96 4.6 22.9 1.0 N D:GLY97 4.6 25.1 1.0 OD1 D:ASN103 4.7 20.4 1.0 CA D:ASP101 4.7 19.1 1.0 CB D:ASP99 4.7 27.3 1.0 CA D:GLU95 4.7 21.1 1.0 C2 H:ZDC101 4.8 22.6 1.0 C5 H:ZDC101 4.8 25.7 1.0 N D:ASP99 4.8 28.6 1.0 C D:ASP101 4.9 19.3 1.0 O2 H:ZDC101 4.9 20.5 1.0 CB D:GLU95 5.0 20.6 1.0 CA D:ASN100 5.0 24.2 1.0 C D:ASP99 5.0 25.6 1.0 CG D:ASP96 5.0 27.1 1.0 N D:ASP104 5.0 17.9 1.0

Calcium binding site 8 out of 8 in the Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:25.9 occ:1.00 OD1 D:ASN103 2.3 20.4 1.0 O D:ASN21 2.4 17.5 1.0 OD1 D:ASP104 2.4 18.0 1.0 OD2 D:ASP101 2.4 20.5 1.0 O3 H:ZDC101 2.5 22.6 1.0 O B:GLY114 2.5 21.5 1.0 O2 H:ZDC101 2.6 20.5 1.0 OD1 D:ASP101 3.0 19.2 1.0 CG D:ASP101 3.0 19.6 1.0 C3 H:ZDC101 3.4 23.6 1.0 CG D:ASN103 3.4 20.3 1.0 C B:GLY114 3.5 21.6 1.0 C2 H:ZDC101 3.5 22.6 1.0 C D:ASN21 3.5 18.4 1.0 CG D:ASP104 3.6 19.0 1.0 CA D:CA301 3.6 23.5 1.0 OXT B:GLY114 3.7 22.1 1.0 C4 H:ZDC101 3.7 23.8 1.0 ND2 D:ASN103 3.9 19.3 1.0 CB D:ASN21 4.1 17.3 1.0 CA D:ASP104 4.1 18.5 1.0 N D:ASP104 4.2 17.9 1.0 O4 H:ZDC101 4.3 21.9 1.0 N D:SER22 4.4 19.7 1.0 CA D:SER22 4.4 20.8 1.0 OD2 D:ASP99 4.4 28.2 1.0 C D:ASN103 4.4 19.7 1.0 CB D:ASP104 4.5 18.2 1.0 CA D:ASN21 4.5 18.5 1.0 OD2 D:ASP104 4.5 20.2 1.0 CB D:ASP101 4.5 18.8 1.0 CB D:SER22 4.7 20.4 1.0 CB D:ASN103 4.7 19.9 1.0 O D:ASN103 4.8 20.3 1.0 C1 H:ZDC101 4.8 23.6 1.0 N D:ASN103 4.8 20.3 1.0 CA B:GLY114 4.9 20.8 1.0 CA D:ASN103 4.9 20.4 1.0

S.Baeriswyl, A.Stocker, J.-L.Reymond. Fucosylated Bicyclic Peptide BP102 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 1.7 Angstrom Resolution To Be Published.