Calcium in PDB 2vud: Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics

The structure of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics, PDB code: 2vud was solved by S.Beha, K.Marotte, C.Sabin, E.P.Mitchell, A.Imberty, R.Roy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.22 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.079, 73.179, 55.367, 90.00, 93.86, 90.00
R / Rfree (%)	20.3 / 21.8

The binding sites of Calcium atom in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics (pdb code 2vud). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics, PDB code: 2vud:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1115 b:9.9 occ:1.00 OD1 A:ASP104 2.3 10.5 1.0 OD1 A:ASN103 2.3 8.9 1.0 O A:ASN21 2.3 7.3 1.0 O3 A:FUC1118 2.4 8.4 1.0 OD2 A:ASP101 2.5 9.2 1.0 O B:GLY114 2.6 10.2 1.0 O4 A:FUC1118 2.7 6.9 1.0 CG A:ASP101 3.2 12.8 1.0 OD1 A:ASP101 3.3 10.4 1.0 C3 A:FUC1118 3.4 9.7 1.0 CG A:ASN103 3.4 9.1 1.0 C4 A:FUC1118 3.5 8.7 1.0 C B:GLY114 3.6 10.5 1.0 CG A:ASP104 3.6 8.0 1.0 C A:ASN21 3.6 7.8 1.0 OXT B:GLY114 3.8 10.6 1.0 CA A:CA1116 3.8 8.8 1.0 ND2 A:ASN103 3.8 9.6 1.0 C2 A:FUC1118 3.9 10.3 1.0 N A:ASP104 4.2 7.6 1.0 CB A:ASN21 4.2 7.3 1.0 CA A:ASP104 4.2 7.6 1.0 OD2 A:ASP104 4.4 9.8 1.0 CB A:ASP104 4.5 8.0 1.0 CA A:SER22 4.5 8.2 1.0 N A:SER22 4.5 7.9 1.0 C A:ASN103 4.5 7.5 1.0 CA A:ASN21 4.5 7.5 1.0 OD2 A:ASP99 4.5 10.6 1.0 O A:HOH2167 4.6 19.1 1.0 O2 A:FUC1118 4.6 11.8 1.0 CB A:ASP101 4.7 11.9 1.0 CB A:SER22 4.7 6.9 1.0 CB A:ASN103 4.7 8.5 1.0 C5 A:FUC1118 4.9 8.5 1.0 N A:ASN103 4.9 7.6 1.0 CA B:GLY114 4.9 9.7 1.0 O A:ASN103 5.0 7.8 1.0 CA A:ASN103 5.0 7.8 1.0

Calcium binding site 2 out of 8 in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1116 b:8.8 occ:1.00 OD1 A:ASP101 2.3 10.4 1.0 OD1 A:ASP99 2.3 11.9 1.0 OD2 A:ASP104 2.3 9.8 1.0 OE2 A:GLU95 2.3 10.6 1.0 O3 A:FUC1118 2.6 8.4 1.0 OE1 A:GLU95 2.6 10.7 1.0 O2 A:FUC1118 2.8 11.8 1.0 OD1 A:ASP104 2.8 10.5 1.0 CD A:GLU95 2.8 12.2 1.0 CG A:ASP104 2.9 8.0 1.0 CG A:ASP101 3.4 12.8 1.0 CG A:ASP99 3.4 11.5 1.0 C2 A:FUC1118 3.5 10.3 1.0 C3 A:FUC1118 3.5 9.7 1.0 OD2 A:ASP99 3.7 10.6 1.0 CA A:CA1115 3.8 9.9 1.0 OD2 A:ASP101 3.8 9.2 1.0 OD1 A:ASP96 4.1 12.8 1.0 N A:ASP101 4.1 12.3 1.0 CG A:GLU95 4.3 8.0 1.0 CB A:ASP104 4.4 8.0 1.0 N A:TYR102 4.4 9.5 1.0 N A:ASN100 4.5 11.5 1.0 N A:GLY97 4.5 11.1 1.0 N A:ASP96 4.5 8.2 1.0 O A:HOH2157 4.5 13.4 1.0 CB A:ASP101 4.6 11.9 1.0 CA A:GLU95 4.7 7.3 1.0 CB A:ASP99 4.7 11.7 1.0 OD1 A:ASN103 4.7 8.9 1.0 CA A:ASP101 4.8 11.4 1.0 N A:ASP99 4.8 12.8 1.0 C4 A:FUC1118 4.9 8.7 1.0 CB A:GLU95 4.9 7.7 1.0 C1 A:FUC1118 5.0 12.1 1.0 CA A:GLY97 5.0 11.5 1.0 CG A:ASP96 5.0 10.4 1.0

Calcium binding site 3 out of 8 in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1117 b:9.9 occ:1.00 OD1 B:ASP101 2.4 7.9 1.0 OD1 B:ASP99 2.4 11.5 1.0 O3 B:LZ01115 2.5 13.0 1.0 OE1 B:GLU95 2.5 7.4 1.0 OE2 B:GLU95 2.5 11.0 1.0 OD2 B:ASP104 2.7 8.7 1.0 O2 B:LZ01115 2.8 18.2 1.0 CD B:GLU95 2.9 9.0 1.0 OD1 B:ASP104 2.9 9.9 1.0 CG B:ASP104 3.2 5.3 1.0 C2 B:LZ01115 3.4 18.7 1.0 CG B:ASP99 3.4 11.6 1.0 CG B:ASP101 3.4 9.5 1.0 C3 B:LZ01115 3.4 14.5 1.0 OD2 B:ASP99 3.7 10.6 1.0 CA B:CA1118 3.7 9.5 1.0 OD2 B:ASP101 4.0 7.1 1.0 N B:ASP101 4.1 9.6 1.0 O B:HOH2153 4.3 11.6 1.0 N B:TYR102 4.3 8.4 1.0 OD1 B:ASP96 4.3 10.1 1.0 CG B:GLU95 4.4 8.4 1.0 N B:ASN100 4.4 9.3 1.0 CB B:ASP101 4.6 7.5 1.0 CB B:ASP104 4.6 7.0 1.0 N B:ASP96 4.7 8.4 1.0 CA B:ASP101 4.7 8.9 1.0 N B:GLY97 4.7 9.7 1.0 OD1 B:ASN103 4.7 8.3 1.0 C4 B:LZ01115 4.8 15.6 1.0 CB B:ASP99 4.8 10.4 1.0 CA B:GLU95 4.8 8.3 1.0 O4 B:LZ01115 4.9 12.5 1.0 N B:ASP99 4.9 10.5 1.0 C B:ASP101 4.9 9.2 1.0 C1 B:LZ01115 4.9 17.3 1.0 CA B:ASN100 5.0 9.0 1.0

Calcium binding site 4 out of 8 in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1118 b:9.5 occ:1.00 O B:ASN21 2.3 9.8 1.0 OD1 B:ASN103 2.3 8.3 1.0 OD1 B:ASP104 2.5 9.9 1.0 O4 B:LZ01115 2.5 12.5 1.0 O3 B:LZ01115 2.6 13.0 1.0 O A:GLY114 2.6 11.0 1.0 OD2 B:ASP101 2.8 7.1 1.0 OD1 B:ASP101 3.1 7.9 1.0 CG B:ASP101 3.3 9.5 1.0 CG B:ASN103 3.4 8.9 1.0 C3 B:LZ01115 3.5 14.5 1.0 C4 B:LZ01115 3.5 15.6 1.0 C A:GLY114 3.5 11.9 1.0 C B:ASN21 3.6 9.9 1.0 CG B:ASP104 3.7 5.3 1.0 CA B:CA1117 3.7 9.9 1.0 OXT A:GLY114 3.7 12.2 1.0 C2 B:LZ01115 3.9 18.7 1.0 ND2 B:ASN103 3.9 11.3 1.0 N B:ASP104 4.1 6.7 1.0 CA B:ASP104 4.2 7.1 1.0 CB B:ASN21 4.2 8.5 1.0 CA B:SER22 4.4 10.5 1.0 C B:ASN103 4.4 7.5 1.0 N B:SER22 4.4 9.7 1.0 OD2 B:ASP104 4.5 8.7 1.0 CB B:ASP104 4.5 7.0 1.0 CA B:ASN21 4.5 8.2 1.0 O B:HOH2148 4.6 22.1 1.0 O2 B:LZ01115 4.7 18.2 1.0 CB B:SER22 4.7 8.4 1.0 CB B:ASN103 4.7 7.4 1.0 CB B:ASP101 4.8 7.5 1.0 OD2 B:ASP99 4.8 10.6 1.0 N B:ASN103 4.8 7.2 1.0 C5 B:LZ01115 4.8 16.0 1.0 O B:ASN103 4.9 7.8 1.0 CA B:ASN103 4.9 6.9 1.0 CA A:GLY114 4.9 11.2 1.0

Calcium binding site 5 out of 8 in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1117 b:11.9 occ:1.00 OE2 C:GLU95 2.3 11.4 1.0 OD1 C:ASP99 2.3 11.1 1.0 O2 C:LZ01115 2.3 14.4 1.0 OD1 C:ASP101 2.6 9.9 1.0 O3 C:LZ01115 2.6 11.9 1.0 OD2 C:ASP104 2.6 10.0 1.0 OD1 C:ASP104 2.8 9.5 1.0 OE1 C:GLU95 2.9 9.1 1.0 CD C:GLU95 2.9 12.4 1.0 C2 C:LZ01115 3.1 15.0 1.0 CG C:ASP104 3.1 7.6 1.0 C3 C:LZ01115 3.3 13.3 1.0 CG C:ASP99 3.4 14.9 1.0 CG C:ASP101 3.6 12.2 1.0 OD2 C:ASP99 3.7 13.8 1.0 O C:HOH2120 3.8 19.2 1.0 CA C:CA1118 3.9 10.8 1.0 OD2 C:ASP101 3.9 10.6 1.0 OD1 C:ASP96 4.0 12.4 1.0 CG C:GLU95 4.4 11.2 1.0 N C:ASP101 4.4 12.9 1.0 N C:GLY97 4.5 13.5 1.0 C1 C:LZ01115 4.5 15.2 1.0 N C:ASN100 4.6 13.3 1.0 N C:ASP96 4.6 10.5 1.0 CB C:ASP104 4.6 7.1 1.0 C4 C:LZ01115 4.7 14.8 1.0 CB C:ASP99 4.7 13.1 1.0 N C:TYR102 4.7 9.2 1.0 N C:ASP99 4.7 13.2 1.0 CB C:ASP101 4.8 11.4 1.0 O4 C:LZ01115 4.8 12.0 1.0 CG C:ASP96 4.8 12.4 1.0 CA C:GLU95 4.9 9.8 1.0 CA C:GLY97 4.9 13.8 1.0 OD1 C:ASN103 4.9 8.8 1.0

Calcium binding site 6 out of 8 in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1118 b:10.8 occ:1.00 O C:ASN21 2.3 6.0 1.0 OD1 C:ASN103 2.3 8.8 1.0 OD1 C:ASP104 2.4 9.5 1.0 O4 C:LZ01115 2.6 12.0 1.0 OD2 C:ASP101 2.6 10.6 1.0 O D:GLY114 2.6 10.3 1.0 O3 C:LZ01115 2.6 11.9 1.0 CG C:ASP101 3.3 12.2 1.0 OD1 C:ASP101 3.3 9.9 1.0 CG C:ASN103 3.4 8.1 1.0 C3 C:LZ01115 3.5 13.3 1.0 C C:ASN21 3.6 7.6 1.0 C D:GLY114 3.6 11.4 1.0 C4 C:LZ01115 3.6 14.8 1.0 CG C:ASP104 3.7 7.6 1.0 OXT D:GLY114 3.8 12.6 1.0 C2 C:LZ01115 3.8 15.0 1.0 ND2 C:ASN103 3.8 7.2 1.0 CA C:CA1117 3.9 11.9 1.0 N C:ASP104 4.1 8.2 1.0 CA C:ASP104 4.1 7.5 1.0 CB C:ASN21 4.2 8.8 1.0 C C:ASN103 4.4 8.1 1.0 CA C:SER22 4.5 8.5 1.0 N C:SER22 4.5 8.3 1.0 CB C:ASP104 4.5 7.1 1.0 OD2 C:ASP104 4.5 10.0 1.0 CA C:ASN21 4.5 8.0 1.0 O2 C:LZ01115 4.6 14.4 1.0 CB C:SER22 4.6 8.0 1.0 O D:HOH2153 4.7 20.6 1.0 OD2 C:ASP99 4.7 13.8 1.0 CB C:ASP101 4.7 11.4 1.0 CB C:ASN103 4.7 8.3 1.0 N C:ASN103 4.9 8.2 1.0 O C:ASN103 4.9 8.3 1.0 C5 C:LZ01115 4.9 16.3 1.0 CA C:ASN103 4.9 8.2 1.0 CA D:GLY114 4.9 11.7 1.0

Calcium binding site 7 out of 8 in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1117 b:10.3 occ:1.00 O D:ASN21 2.3 8.6 1.0 OD1 D:ASN103 2.4 8.4 1.0 OD1 D:ASP104 2.4 9.2 1.0 O4 D:LZ01115 2.6 12.9 1.0 O C:GLY114 2.6 9.4 1.0 O3 D:LZ01115 2.6 12.1 1.0 OD2 D:ASP101 2.7 11.4 1.0 OD1 D:ASP101 3.2 10.5 1.0 CG D:ASP101 3.3 12.0 1.0 C3 D:LZ01115 3.5 14.8 1.0 CG D:ASN103 3.5 11.0 1.0 C C:GLY114 3.5 12.4 1.0 C D:ASN21 3.5 9.5 1.0 C4 D:LZ01115 3.5 15.9 1.0 CG D:ASP104 3.7 8.8 1.0 OXT C:GLY114 3.7 12.8 1.0 CA D:CA1118 3.9 10.5 1.0 C2 D:LZ01115 3.9 17.5 1.0 ND2 D:ASN103 4.0 14.4 1.0 N D:ASP104 4.0 7.8 1.0 CB D:ASN21 4.0 9.5 1.0 CA D:ASP104 4.1 8.5 1.0 C D:ASN103 4.4 8.3 1.0 CA D:ASN21 4.4 8.8 1.0 N D:SER22 4.4 10.0 1.0 CB D:ASP104 4.5 8.1 1.0 CA D:SER22 4.5 10.8 1.0 OD2 D:ASP104 4.5 11.2 1.0 O2 D:LZ01115 4.6 19.6 1.0 O D:HOH2148 4.6 16.4 1.0 CB D:SER22 4.6 11.2 1.0 OD2 D:ASP99 4.7 15.6 1.0 CB D:ASP101 4.7 11.1 1.0 CB D:ASN103 4.8 9.5 1.0 O D:ASN103 4.8 7.8 1.0 N D:ASN103 4.8 8.5 1.0 CA D:ASN103 4.9 8.2 1.0 C5 D:LZ01115 4.9 15.3 1.0 CA C:GLY114 4.9 11.9 1.0

Calcium binding site 8 out of 8 in the Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Pa-Iil Lectin From Pseudomonas Aeruginosa Complexed with Fucose- Derived Glycomimetics within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1118 b:10.5 occ:1.00 OD1 D:ASP99 2.3 13.2 1.0 OD1 D:ASP101 2.3 10.5 1.0 OE2 D:GLU95 2.3 12.1 1.0 O3 D:LZ01115 2.6 12.1 1.0 OE1 D:GLU95 2.6 9.5 1.0 O2 D:LZ01115 2.7 19.6 1.0 OD2 D:ASP104 2.7 11.2 1.0 CD D:GLU95 2.8 11.6 1.0 OD1 D:ASP104 2.9 9.2 1.0 CG D:ASP104 3.2 8.8 1.0 CG D:ASP99 3.3 14.6 1.0 CG D:ASP101 3.4 12.0 1.0 C2 D:LZ01115 3.4 17.5 1.0 C3 D:LZ01115 3.5 14.8 1.0 OD2 D:ASP99 3.6 15.6 1.0 CA D:CA1117 3.9 10.3 1.0 OD2 D:ASP101 4.0 11.4 1.0 N D:ASP101 4.0 11.7 1.0 O D:HOH2143 4.2 15.4 1.0 CG D:GLU95 4.3 9.0 1.0 OD1 D:ASP96 4.3 9.5 1.0 N D:ASN100 4.3 12.4 1.0 N D:TYR102 4.4 9.8 1.0 N D:GLY97 4.5 12.3 1.0 CB D:ASP101 4.5 11.1 1.0 N D:ASP96 4.6 10.0 1.0 CA D:ASP101 4.6 11.2 1.0 CB D:ASP99 4.7 12.4 1.0 CB D:ASP104 4.7 8.1 1.0 N D:ASP99 4.7 13.4 1.0 CA D:GLU95 4.8 8.7 1.0 C4 D:LZ01115 4.8 15.9 1.0 OD1 D:ASN103 4.9 8.4 1.0 CA D:GLY97 4.9 12.7 1.0 C D:ASP99 4.9 12.2 1.0 C D:ASP101 4.9 10.6 1.0 C1 D:LZ01115 4.9 17.9 1.0 CA D:ASN100 4.9 12.5 1.0 CA D:ASP99 4.9 12.8 1.0 CB D:GLU95 5.0 9.7 1.0 O4 D:LZ01115 5.0 12.9 1.0 C D:ASN100 5.0 12.1 1.0

S.Beha, K.Marotte, C.Sabin, E.P.Mitchell, A.Imberty, R.Roy. Fucose-Derived Glycomimetics As High Affinity Ligands For Bacterial Lectin Pa-Iil From Pseudomonas Aeruginosa To Be Published.