Calcium in PDB 5may: Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)

The structure of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl), PDB code: 5may was solved by R.Sommer, A.Imberty, A.Titz, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.59 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.089, 65.520, 109.173, 90.00, 90.00, 90.00
R / Rfree (%)	13.5 / 17.3

The binding sites of Calcium atom in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) (pdb code 5may). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl), PDB code: 5may:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca200 b:9.4 occ:1.00 OD1 A:ASN103 2.4 8.6 1.0 OD1 A:ASP104 2.4 9.1 1.0 O A:ASN21 2.4 9.4 1.0 O B:GLY114 2.4 9.4 1.0 OD2 A:ASP101 2.5 10.2 1.0 O4 A:FUL202 2.5 10.7 1.0 O3 A:FUL202 2.5 11.8 1.0 OD1 A:ASP101 3.1 10.6 1.0 CG A:ASP101 3.1 10.6 1.0 CG A:ASN103 3.4 8.5 1.0 C3 A:FUL202 3.4 11.3 1.0 C4 A:FUL202 3.4 11.0 1.0 C B:GLY114 3.4 10.9 1.0 C A:ASN21 3.6 8.2 1.0 CG A:ASP104 3.6 8.5 1.0 OXT B:GLY114 3.7 10.9 1.0 ND2 A:ASN103 3.7 8.9 1.0 CA A:CA201 3.8 10.3 1.0 C2 A:FUL202 3.9 10.7 1.0 CB A:ASN21 4.2 8.0 1.0 CA A:ASP104 4.2 7.4 1.0 N A:ASP104 4.3 7.7 1.0 O A:HOH313 4.4 19.6 1.0 CA A:SER22 4.4 9.4 1.0 OD2 A:ASP104 4.4 8.4 1.0 N A:SER22 4.4 8.4 1.0 O2 A:FUL202 4.4 10.4 1.0 C A:ASN103 4.4 7.5 1.0 CB A:ASP104 4.5 8.0 1.0 CB A:ASP101 4.5 9.4 1.0 CA A:ASN21 4.6 7.9 1.0 OD2 A:ASP99 4.6 13.2 1.0 CB A:SER22 4.7 9.6 1.0 CB A:ASN103 4.7 8.5 1.0 O A:ASN103 4.8 8.0 1.0 C5 A:FUL202 4.8 10.7 1.0 CA B:GLY114 4.8 9.4 1.0 N A:ASN103 4.9 7.9 1.0 CA A:ASN103 4.9 8.2 1.0

Calcium binding site 2 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:10.3 occ:1.00 OE2 A:GLU95 2.4 10.8 1.0 OD1 A:ASP99 2.4 13.2 1.0 OD1 A:ASP101 2.4 10.6 1.0 OD2 A:ASP104 2.4 8.4 1.0 O3 A:FUL202 2.5 11.8 1.0 O2 A:FUL202 2.5 10.4 1.0 OE1 A:GLU95 2.5 10.4 1.0 OD1 A:ASP104 2.7 9.1 1.0 CD A:GLU95 2.8 9.9 1.0 CG A:ASP104 2.9 8.5 1.0 C3 A:FUL202 3.3 11.3 1.0 C2 A:FUL202 3.4 10.7 1.0 CG A:ASP99 3.4 13.5 1.0 CG A:ASP101 3.5 10.6 1.0 OD2 A:ASP99 3.7 13.2 1.0 CA A:CA200 3.8 9.4 1.0 OD1 A:ASP96 4.0 10.0 1.0 OD2 A:ASP101 4.0 10.2 1.0 N A:ASP101 4.2 9.3 1.0 CG A:GLU95 4.2 8.6 1.0 CB A:ASP104 4.4 8.0 1.0 N A:ASP96 4.5 8.0 1.0 N A:ASN100 4.5 11.2 1.0 N A:TYR102 4.5 8.7 1.0 CB A:ASP101 4.6 9.4 1.0 N A:SER97 4.7 10.9 1.0 CA A:GLU95 4.7 7.7 1.0 C4 A:FUL202 4.7 11.0 1.0 OD1 A:ASN103 4.7 8.6 1.0 CB A:ASP99 4.7 13.1 1.0 CB A:SER97 4.7 15.3 1.0 CA A:ASP101 4.8 9.0 1.0 C1 A:FUL202 4.8 10.6 1.0 O4 A:FUL202 4.8 10.7 1.0 N A:ASP99 4.9 12.5 1.0 CG A:ASP96 4.9 10.1 1.0 CB A:GLU95 4.9 8.5 1.0

Calcium binding site 3 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca200 b:8.6 occ:1.00 O B:ASN21 2.3 7.4 1.0 OD1 B:ASN103 2.4 8.8 1.0 OD1 B:ASP104 2.4 8.3 1.0 O A:GLY114 2.4 8.5 1.0 O3 B:FUL202 2.5 8.9 1.0 OD2 B:ASP101 2.5 7.6 1.0 O4 B:FUL202 2.5 9.0 1.0 OD1 B:ASP101 3.1 8.5 1.0 CG B:ASP101 3.1 8.5 1.0 CG B:ASN103 3.4 8.5 1.0 C3 B:FUL202 3.4 9.4 1.0 C4 B:FUL202 3.4 9.0 1.0 C A:GLY114 3.4 9.4 1.0 C B:ASN21 3.5 7.2 1.0 CG B:ASP104 3.6 7.3 1.0 ND2 B:ASN103 3.7 8.9 1.0 OXT A:GLY114 3.7 10.1 1.0 CA B:CA201 3.7 9.4 1.0 C2 B:FUL202 3.8 9.9 1.0 CB B:ASN21 4.1 7.3 1.0 CA B:ASP104 4.2 7.1 1.0 N B:ASP104 4.3 7.4 1.0 O B:HOH311 4.4 17.9 1.0 CA B:SER22 4.4 8.0 1.0 O2 B:FUL202 4.4 9.2 1.0 N B:SER22 4.4 7.6 1.0 OD2 B:ASP104 4.4 8.8 1.0 C B:ASN103 4.5 7.3 1.0 CB B:ASP104 4.5 7.2 1.0 CA B:ASN21 4.5 7.2 1.0 CB B:ASP101 4.6 8.3 1.0 OD2 B:ASP99 4.6 10.9 1.0 CB B:SER22 4.7 8.7 1.0 CB B:ASN103 4.7 8.5 1.0 O B:ASN103 4.7 6.7 1.0 C5 B:FUL202 4.8 9.4 1.0 CA A:GLY114 4.8 9.4 1.0 N B:ASN103 4.9 8.2 1.0 CA B:ASN103 4.9 7.9 1.0

Calcium binding site 4 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:9.4 occ:1.00 OD1 B:ASP101 2.3 8.5 1.0 OD1 B:ASP99 2.3 11.4 1.0 OE2 B:GLU95 2.4 8.9 1.0 OD2 B:ASP104 2.4 8.8 1.0 O3 B:FUL202 2.5 8.9 1.0 O2 B:FUL202 2.5 9.2 1.0 OE1 B:GLU95 2.5 9.0 1.0 OD1 B:ASP104 2.6 8.3 1.0 CD B:GLU95 2.8 8.9 1.0 CG B:ASP104 2.9 7.3 1.0 C2 B:FUL202 3.3 9.9 1.0 C3 B:FUL202 3.3 9.4 1.0 CG B:ASP99 3.4 11.0 1.0 CG B:ASP101 3.4 8.5 1.0 OD2 B:ASP99 3.7 10.9 1.0 CA B:CA200 3.7 8.6 1.0 OD2 B:ASP101 4.0 7.6 1.0 OD1 B:ASP96 4.0 9.3 1.0 N B:ASP101 4.2 9.2 1.0 CG B:GLU95 4.3 8.5 1.0 CB B:ASP104 4.4 7.2 1.0 N B:ASN100 4.5 10.0 1.0 N B:TYR102 4.5 8.7 1.0 N B:ASP96 4.5 7.5 1.0 CB B:ASP101 4.6 8.3 1.0 OD1 B:ASN103 4.6 8.8 1.0 C4 B:FUL202 4.6 9.0 1.0 N B:SER97 4.7 9.5 1.0 CB B:ASP99 4.7 9.9 1.0 CA B:ASP101 4.7 8.5 1.0 CA B:GLU95 4.7 7.7 1.0 C1 B:FUL202 4.8 10.4 1.0 N B:ASP99 4.8 9.9 1.0 CB B:SER97 4.8 12.6 1.0 O4 B:FUL202 4.8 9.0 1.0 CG B:ASP96 4.9 8.3 1.0 CB B:GLU95 4.9 8.7 1.0

Calcium binding site 5 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca200 b:12.0 occ:1.00 O C:ASN21 2.3 8.9 1.0 OD1 C:ASP104 2.3 11.9 1.0 OD1 C:ASN103 2.3 9.9 1.0 O4 C:FUL202 2.4 14.1 1.0 OD2 C:ASP101 2.5 14.7 1.0 O D:GLY114 2.5 12.5 1.0 O3 C:FUL202 2.5 15.2 1.0 OD1 C:ASP101 3.1 15.1 1.0 CG C:ASP101 3.1 15.4 1.0 C3 C:FUL202 3.4 13.9 1.0 CG C:ASN103 3.4 10.4 1.0 C4 C:FUL202 3.4 14.8 1.0 C D:GLY114 3.5 14.0 1.0 C C:ASN21 3.5 9.6 1.0 CG C:ASP104 3.6 11.0 1.0 OXT D:GLY114 3.7 15.0 1.0 CA C:CA201 3.7 14.3 1.0 ND2 C:ASN103 3.8 9.9 1.0 C2 C:FUL202 3.9 13.3 1.0 CA C:ASP104 4.1 9.5 1.0 CB C:ASN21 4.2 9.3 1.0 N C:ASP104 4.2 9.2 1.0 CA C:SER22 4.3 9.8 1.0 N C:SER22 4.4 9.6 1.0 OD2 C:ASP104 4.4 11.1 1.0 CB C:ASP104 4.4 10.4 1.0 O C:HOH317 4.4 22.6 1.0 C C:ASN103 4.4 9.4 1.0 O2 C:FUL202 4.5 15.0 1.0 CA C:ASN21 4.5 9.4 1.0 CB C:ASP101 4.5 14.5 1.0 OD2 C:ASP99 4.5 15.5 1.0 CB C:SER22 4.6 9.1 1.0 CB C:ASN103 4.7 10.2 1.0 O C:ASN103 4.7 9.1 1.0 C5 C:FUL202 4.8 13.9 1.0 CA D:GLY114 4.8 12.8 1.0 N C:ASN103 4.9 9.9 1.0 CA C:ASN103 4.9 9.5 1.0

Calcium binding site 6 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:14.3 occ:1.00 OD1 C:ASP99 2.3 15.3 1.0 OD1 C:ASP101 2.4 15.1 1.0 OD2 C:ASP104 2.4 11.1 1.0 OE2 C:GLU95 2.4 15.3 1.0 O3 C:FUL202 2.5 15.2 1.0 OE1 C:GLU95 2.5 14.3 1.0 O2 C:FUL202 2.5 15.0 1.0 OD1 C:ASP104 2.6 11.9 1.0 CD C:GLU95 2.8 14.2 1.0 CG C:ASP104 2.9 11.0 1.0 C2 C:FUL202 3.3 13.3 1.0 CG C:ASP99 3.3 15.6 1.0 C3 C:FUL202 3.4 13.9 1.0 CG C:ASP101 3.4 15.4 1.0 OD2 C:ASP99 3.7 15.5 1.0 CA C:CA200 3.7 12.0 1.0 OD2 C:ASP101 4.0 14.7 1.0 OD1 C:ASP96 4.0 13.5 1.0 O C:HOH381 4.0 25.1 1.0 N C:ASP101 4.1 16.2 1.0 CG C:GLU95 4.3 13.5 1.0 CB C:ASP104 4.4 10.4 1.0 N C:ASP96 4.5 11.5 1.0 N C:ASN100 4.5 16.9 1.0 CB C:ASP101 4.6 14.5 1.0 N C:TYR102 4.6 11.8 1.0 OD1 C:ASN103 4.7 9.9 1.0 CA C:GLU95 4.7 10.5 1.0 CB C:ASP99 4.7 16.6 1.0 C4 C:FUL202 4.7 14.8 1.0 N C:SER97 4.7 14.7 1.0 CA C:ASP101 4.7 14.0 1.0 C1 C:FUL202 4.8 14.8 1.0 O4 C:FUL202 4.8 14.1 1.0 N C:ASP99 4.8 18.4 1.0 CG C:ASP96 4.9 13.2 1.0 CB C:GLU95 4.9 11.7 1.0 CB C:SER97 4.9 18.7 1.0

Calcium binding site 7 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca200 b:16.9 occ:1.00 O D:ASN21 2.3 12.8 1.0 OD1 D:ASN103 2.3 14.2 1.0 OD1 D:ASP104 2.3 13.4 1.0 O3 D:FUL202 2.4 12.7 0.7 O4 D:FUL202 2.4 12.8 0.7 OD2 D:ASP101 2.5 21.6 1.0 O C:GLY114 2.5 16.6 1.0 OD1 D:ASP101 3.1 21.3 1.0 CG D:ASP101 3.2 24.3 1.0 CG D:ASN103 3.4 12.7 1.0 C3 D:FUL202 3.4 12.9 0.7 C4 D:FUL202 3.4 12.2 0.7 C C:GLY114 3.5 17.1 1.0 C D:ASN21 3.5 12.4 1.0 CG D:ASP104 3.5 14.0 1.0 OXT C:GLY114 3.6 18.0 1.0 ND2 D:ASN103 3.8 12.4 1.0 CA D:CA201 3.8 21.4 1.0 C2 D:FUL202 3.9 13.1 0.7 CB D:ASN21 4.1 10.8 1.0 CA D:ASP104 4.1 12.1 1.0 N D:ASP104 4.2 11.6 1.0 C D:ASN103 4.4 12.1 1.0 CA D:SER22 4.4 12.8 1.0 N D:SER22 4.4 12.0 1.0 CB D:ASP104 4.4 12.3 1.0 OD2 D:ASP104 4.4 15.5 1.0 O D:HOH333 4.5 25.7 1.0 CA D:ASN21 4.5 11.2 1.0 O2 D:FUL202 4.5 13.7 0.7 CB D:ASP101 4.6 22.3 1.0 OD2 D:ASP99 4.6 24.1 1.0 CB D:SER22 4.6 13.7 1.0 O D:ASN103 4.7 11.7 1.0 CB D:ASN103 4.7 12.3 1.0 C5 D:FUL202 4.8 12.2 0.7 CA C:GLY114 4.9 14.8 1.0 N D:ASN103 4.9 12.2 1.0 CA D:ASN103 4.9 11.4 1.0

Calcium binding site 8 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with 2-Thiophenesulfonamide-N-(Beta-L-Fucopyranosyl Methyl) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:21.4 occ:1.00 OD2 D:ASP104 2.3 15.5 1.0 OD1 D:ASP99 2.4 26.3 1.0 OE2 D:GLU95 2.4 20.5 1.0 OD1 D:ASP101 2.4 21.3 1.0 O3 D:FUL202 2.5 12.7 0.7 OE1 D:GLU95 2.5 17.6 1.0 O2 D:FUL202 2.5 13.7 0.7 OD1 D:ASP104 2.6 13.4 1.0 CD D:GLU95 2.8 19.5 1.0 CG D:ASP104 2.8 14.0 1.0 C2 D:FUL202 3.3 13.1 0.7 C3 D:FUL202 3.3 12.9 0.7 CG D:ASP99 3.4 25.5 1.0 CG D:ASP101 3.5 24.3 1.0 OD2 D:ASP99 3.7 24.1 1.0 CA D:CA200 3.8 16.9 1.0 OD1 D:ASP96 3.9 20.8 1.0 OD2 D:ASP101 4.0 21.6 1.0 N D:ASP101 4.2 22.1 1.0 CG D:GLU95 4.3 15.6 1.0 CB D:ASP104 4.3 12.3 1.0 N D:ASP96 4.4 14.6 1.0 N D:ASN100 4.6 23.9 1.0 N D:SER97 4.6 21.9 1.0 N D:TYR102 4.6 15.8 1.0 CA D:GLU95 4.6 13.2 1.0 CB D:ASP101 4.7 22.3 1.0 C4 D:FUL202 4.7 12.2 0.7 OD1 D:ASN103 4.7 14.2 1.0 C1 D:FUL202 4.7 12.3 0.7 CB D:ASP99 4.7 24.8 1.0 CG D:ASP96 4.8 19.0 1.0 CA D:ASP101 4.8 21.8 1.0 O4 D:FUL202 4.8 12.8 0.7 CB D:SER97 4.8 27.6 1.0 N D:ASP99 4.9 26.9 1.0 CB D:GLU95 4.9 14.6 1.0

R.Sommer, S.Wagner, K.Rox, A.Varrot, D.Hauck, E.C.Wamhoff, J.Schreiber, T.Ryckmans, T.Brunner, C.Rademacher, R.W.Hartmann, M.Bronstrup, A.Imberty, A.Titz. Glycomimetic, Orally Bioavailable Lecb Inhibitors Block Biofilm Formation of Pseudomonas Aeruginosa. J. Am. Chem. Soc. V. 140 2537 2018.
ISSN: ESSN 1520-5126
PubMed: 29272578
DOI: 10.1021/JACS.7B11133