Calcium in PDB 4ut5: Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide

The structure of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide, PDB code: 4ut5 was solved by A.M.Boukerb, A.Decor, R.Tabaroni, A.Varrot, S.Debentzmann, S.Vidal, A.Imberty, B.Cournoyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.23 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.790, 70.370, 54.660, 90.00, 90.50, 90.00
R / Rfree (%)	14.752 / 18.345

The binding sites of Calcium atom in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide (pdb code 4ut5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide, PDB code: 4ut5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide


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 Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca200 b:9.1 occ:1.00 OD1 A:ASN103 2.3 7.8 1.0 OD1 A:ASP104 2.3 7.8 1.0 O A:ASN21 2.4 7.1 1.0 O B:GLY114 2.4 9.1 1.0 OD2 A:ASP101 2.4 9.2 1.0 O4 A:FUC403 2.5 11.6 1.0 O3 A:FUC403 2.5 10.0 1.0 OD1 A:ASP101 3.1 9.5 1.0 CG A:ASP101 3.1 9.9 1.0 CG A:ASN103 3.3 8.4 1.0 C3 A:FUC403 3.3 10.8 1.0 C4 A:FUC403 3.4 11.2 1.0 C B:GLY114 3.4 10.3 1.0 C A:ASN21 3.6 7.2 1.0 CG A:ASP104 3.6 7.4 1.0 ND2 A:ASN103 3.7 7.9 1.0 OXT B:GLY114 3.7 11.7 1.0 CA A:CA201 3.7 10.3 1.0 C2 A:FUC403 3.7 10.6 1.0 CB A:ASN21 4.2 6.6 1.0 CA A:ASP104 4.2 7.0 1.0 N A:ASP104 4.3 7.2 1.0 O2 A:FUC403 4.3 10.2 1.0 O A:HOH2204 4.4 21.7 1.0 OD2 A:ASP104 4.4 7.4 1.0 CA A:SER22 4.4 7.6 1.0 N A:SER22 4.5 7.6 1.0 OD2 A:ASP99 4.5 11.6 1.0 C A:ASN103 4.5 7.5 1.0 CB A:ASP104 4.5 7.3 1.0 CB A:ASP101 4.6 9.6 1.0 CA A:ASN21 4.6 6.6 1.0 CB A:ASN103 4.7 8.1 1.0 CB A:SER22 4.7 7.0 1.0 C5 A:FUC403 4.7 11.6 1.0 CA B:GLY114 4.8 10.5 1.0 O A:ASN103 4.8 7.4 1.0 N A:ASN103 4.9 7.9 1.0 CA A:ASN103 4.9 7.8 1.0 C1 A:FUC403 5.0 11.7 1.0 O5 A:FUC403 5.0 11.1 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide


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 Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:10.3 occ:1.00 OD1 A:ASP99 2.3 11.8 1.0 OD1 A:ASP101 2.4 9.5 1.0 OE2 A:GLU95 2.4 10.4 1.0 OD2 A:ASP104 2.4 7.4 1.0 O2 A:FUC403 2.5 10.2 1.0 OE1 A:GLU95 2.5 10.8 1.0 O3 A:FUC403 2.5 10.0 1.0 OD1 A:ASP104 2.7 7.8 1.0 CD A:GLU95 2.8 9.6 1.0 CG A:ASP104 2.9 7.4 1.0 CG A:ASP99 3.3 12.2 1.0 C2 A:FUC403 3.3 10.6 1.0 C3 A:FUC403 3.4 10.8 1.0 CG A:ASP101 3.5 9.9 1.0 OD2 A:ASP99 3.6 11.6 1.0 CA A:CA200 3.7 9.1 1.0 OD2 A:ASP101 4.0 9.2 1.0 OD1 A:ASP96 4.1 10.1 1.0 N A:ASP101 4.2 10.5 1.0 CG A:GLU95 4.3 9.2 1.0 CB A:ASP104 4.4 7.3 1.0 N A:ASN100 4.5 11.5 1.0 N A:ASP96 4.5 8.5 1.0 N A:TYR102 4.5 9.3 1.0 O A:HOH2193 4.6 25.9 1.0 OD1 A:ASN103 4.6 7.8 1.0 N A:SER97 4.6 10.4 1.0 CB A:SER97 4.6 11.3 1.0 CB A:ASP101 4.6 9.6 1.0 CA A:GLU95 4.7 8.3 1.0 CB A:ASP99 4.7 11.6 1.0 C4 A:FUC403 4.8 11.2 1.0 C1 A:FUC403 4.8 11.7 1.0 N A:ASP99 4.8 11.4 1.0 CA A:ASP101 4.8 10.1 1.0 O4 A:FUC403 4.9 11.6 1.0 CB A:GLU95 4.9 8.4 1.0 C A:ASP99 4.9 11.8 1.0 CG A:ASP96 5.0 9.4 1.0 CA A:ASP99 5.0 11.6 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide


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 Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca200 b:10.7 occ:1.00 OD1 B:ASP99 2.3 14.0 1.0 OD1 B:ASP101 2.3 10.2 1.0 OD2 B:ASP104 2.4 8.2 1.0 O3 B:FUC403 2.4 10.4 1.0 O2 B:FUC403 2.5 9.2 1.0 OE2 B:GLU95 2.5 9.0 1.0 OE1 B:GLU95 2.5 9.9 1.0 OD1 B:ASP104 2.6 7.7 1.0 CD B:GLU95 2.9 8.9 1.0 CG B:ASP104 2.9 7.2 1.0 CG B:ASP99 3.3 13.5 1.0 C2 B:FUC403 3.3 10.1 1.0 C3 B:FUC403 3.4 10.0 1.0 CG B:ASP101 3.4 10.6 1.0 OD2 B:ASP99 3.6 13.5 1.0 CA B:CA201 3.7 10.3 1.0 OD2 B:ASP101 4.0 9.7 1.0 OD1 B:ASP96 4.2 9.0 1.0 N B:ASP101 4.2 9.9 1.0 CG B:GLU95 4.3 8.1 1.0 CB B:ASP104 4.4 7.0 1.0 N B:ASN100 4.5 12.1 1.0 N B:ASP96 4.6 8.3 1.0 N B:TYR102 4.6 8.5 1.0 OD1 B:ASN103 4.6 7.5 1.0 CB B:ASP101 4.6 10.2 1.0 CB B:ASP99 4.7 13.4 1.0 C4 B:FUC403 4.7 10.1 1.0 CB B:SER97 4.7 10.9 1.0 N B:SER97 4.7 9.2 1.0 O B:HOH2163 4.7 23.6 1.0 CA B:GLU95 4.7 7.4 1.0 N B:ASP99 4.8 12.6 1.0 C1 B:FUC403 4.8 10.8 1.0 CA B:ASP101 4.8 10.2 1.0 O4 B:FUC403 4.8 10.2 1.0 CG B:ASP96 4.9 8.5 1.0 C B:ASP99 5.0 12.9 1.0 CB B:GLU95 5.0 7.8 1.0 CA B:ASP99 5.0 12.6 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide


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 Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:10.3 occ:1.00 OD1 B:ASN103 2.3 7.5 1.0 OD1 B:ASP104 2.4 7.7 1.0 O B:ASN21 2.4 6.5 1.0 O A:GLY114 2.4 10.7 1.0 OD2 B:ASP101 2.4 9.7 1.0 O4 B:FUC403 2.5 10.2 1.0 O3 B:FUC403 2.6 10.4 1.0 OD1 B:ASP101 3.1 10.2 1.0 CG B:ASP101 3.1 10.6 1.0 CG B:ASN103 3.3 6.8 1.0 C3 B:FUC403 3.4 10.0 1.0 C A:GLY114 3.4 11.9 1.0 C4 B:FUC403 3.4 10.1 1.0 C B:ASN21 3.6 6.6 1.0 ND2 B:ASN103 3.6 8.1 1.0 CG B:ASP104 3.6 7.2 1.0 OXT A:GLY114 3.7 10.9 1.0 CA B:CA200 3.7 10.7 1.0 C2 B:FUC403 3.8 10.1 1.0 CB B:ASN21 4.1 6.2 1.0 CA B:ASP104 4.2 6.6 1.0 N B:ASP104 4.3 6.3 1.0 O A:HOH2207 4.4 21.7 1.0 O2 B:FUC403 4.4 9.2 1.0 OD2 B:ASP104 4.4 8.2 1.0 CA B:SER22 4.4 7.6 1.0 N B:SER22 4.4 7.1 1.0 C B:ASN103 4.5 6.4 1.0 CB B:ASP104 4.5 7.0 1.0 OD2 B:ASP99 4.5 13.5 1.0 CA B:ASN21 4.5 6.2 1.0 CB B:ASP101 4.6 10.2 1.0 CB B:ASN103 4.6 6.7 1.0 CB B:SER22 4.7 7.5 1.0 CA A:GLY114 4.8 9.7 1.0 C5 B:FUC403 4.8 10.0 1.0 O B:ASN103 4.8 6.1 1.0 N B:ASN103 4.9 6.8 1.0 CA B:ASN103 4.9 6.5 1.0 O5 B:FUC403 5.0 9.4 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca200 b:16.0 occ:1.00 OD2 C:ASP104 2.4 12.3 1.0 OD1 C:ASP99 2.4 15.0 1.0 OE2 C:GLU95 2.4 13.9 1.0 OD1 C:ASP101 2.4 13.7 1.0 OE1 C:GLU95 2.5 15.4 1.0 O3 C:FUC403 2.5 15.2 1.0 O2 C:FUC403 2.5 13.3 1.0 OD1 C:ASP104 2.7 11.1 1.0 CD C:GLU95 2.8 15.7 1.0 CG C:ASP104 2.9 11.1 1.0 C2 C:FUC403 3.3 13.9 1.0 C3 C:FUC403 3.4 14.9 1.0 CG C:ASP99 3.4 15.0 1.0 CG C:ASP101 3.5 13.4 1.0 OD2 C:ASP99 3.7 16.2 1.0 CA C:CA201 3.7 14.3 1.0 OD2 C:ASP101 4.1 13.5 1.0 OD1 C:ASP96 4.1 16.2 1.0 N C:ASP101 4.2 13.1 1.0 CG C:GLU95 4.2 14.7 1.0 CB C:ASP104 4.4 10.1 1.0 N C:ASN100 4.4 15.3 1.0 N C:ASP96 4.5 13.1 1.0 N C:TYR102 4.5 11.3 1.0 CA C:GLU95 4.6 12.2 1.0 N C:SER97 4.7 14.5 1.0 CB C:SER97 4.7 16.4 1.0 OD1 C:ASN103 4.7 11.1 1.0 CB C:ASP101 4.7 13.0 1.0 C4 C:FUC403 4.7 15.5 1.0 C1 C:FUC403 4.7 14.2 1.0 CB C:ASP99 4.7 15.9 1.0 O C:HOH2122 4.8 22.1 1.0 CA C:ASP101 4.8 12.8 1.0 N C:ASP99 4.8 15.3 1.0 CB C:GLU95 4.8 14.1 1.0 O4 C:FUC403 4.9 13.2 1.0 CG C:ASP96 4.9 13.9 1.0 C C:ASP99 5.0 17.2 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:14.3 occ:1.00 OD1 C:ASN103 2.3 11.1 1.0 OD1 C:ASP104 2.3 11.1 1.0 O C:ASN21 2.4 11.2 1.0 O4 C:FUC403 2.5 13.2 1.0 OD2 C:ASP101 2.5 13.5 1.0 O D:GLY114 2.5 14.5 1.0 O3 C:FUC403 2.5 15.2 1.0 OD1 C:ASP101 3.1 13.7 1.0 CG C:ASP101 3.2 13.4 1.0 CG C:ASN103 3.3 10.7 1.0 C3 C:FUC403 3.4 14.9 1.0 C4 C:FUC403 3.4 15.5 1.0 CG C:ASP104 3.5 11.1 1.0 C D:GLY114 3.5 15.4 1.0 C C:ASN21 3.6 10.4 1.0 ND2 C:ASN103 3.7 11.9 1.0 C2 C:FUC403 3.7 13.9 1.0 CA C:CA200 3.7 16.0 1.0 OXT D:GLY114 3.8 16.0 1.0 CA C:ASP104 4.1 8.9 1.0 N C:ASP104 4.2 8.6 1.0 CB C:ASN21 4.2 9.8 1.0 OD2 C:ASP104 4.4 12.3 1.0 O2 C:FUC403 4.4 13.3 1.0 C C:ASN103 4.4 8.6 1.0 CB C:ASP104 4.4 10.1 1.0 CA C:SER22 4.5 10.5 1.0 O C:HOH2129 4.5 21.3 1.0 N C:SER22 4.5 10.2 1.0 OD2 C:ASP99 4.6 16.2 1.0 CB C:ASP101 4.6 13.0 1.0 CA C:ASN21 4.6 9.6 1.0 CB C:ASN103 4.6 9.5 1.0 CB C:SER22 4.7 10.9 1.0 O C:ASN103 4.7 8.2 1.0 C5 C:FUC403 4.8 15.7 1.0 N C:ASN103 4.8 8.8 1.0 CA C:ASN103 4.9 9.1 1.0 CA D:GLY114 4.9 14.3 1.0 O5 C:FUC403 5.0 14.6 1.0 C1 C:FUC403 5.0 14.2 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca200 b:22.2 occ:1.00 OD2 D:ASP104 2.4 15.3 1.0 OD1 D:ASP99 2.4 22.0 1.0 OE2 D:GLU95 2.4 23.5 1.0 OD1 D:ASP101 2.4 18.9 1.0 O3 D:FUC403 2.5 20.0 1.0 O2 D:FUC403 2.5 18.7 1.0 OE1 D:GLU95 2.5 22.8 1.0 OD1 D:ASP104 2.7 12.0 1.0 CD D:GLU95 2.8 20.0 1.0 CG D:ASP104 2.9 12.3 1.0 C2 D:FUC403 3.2 18.6 1.0 C3 D:FUC403 3.3 18.2 1.0 CG D:ASP99 3.4 23.6 1.0 CG D:ASP101 3.5 17.5 1.0 OD2 D:ASP99 3.7 21.6 1.0 CA D:CA201 3.8 16.9 1.0 OD2 D:ASP101 4.1 18.3 1.0 N D:ASP101 4.1 18.1 1.0 OD1 D:ASP96 4.2 20.0 1.0 CG D:GLU95 4.2 17.6 1.0 N D:ASN100 4.4 23.7 1.0 CB D:ASP104 4.4 11.4 1.0 N D:ASP96 4.5 13.4 1.0 N D:TYR102 4.5 10.3 1.0 O D:HOH2106 4.5 30.2 1.0 CA D:GLU95 4.6 13.2 1.0 CB D:SER97 4.7 24.4 1.0 OD1 D:ASN103 4.7 13.4 1.0 C4 D:FUC403 4.7 18.1 1.0 CB D:ASP101 4.7 16.5 1.0 C1 D:FUC403 4.7 19.9 1.0 N D:SER97 4.7 17.9 1.0 CB D:ASP99 4.7 22.8 1.0 N D:ASP99 4.8 21.9 1.0 CA D:ASP101 4.8 15.9 1.0 CB D:GLU95 4.9 15.3 1.0 O4 D:FUC403 4.9 16.4 1.0 CG D:ASP96 4.9 16.9 1.0 C D:ASP99 5.0 23.5 1.0 N D:ASP104 5.0 10.6 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA7 in Complex with Lewis A Tetrasaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:16.9 occ:1.00 OD1 D:ASN103 2.2 13.4 1.0 OD1 D:ASP104 2.3 12.0 1.0 O D:ASN21 2.4 13.4 1.0 O4 D:FUC403 2.5 16.4 1.0 O C:GLY114 2.5 17.1 1.0 O3 D:FUC403 2.5 20.0 1.0 OD2 D:ASP101 2.5 18.3 1.0 OD1 D:ASP101 3.2 18.9 1.0 CG D:ASP101 3.2 17.5 1.0 CG D:ASN103 3.2 12.3 1.0 C3 D:FUC403 3.4 18.2 1.0 C4 D:FUC403 3.4 18.1 1.0 C C:GLY114 3.4 17.9 1.0 CG D:ASP104 3.5 12.3 1.0 C D:ASN21 3.6 11.6 1.0 ND2 D:ASN103 3.6 11.9 1.0 OXT C:GLY114 3.6 19.0 1.0 C2 D:FUC403 3.8 18.6 1.0 CA D:CA200 3.8 22.2 1.0 CB D:ASN21 4.1 10.3 1.0 N D:ASP104 4.1 10.6 1.0 CA D:ASP104 4.1 10.8 1.0 C D:ASN103 4.3 10.8 1.0 OD2 D:ASP104 4.4 15.3 1.0 CB D:ASP104 4.4 11.4 1.0 CA D:SER22 4.5 11.6 1.0 O2 D:FUC403 4.5 18.7 1.0 N D:SER22 4.5 11.9 1.0 CA D:ASN21 4.5 10.6 1.0 CB D:ASN103 4.6 11.4 1.0 OD2 D:ASP99 4.6 21.6 1.0 CB D:ASP101 4.6 16.5 1.0 O D:ASN103 4.7 11.4 1.0 O C:HOH2132 4.7 30.1 1.0 C5 D:FUC403 4.7 19.2 1.0 CB D:SER22 4.7 11.8 1.0 N D:ASN103 4.8 10.1 1.0 CA C:GLY114 4.8 15.3 1.0 CA D:ASN103 4.8 11.1 1.0 O5 D:FUC403 4.9 18.8 1.0 C1 D:FUC403 5.0 19.9 1.0

A.M.Boukerb, A.Decor, S.Ribun, R.Tabaroni, A.Rousset, L.Commin, S.Buff, A.Doleans-Jordheim, S.Vidal, A.Varrot, A.Imberty, B.Cournoyer. Genomic Rearrangements and Functional Diversification of Leca and Lecb Lectin-Coding Regions Impacting the Efficacy of Glycomimetics Directed Against Pseudomonas Aeruginosa. Front.Microbiol. V. 7 811 2016.
ISSN: ISSN 1664-302X
PubMed: 27303392
DOI: 10.3389/FMICB.2016.00811