Calcium in PDB 5a3o: Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom

The structure of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom, PDB code: 5a3o was solved by R.Sommer, D.Hauck, A.Varrot, A.Audfray, A.Imberty, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.25 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	44.954, 51.111, 52.348, 101.80, 99.40, 115.95
R / Rfree (%)	16.71 / 20.435

The structure of Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom (pdb code 5a3o). 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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom, PDB code: 5a3o:
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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom


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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca199 b:6.1 occ:1.00 OD1 A:ASP101 2.3 6.0 1.0 OD1 A:ASP99 2.4 7.9 1.0 O3 A:MMA201 2.4 7.2 1.0 OD2 A:ASP104 2.4 5.8 1.0 OE2 A:GLU95 2.5 5.5 1.0 OE1 A:GLU95 2.5 6.3 1.0 O4 A:MMA201 2.7 8.3 1.0 OD1 A:ASP104 2.7 6.1 1.0 CD A:GLU95 2.8 5.7 1.0 CG A:ASP104 2.9 5.2 1.0 CG A:ASP99 3.3 8.0 1.0 CG A:ASP101 3.4 6.3 1.0 C4 A:MMA201 3.4 7.9 1.0 C3 A:MMA201 3.4 7.6 1.0 CA A:CA200 3.7 6.3 1.0 OD2 A:ASP99 3.7 8.1 1.0 OD1 A:ASP96 3.9 6.5 1.0 OD2 A:ASP101 3.9 5.9 1.0 O A:HOH2159 4.0 8.9 1.0 N A:ASP101 4.1 7.3 1.0 CG A:GLU95 4.3 5.4 1.0 CB A:ASP104 4.4 5.0 1.0 N A:TYR102 4.4 5.9 1.0 CB A:ASP101 4.4 6.5 1.0 N A:ASN100 4.5 8.3 1.0 N A:ASP96 4.6 6.0 1.0 CA A:ASP101 4.6 6.7 1.0 N A:GLY97 4.7 7.5 1.0 C2 A:MMA201 4.7 7.3 1.0 CB A:ASP99 4.7 8.4 1.0 OD1 A:ASN103 4.7 5.3 1.0 O2 A:MMA201 4.7 6.5 1.0 CA A:GLU95 4.7 5.6 1.0 N A:ASP99 4.8 8.5 1.0 CG A:ASP96 4.8 6.5 1.0 C5 A:MMA201 4.8 7.9 1.0 C A:ASP101 4.9 6.4 1.0 C A:ASP99 5.0 8.5 1.0 CA A:GLY97 5.0 7.7 1.0 CA A:ASP99 5.0 8.4 1.0 CB A:GLU95 5.0 5.4 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom


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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca200 b:6.3 occ:1.00 O A:ASN21 2.3 5.7 1.0 OD1 A:ASN103 2.3 5.3 1.0 OD1 A:ASP104 2.3 6.1 1.0 OD2 A:ASP101 2.4 5.9 1.0 O B:GLY114 2.4 7.1 1.0 O2 A:MMA201 2.5 6.5 1.0 O3 A:MMA201 2.5 7.2 1.0 OD1 A:ASP101 3.0 6.0 1.0 CG A:ASP101 3.0 6.3 1.0 CG A:ASN103 3.4 5.2 1.0 C2 A:MMA201 3.4 7.3 1.0 C B:GLY114 3.4 7.2 1.0 C3 A:MMA201 3.4 7.6 1.0 C A:ASN21 3.5 5.6 1.0 CG A:ASP104 3.6 5.2 1.0 OXT B:GLY114 3.7 7.4 1.0 CA A:CA199 3.7 6.1 1.0 ND2 A:ASN103 3.7 5.1 1.0 C4 A:MMA201 4.0 7.9 1.0 CA A:ASP104 4.1 4.8 1.0 CB A:ASN21 4.2 5.6 1.0 N A:ASP104 4.3 4.7 1.0 CA A:SER22 4.3 6.0 1.0 N A:SER22 4.4 5.8 1.0 OD2 A:ASP104 4.4 5.8 1.0 O A:HOH2168 4.4 14.0 1.0 C A:ASN103 4.4 5.2 1.0 CB A:ASP104 4.5 5.0 1.0 CB A:ASP101 4.5 6.5 1.0 CA A:ASN21 4.5 5.6 1.0 O A:HOH2163 4.5 25.1 1.0 OD2 A:ASP99 4.5 8.1 1.0 CB A:SER22 4.6 6.0 1.0 O4 A:MMA201 4.7 8.3 1.0 CB A:ASN103 4.7 5.2 1.0 O A:ASN103 4.7 5.3 1.0 C1 A:MMA201 4.8 7.4 1.0 CA B:GLY114 4.8 7.2 1.0 N A:ASN103 4.9 5.7 1.0 CA A:ASN103 4.9 5.3 1.0 OD1 A:ASP99 5.0 7.9 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom


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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca199 b:7.3 occ:1.00 OD1 B:ASP99 2.4 8.2 1.0 OD1 B:ASP101 2.4 6.4 1.0 OD2 B:ASP104 2.4 6.3 1.0 OE2 B:GLU95 2.4 6.5 1.0 OE1 B:GLU95 2.4 6.7 1.0 O3 B:MMA201 2.5 7.2 1.0 O4 B:MMA201 2.6 6.8 1.0 OD1 B:ASP104 2.6 6.1 1.0 CD B:GLU95 2.8 6.6 1.0 CG B:ASP104 2.8 5.8 1.0 CG B:ASP99 3.4 8.6 1.0 CG B:ASP101 3.4 7.2 1.0 C4 B:MMA201 3.4 7.5 1.0 C3 B:MMA201 3.5 7.5 1.0 CA B:CA200 3.7 6.8 1.0 OD2 B:ASP99 3.7 8.5 1.0 OD2 B:ASP101 3.9 7.3 1.0 O B:HOH2139 4.0 7.6 1.0 OD1 B:ASP96 4.1 7.1 1.0 N B:ASP101 4.2 8.3 1.0 CG B:GLU95 4.3 6.4 1.0 CB B:ASP104 4.4 5.4 1.0 N B:TYR102 4.4 6.7 1.0 N B:ASN100 4.5 9.7 1.0 CB B:ASP101 4.6 7.3 1.0 N B:ASP96 4.6 6.3 1.0 N B:GLY97 4.6 6.9 1.0 OD1 B:ASN103 4.6 5.9 1.0 C2 B:MMA201 4.7 7.5 1.0 CA B:ASP101 4.7 7.8 1.0 CA B:GLU95 4.7 6.2 1.0 CB B:ASP99 4.7 8.7 1.0 N B:ASP99 4.8 9.0 1.0 O2 B:MMA201 4.8 7.1 1.0 C5 B:MMA201 4.9 7.7 1.0 CA B:GLY97 4.9 6.7 1.0 CB B:GLU95 4.9 6.3 1.0 CG B:ASP96 5.0 6.9 1.0 C B:ASP101 5.0 7.0 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom


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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca200 b:6.8 occ:1.00 OD1 B:ASN103 2.2 5.9 1.0 OD1 B:ASP104 2.4 6.1 1.0 O B:ASN21 2.4 4.8 1.0 O A:GLY114 2.4 6.2 1.0 OD2 B:ASP101 2.4 7.3 1.0 O3 B:MMA201 2.5 7.2 1.0 O2 B:MMA201 2.6 7.1 1.0 OD1 B:ASP101 3.1 6.4 1.0 CG B:ASP101 3.1 7.2 1.0 CG B:ASN103 3.3 5.5 1.0 C A:GLY114 3.4 6.4 1.0 C2 B:MMA201 3.4 7.5 1.0 C3 B:MMA201 3.5 7.5 1.0 C B:ASN21 3.6 5.0 1.0 CG B:ASP104 3.6 5.8 1.0 OXT A:GLY114 3.6 7.0 1.0 ND2 B:ASN103 3.6 5.7 1.0 CA B:CA199 3.7 7.3 1.0 C4 B:MMA201 4.0 7.5 1.0 CB B:ASN21 4.1 5.0 1.0 CA B:ASP104 4.2 5.2 1.0 N B:ASP104 4.3 5.0 1.0 OD2 B:ASP99 4.4 8.5 1.0 OD2 B:ASP104 4.4 6.3 1.0 O A:HOH2173 4.4 12.1 1.0 CA B:SER22 4.4 5.5 1.0 N B:SER22 4.4 5.0 1.0 C B:ASN103 4.4 5.2 1.0 CB B:ASP104 4.5 5.4 1.0 CA B:ASN21 4.5 4.9 1.0 O4 B:MMA201 4.5 6.8 1.0 CB B:ASP101 4.5 7.3 1.0 CB B:ASN103 4.6 5.4 1.0 O B:HOH2142 4.7 20.9 1.0 CB B:SER22 4.7 5.5 1.0 CA A:GLY114 4.8 6.6 1.0 C1 B:MMA201 4.8 7.5 1.0 O B:ASN103 4.8 5.1 1.0 N B:ASN103 4.9 5.8 1.0 OD1 B:ASP99 4.9 8.2 1.0 CA B:ASN103 4.9 5.3 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom


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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca199 b:7.2 occ:1.00 OD1 C:ASP101 2.3 7.1 1.0 OD1 C:ASP99 2.4 9.3 1.0 OD2 C:ASP104 2.4 6.5 1.0 OE1 C:GLU95 2.5 7.8 1.0 O3 C:MMA201 2.5 7.8 1.0 OD1 C:ASP104 2.5 6.2 1.0 OE2 C:GLU95 2.6 7.5 1.0 O4 C:MMA201 2.6 7.9 1.0 CG C:ASP104 2.8 6.1 1.0 CD C:GLU95 2.9 7.2 1.0 C4 C:MMA201 3.3 8.2 1.0 CG C:ASP101 3.4 7.7 1.0 C3 C:MMA201 3.4 8.4 1.0 CG C:ASP99 3.4 10.2 1.0 CA C:CA200 3.6 6.6 1.0 OD2 C:ASP99 3.7 9.1 1.0 OD2 C:ASP101 3.9 7.8 1.0 OD1 C:ASP96 4.0 7.7 1.0 N C:ASP101 4.0 9.6 1.0 O C:HOH2150 4.0 11.0 1.0 CB C:ASP104 4.3 5.7 1.0 CG C:GLU95 4.4 7.1 1.0 N C:TYR102 4.4 7.8 1.0 CB C:ASP101 4.5 8.0 1.0 N C:ASN100 4.5 10.0 1.0 N C:ASP96 4.6 7.2 1.0 CA C:ASP101 4.6 8.3 1.0 OD1 C:ASN103 4.7 6.4 1.0 N C:ASP99 4.7 10.7 1.0 N C:GLY97 4.7 9.4 1.0 CB C:ASP99 4.7 10.4 1.0 C5 C:MMA201 4.8 8.3 1.0 C2 C:MMA201 4.8 8.1 1.0 CA C:GLU95 4.8 6.8 1.0 O2 C:MMA201 4.8 7.9 1.0 CG C:ASP96 4.9 7.7 1.0 C C:ASP101 4.9 8.0 1.0 C C:ASP99 5.0 10.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom


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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca200 b:6.6 occ:1.00 OD1 C:ASN103 2.3 6.4 1.0 OD2 C:ASP101 2.4 7.8 1.0 OD1 C:ASP104 2.4 6.2 1.0 O C:ASN21 2.4 6.8 1.0 O D:GLY114 2.4 7.3 1.0 O3 C:MMA201 2.5 7.8 1.0 O2 C:MMA201 2.6 7.9 1.0 OD1 C:ASP101 3.0 7.1 1.0 CG C:ASP101 3.1 7.7 1.0 C3 C:MMA201 3.2 8.4 1.0 CG C:ASN103 3.3 6.3 1.0 C D:GLY114 3.5 7.9 1.0 C2 C:MMA201 3.5 8.1 1.0 C C:ASN21 3.6 7.1 1.0 CG C:ASP104 3.6 6.1 1.0 CA C:CA199 3.6 7.2 1.0 ND2 C:ASN103 3.7 6.2 1.0 OXT D:GLY114 3.7 7.7 1.0 C4 C:MMA201 3.8 8.2 1.0 CB C:ASN21 4.1 6.5 1.0 CA C:ASP104 4.2 5.6 1.0 N C:ASP104 4.3 5.5 1.0 O C:HOH2159 4.4 13.3 1.0 OD2 C:ASP104 4.4 6.5 1.0 CB C:ASP104 4.4 5.7 1.0 C C:ASN103 4.4 5.7 1.0 CB C:ASP101 4.5 8.0 1.0 N C:SER22 4.5 7.5 1.0 O4 C:MMA201 4.5 7.9 1.0 CA C:SER22 4.5 8.3 1.0 CA C:ASN21 4.5 6.4 1.0 OD2 C:ASP99 4.5 9.1 1.0 O C:HOH2155 4.6 28.9 1.0 CB C:ASN103 4.7 6.0 1.0 CB C:SER22 4.8 8.3 1.0 O C:ASN103 4.8 5.2 1.0 C1 C:MMA201 4.8 8.5 1.0 CA D:GLY114 4.8 7.5 1.0 N C:ASN103 4.9 6.5 1.0 CA C:ASN103 4.9 6.1 1.0 OD1 C:ASP99 4.9 9.3 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom


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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca199 b:7.3 occ:1.00 OD1 D:ASP101 2.3 7.3 1.0 OD1 D:ASP99 2.3 7.8 1.0 OE2 D:GLU95 2.4 7.6 1.0 OD2 D:ASP104 2.5 5.1 1.0 OE1 D:GLU95 2.5 6.9 1.0 OD1 D:ASP104 2.6 5.7 1.0 O3 D:MMA201 2.6 7.5 1.0 O4 D:MMA201 2.6 8.4 1.0 CD D:GLU95 2.7 7.1 1.0 CG D:ASP104 2.9 5.3 1.0 CG D:ASP99 3.4 8.2 1.0 CG D:ASP101 3.4 7.9 1.0 C4 D:MMA201 3.4 8.2 1.0 C3 D:MMA201 3.4 8.3 1.0 CA D:CA200 3.7 6.2 1.0 OD2 D:ASP99 3.7 8.2 1.0 O D:HOH2115 3.9 11.4 1.0 OD2 D:ASP101 3.9 7.8 1.0 N D:ASP101 4.0 7.9 1.0 OD1 D:ASP96 4.0 7.7 1.0 CG D:GLU95 4.3 6.7 1.0 N D:TYR102 4.3 7.1 1.0 CB D:ASP104 4.4 5.3 1.0 N D:ASN100 4.4 9.2 1.0 CB D:ASP101 4.5 7.5 1.0 CA D:ASP101 4.6 7.6 1.0 N D:ASP96 4.6 6.8 1.0 OD1 D:ASN103 4.6 6.7 1.0 N D:GLY97 4.7 7.9 1.0 CB D:ASP99 4.7 8.5 1.0 C2 D:MMA201 4.7 8.2 1.0 CA D:GLU95 4.7 6.5 1.0 N D:ASP99 4.8 9.5 1.0 O2 D:MMA201 4.8 8.0 1.0 C5 D:MMA201 4.9 9.0 1.0 C D:ASP99 4.9 8.9 1.0 C D:ASP101 4.9 7.3 1.0 CG D:ASP96 4.9 8.0 1.0 CB D:GLU95 4.9 6.6 1.0 CA D:ASP99 4.9 8.8 1.0 C D:ASN100 5.0 8.6 1.0 CA D:ASN100 5.0 9.1 1.0 CA D:GLY97 5.0 8.6 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of the Lecb Lectin From Pseudomonas Aeruginosa in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom


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 in Complex with Methyl 6-(Cinnamido)-6-Deoxy- Alpha-D-Mannopyranoside at 1.6 Ansgtrom within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca200 b:6.2 occ:1.00 OD1 D:ASN103 2.3 6.7 1.0 O D:ASN21 2.3 5.8 1.0 OD1 D:ASP104 2.3 5.7 1.0 O3 D:MMA201 2.4 7.5 1.0 OD2 D:ASP101 2.5 7.8 1.0 O C:GLY114 2.5 6.8 1.0 O2 D:MMA201 2.5 8.0 1.0 OD1 D:ASP101 3.0 7.3 1.0 CG D:ASP101 3.1 7.9 1.0 CG D:ASN103 3.4 6.7 1.0 C3 D:MMA201 3.4 8.3 1.0 C2 D:MMA201 3.4 8.2 1.0 C C:GLY114 3.5 6.9 1.0 C D:ASN21 3.5 6.4 1.0 CG D:ASP104 3.6 5.3 1.0 CA D:CA199 3.7 7.3 1.0 OXT C:GLY114 3.8 7.6 1.0 ND2 D:ASN103 3.8 6.9 1.0 C4 D:MMA201 3.9 8.2 1.0 CA D:ASP104 4.1 5.3 1.0 CB D:ASN21 4.1 6.2 1.0 N D:ASP104 4.2 5.6 1.0 CA D:SER22 4.4 7.3 1.0 N D:SER22 4.4 6.7 1.0 OD2 D:ASP104 4.4 5.1 1.0 C D:ASN103 4.4 5.8 1.0 CB D:ASP104 4.4 5.3 1.0 O4 D:MMA201 4.4 8.4 1.0 O C:HOH2162 4.4 16.5 1.0 CA D:ASN21 4.5 6.3 1.0 CB D:ASP101 4.5 7.5 1.0 OD2 D:ASP99 4.6 8.2 1.0 CB D:ASN103 4.7 6.5 1.0 O D:ASN103 4.7 5.5 1.0 CB D:SER22 4.8 7.5 1.0 C1 D:MMA201 4.8 8.6 1.0 N D:ASN103 4.8 6.4 1.0 CA C:GLY114 4.9 6.7 1.0 CA D:ASN103 4.9 6.1 1.0 OD1 D:ASP99 4.9 7.8 1.0

R.Sommer, D.Hauck, A.Varrot, S.Wagner, A.Audfray, A.Prestel, H.M.Moleer, A.Imberty, A.Titz. Cinnamide Derivatives of D-Mannose As Inhibitors of the Bacterial Virulence Factor Lecb From Pseudomonas Aeruginosa Chemistryopen V. 4 756 2015.
ISSN: ISSN 2191-1363
PubMed: 27308201
DOI: 10.1002/OPEN.201500162