Calcium in PDB 5a6y: Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE

The structure of Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE, PDB code: 5a6y was solved by R.Sommer, S.Wagner, A.Varrot, A.Khaledi, S.Haussler, A.Imberty, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.52 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.979, 49.779, 75.438, 90.00, 93.34, 90.00
R / Rfree (%)	12.2 / 16.3

The binding sites of Calcium atom in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE (pdb code 5a6y). 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 Mannose-ALPHA1,3MANNOSIDE, PDB code: 5a6y:
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 Mannose-ALPHA1,3MANNOSIDE


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 Mannose-ALPHA1,3MANNOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca199 b:9.3 occ:1.00 OD1 A:ASP101 2.4 8.5 1.0 OD1 A:ASP99 2.4 14.0 1.0 OE2 A:GLU95 2.4 9.8 1.0 OD2 A:ASP104 2.4 7.9 1.0 O3 A:GOL203 2.4 10.5 0.5 O2 A:GOL203 2.5 9.9 0.5 OE1 A:GLU95 2.5 9.0 1.0 O3 A:MAN202 2.5 10.3 0.5 O4 A:MAN202 2.5 13.8 0.5 OD1 A:ASP104 2.6 7.3 1.0 CD A:GLU95 2.8 8.7 1.0 CG A:ASP104 2.9 7.8 1.0 C3 A:GOL203 3.3 13.5 0.5 C2 A:GOL203 3.4 12.7 0.5 CG A:ASP99 3.4 13.3 1.0 CG A:ASP101 3.4 9.4 1.0 C3 A:MAN202 3.4 13.2 0.5 C4 A:MAN202 3.4 15.2 0.5 CA A:CA200 3.7 8.5 1.0 OD2 A:ASP99 3.7 13.4 1.0 OD2 A:ASP101 4.0 9.2 1.0 OD1 A:ASP96 4.1 11.8 1.0 N A:ASP101 4.2 10.5 1.0 CG A:GLU95 4.3 8.2 1.0 CB A:ASP104 4.4 7.8 1.0 N A:TYR102 4.5 8.6 1.0 N A:ASP96 4.5 9.0 1.0 CB A:ASP101 4.6 11.2 1.0 N A:ASN100 4.6 13.9 1.0 N A:SER97 4.6 11.6 1.0 CA A:GLU95 4.7 8.5 1.0 C1 A:GOL203 4.7 13.3 0.5 CA A:ASP101 4.7 10.6 1.0 OD1 A:ASN103 4.7 7.5 1.0 N A:ASP99 4.7 13.6 1.0 C2 A:MAN202 4.8 13.6 0.5 CB A:ASP99 4.8 13.9 1.0 O1 A:GOL203 4.8 11.9 0.5 O2 A:MAN202 4.8 10.9 0.5 CB A:SER97 4.9 15.2 1.0 C5 A:MAN202 4.9 16.3 0.5 O A:HOH2163 4.9 30.1 1.0 CB A:GLU95 4.9 8.3 1.0 CG A:ASP96 5.0 9.0 1.0

Calcium binding site 2 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE


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 Mannose-ALPHA1,3MANNOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca200 b:8.5 occ:1.00 OD1 A:ASP104 2.3 7.3 1.0 OD1 A:ASN103 2.3 7.5 1.0 O A:ASN21 2.4 8.0 1.0 O3 A:MAN202 2.4 10.3 0.5 O B:GLY114 2.4 8.7 1.0 O2 A:GOL203 2.4 9.9 0.5 O2 A:MAN202 2.4 10.9 0.5 OD2 A:ASP101 2.5 9.2 1.0 O1 A:GOL203 2.5 11.9 0.5 OD1 A:ASP101 3.1 8.5 1.0 CG A:ASP101 3.1 9.4 1.0 C3 A:MAN202 3.3 13.2 0.5 C2 A:GOL203 3.4 12.7 0.5 C1 A:GOL203 3.4 13.3 0.5 CG A:ASN103 3.4 7.1 1.0 C2 A:MAN202 3.4 13.6 0.5 C B:GLY114 3.4 9.3 1.0 CG A:ASP104 3.6 7.8 1.0 C A:ASN21 3.6 8.2 1.0 OXT B:GLY114 3.7 11.8 1.0 CA A:CA199 3.7 9.3 1.0 ND2 A:ASN103 3.8 7.1 1.0 C3 A:GOL203 3.8 13.5 0.5 C4 A:MAN202 3.9 15.2 0.5 CB A:ASN21 4.2 7.0 1.0 CA A:ASP104 4.2 6.8 1.0 N A:ASP104 4.3 6.7 1.0 O3 A:GOL203 4.4 10.5 0.5 O A:HOH2170 4.4 10.3 0.5 O4 A:MAN202 4.4 13.8 0.5 OD2 A:ASP104 4.4 7.9 1.0 CB A:ASP104 4.4 7.8 1.0 N A:SER22 4.4 9.4 1.0 CA A:SER22 4.5 9.8 1.0 C A:ASN103 4.5 6.1 1.0 CA A:ASN21 4.5 7.3 1.0 OD2 A:ASP99 4.5 13.4 1.0 CB A:ASP101 4.6 11.2 1.0 CB A:SER22 4.7 10.5 1.0 CB A:ASN103 4.7 6.2 1.0 C1 A:MAN202 4.7 16.6 0.5 CA B:GLY114 4.8 8.5 1.0 O A:ASN103 4.8 7.1 1.0 N A:ASN103 4.9 6.4 1.0 CA A:ASN103 4.9 5.9 1.0 O A:HOH2168 5.0 11.6 0.4 OD1 A:ASP99 5.0 14.0 1.0

Calcium binding site 3 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE


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 Mannose-ALPHA1,3MANNOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca199 b:9.4 occ:1.00 OD1 B:ASP101 2.3 9.2 1.0 OD1 B:ASP99 2.4 14.6 1.0 OE2 B:GLU95 2.4 9.4 1.0 OD2 B:ASP104 2.4 7.1 1.0 O4 B:MAN202 2.5 10.8 1.0 OE1 B:GLU95 2.5 8.6 1.0 O3 B:MAN202 2.5 9.5 1.0 OD1 B:ASP104 2.7 8.2 1.0 CD B:GLU95 2.8 8.6 1.0 CG B:ASP104 2.9 7.2 1.0 C4 B:MAN202 3.3 11.1 1.0 CG B:ASP99 3.4 12.6 1.0 CG B:ASP101 3.4 8.8 1.0 C3 B:MAN202 3.4 10.2 1.0 OD2 B:ASP99 3.7 12.7 1.0 CA B:CA200 3.8 8.6 1.0 OD2 B:ASP101 4.0 10.2 1.0 O B:HOH2167 4.0 26.2 1.0 OD1 B:ASP96 4.1 12.0 1.0 N B:ASP101 4.2 11.1 1.0 CG B:GLU95 4.2 8.0 1.0 CB B:ASP104 4.4 6.6 1.0 N B:TYR102 4.5 8.2 1.0 N B:ASP96 4.5 8.8 1.0 CB B:ASP101 4.5 10.0 1.0 N B:ASN100 4.5 13.1 1.0 CA B:GLU95 4.7 7.2 1.0 CA B:ASP101 4.7 9.9 1.0 CB B:ASP99 4.7 13.6 1.0 N B:SER97 4.7 11.5 1.0 OD1 B:ASN103 4.7 8.2 1.0 C2 B:MAN202 4.7 10.2 1.0 N B:ASP99 4.8 12.9 1.0 C5 B:MAN202 4.8 13.4 1.0 O2 B:MAN202 4.9 9.0 1.0 CB B:GLU95 4.9 8.0 1.0 CG B:ASP96 4.9 9.5 1.0 C B:ASP101 5.0 9.0 1.0

Calcium binding site 4 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE


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 Mannose-ALPHA1,3MANNOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca200 b:8.6 occ:1.00 OD1 B:ASN103 2.3 8.2 1.0 OD1 B:ASP104 2.4 8.2 1.0 O B:ASN21 2.4 8.6 1.0 O A:GLY114 2.4 9.6 1.0 OD2 B:ASP101 2.4 10.2 1.0 O3 B:MAN202 2.5 9.5 1.0 O2 B:MAN202 2.5 9.0 1.0 OD1 B:ASP101 3.1 9.2 1.0 CG B:ASP101 3.1 8.8 1.0 CG B:ASN103 3.4 7.3 1.0 C A:GLY114 3.4 11.9 1.0 C3 B:MAN202 3.4 10.2 1.0 C2 B:MAN202 3.4 10.2 1.0 C B:ASN21 3.6 8.0 1.0 CG B:ASP104 3.6 7.2 1.0 OXT A:GLY114 3.7 12.7 1.0 CA B:CA199 3.8 9.4 1.0 ND2 B:ASN103 3.8 8.0 1.0 C4 B:MAN202 3.9 11.1 1.0 CB B:ASN21 4.2 7.7 1.0 CA B:ASP104 4.2 6.4 1.0 N B:ASP104 4.3 7.0 1.0 O4 B:MAN202 4.4 10.8 1.0 CA B:SER22 4.4 9.4 1.0 N B:SER22 4.4 8.3 1.0 OD2 B:ASP104 4.4 7.1 1.0 CB B:ASP104 4.4 6.6 1.0 O A:HOH2174 4.5 23.8 1.0 C B:ASN103 4.5 7.0 1.0 OD2 B:ASP99 4.6 12.7 1.0 CA B:ASN21 4.6 7.8 1.0 CB B:ASP101 4.6 10.0 1.0 CB B:SER22 4.7 9.7 1.0 CB B:ASN103 4.7 7.1 1.0 CA A:GLY114 4.8 10.0 1.0 O B:ASN103 4.8 6.4 1.0 C1 B:MAN202 4.8 13.2 1.0 N B:ASN103 4.9 6.3 1.0 CA B:ASN103 4.9 7.0 1.0

Calcium binding site 5 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE


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 Mannose-ALPHA1,3MANNOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca199 b:5.4 occ:1.00 OD1 C:ASP99 2.3 9.2 1.0 OD1 C:ASP101 2.3 6.1 1.0 OE2 C:GLU95 2.4 4.9 1.0 OD2 C:ASP104 2.4 4.8 1.0 OE1 C:GLU95 2.5 5.6 1.0 O4 C:MAN202 2.5 6.6 1.0 O3 C:MAN202 2.5 5.9 1.0 OD1 C:ASP104 2.7 5.0 1.0 CD C:GLU95 2.8 6.0 1.0 CG C:ASP104 2.9 4.4 1.0 C4 C:MAN202 3.3 6.6 1.0 CG C:ASP99 3.4 7.2 1.0 C3 C:MAN202 3.4 7.1 1.0 CG C:ASP101 3.4 5.8 1.0 OD2 C:ASP99 3.7 7.1 1.0 CA C:CA200 3.7 5.2 1.0 OD2 C:ASP101 3.9 6.0 1.0 O C:HOH2159 4.0 14.7 1.0 OD1 C:ASP96 4.1 6.5 1.0 N C:ASP101 4.2 6.3 1.0 CG C:GLU95 4.3 5.3 1.0 CB C:ASP104 4.4 4.4 1.0 N C:TYR102 4.5 5.2 1.0 CB C:ASP101 4.5 6.4 1.0 N C:ASP96 4.5 5.1 1.0 N C:ASN100 4.6 7.1 1.0 CA C:GLU95 4.7 5.2 1.0 CA C:ASP101 4.7 6.2 1.0 OD1 C:ASN103 4.7 5.1 1.0 CB C:ASP99 4.7 7.6 1.0 N C:ASP99 4.7 7.4 1.0 N C:SER97 4.7 6.7 1.0 C2 C:MAN202 4.7 7.6 1.0 C5 C:MAN202 4.8 8.5 1.0 O2 C:MAN202 4.9 6.7 1.0 CG C:ASP96 4.9 6.6 1.0 CB C:GLU95 4.9 4.9 1.0 C C:ASP101 5.0 5.6 1.0 CA C:ASP99 5.0 7.5 1.0 C C:ASP99 5.0 7.6 1.0

Calcium binding site 6 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE


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 Mannose-ALPHA1,3MANNOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca200 b:5.2 occ:1.00 OD1 C:ASN103 2.3 5.1 1.0 OD1 C:ASP104 2.3 5.0 1.0 O C:ASN21 2.4 4.8 1.0 O D:GLY114 2.4 6.5 1.0 OD2 C:ASP101 2.4 6.0 1.0 O3 C:MAN202 2.4 5.9 1.0 O2 C:MAN202 2.5 6.7 1.0 OD1 C:ASP101 3.1 6.1 1.0 CG C:ASP101 3.1 5.8 1.0 C3 C:MAN202 3.4 7.1 1.0 C D:GLY114 3.4 6.8 1.0 CG C:ASN103 3.4 5.1 1.0 C2 C:MAN202 3.4 7.6 1.0 CG C:ASP104 3.6 4.4 1.0 C C:ASN21 3.6 5.3 1.0 OXT D:GLY114 3.6 8.5 1.0 CA C:CA199 3.7 5.4 1.0 ND2 C:ASN103 3.7 5.5 1.0 C4 C:MAN202 3.9 6.6 1.0 CB C:ASN21 4.2 5.3 1.0 CA C:ASP104 4.2 4.5 1.0 N C:ASP104 4.3 4.0 1.0 OD2 C:ASP104 4.4 4.8 1.0 CA C:SER22 4.4 5.9 1.0 O C:HOH2172 4.4 15.9 1.0 N C:SER22 4.4 5.5 1.0 CB C:ASP104 4.5 4.4 1.0 O4 C:MAN202 4.5 6.6 1.0 C C:ASN103 4.5 4.4 1.0 OD2 C:ASP99 4.5 7.1 1.0 CB C:ASP101 4.6 6.4 1.0 CA C:ASN21 4.6 5.4 1.0 CB C:SER22 4.7 6.0 1.0 CB C:ASN103 4.7 5.0 1.0 CA D:GLY114 4.7 5.8 1.0 C1 C:MAN202 4.8 9.9 1.0 O C:ASN103 4.8 5.2 1.0 N C:ASN103 4.9 4.6 1.0 CA C:ASN103 4.9 4.7 1.0 OD1 C:ASP99 4.9 9.2 1.0

Calcium binding site 7 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE


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 Mannose-ALPHA1,3MANNOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca199 b:5.7 occ:1.00 OD1 D:ASP99 2.3 10.0 1.0 OD1 D:ASP101 2.4 6.3 1.0 OE2 D:GLU95 2.4 4.4 1.0 OD2 D:ASP104 2.4 5.6 1.0 O3 D:MAN202 2.5 6.4 1.0 OE1 D:GLU95 2.5 6.0 1.0 O4 D:MAN202 2.5 7.6 1.0 OD1 D:ASP104 2.7 5.1 1.0 CD D:GLU95 2.8 5.4 1.0 CG D:ASP104 2.9 4.6 1.0 C4 D:MAN202 3.4 8.3 1.0 CG D:ASP99 3.4 8.3 1.0 C3 D:MAN202 3.4 8.3 1.0 CG D:ASP101 3.4 6.0 1.0 OD2 D:ASP99 3.7 8.5 1.0 CA D:CA200 3.7 5.6 1.0 OD2 D:ASP101 3.9 6.3 1.0 O D:HOH2128 4.1 16.6 1.0 OD1 D:ASP96 4.1 6.8 1.0 N D:ASP101 4.2 6.8 1.0 CG D:GLU95 4.3 5.3 1.0 CB D:ASP104 4.4 4.8 1.0 N D:TYR102 4.5 5.6 1.0 N D:ASP96 4.5 5.4 1.0 CB D:ASP101 4.5 6.7 1.0 N D:ASN100 4.6 7.8 1.0 CA D:ASP101 4.7 6.7 1.0 CB D:ASP99 4.7 8.3 1.0 CA D:GLU95 4.7 4.9 1.0 OD1 D:ASN103 4.7 5.4 1.0 N D:ASP99 4.7 7.3 1.0 C2 D:MAN202 4.7 8.5 1.0 N D:SER97 4.7 6.9 1.0 C5 D:MAN202 4.8 9.1 1.0 O2 D:MAN202 4.8 7.6 1.0 CB D:GLU95 4.9 5.1 1.0 CG D:ASP96 4.9 6.4 1.0 C D:ASP101 5.0 5.7 1.0

Calcium binding site 8 out of 8 in the Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 in Complex with Mannose-ALPHA1,3MANNOSIDE


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 Mannose-ALPHA1,3MANNOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca200 b:5.6 occ:1.00 OD1 D:ASN103 2.3 5.4 1.0 OD1 D:ASP104 2.4 5.1 1.0 O D:ASN21 2.4 5.7 1.0 OD2 D:ASP101 2.4 6.3 1.0 O C:GLY114 2.4 6.2 1.0 O3 D:MAN202 2.5 6.4 1.0 O2 D:MAN202 2.5 7.6 1.0 OD1 D:ASP101 3.1 6.3 1.0 CG D:ASP101 3.1 6.0 1.0 CG D:ASN103 3.4 5.2 1.0 C C:GLY114 3.4 7.7 1.0 C3 D:MAN202 3.4 8.3 1.0 C2 D:MAN202 3.4 8.5 1.0 C D:ASN21 3.5 5.5 1.0 CG D:ASP104 3.6 4.6 1.0 OXT C:GLY114 3.6 9.4 1.0 CA D:CA199 3.7 5.7 1.0 ND2 D:ASN103 3.8 5.8 1.0 C4 D:MAN202 3.9 8.3 1.0 CB D:ASN21 4.2 5.4 1.0 CA D:ASP104 4.2 4.8 1.0 N D:ASP104 4.3 4.8 1.0 CA D:SER22 4.4 6.3 1.0 N D:SER22 4.4 5.4 1.0 OD2 D:ASP104 4.4 5.6 1.0 O4 D:MAN202 4.4 7.6 1.0 C D:ASN103 4.5 4.4 1.0 CB D:ASP104 4.5 4.8 1.0 O C:HOH2174 4.5 19.7 1.0 CA D:ASN21 4.5 5.5 1.0 CB D:ASP101 4.6 6.7 1.0 OD2 D:ASP99 4.6 8.5 1.0 CB D:SER22 4.7 7.0 1.0 CB D:ASN103 4.7 4.7 1.0 O C:HOH2092 4.8 41.8 1.0 CA C:GLY114 4.8 6.7 1.0 C1 D:MAN202 4.8 9.0 1.0 O D:ASN103 4.8 5.0 1.0 N D:ASN103 4.9 5.1 1.0 CA D:ASN103 4.9 4.8 1.0 OD1 D:ASP99 5.0 10.0 1.0

R.Sommer, S.Wagner, A.Varrot, C.M.Nycholat, A.Khaledi, S.Haussler, J.C.Paulson, A.Imberty, A.Titz. The Virulence Factor Lecb Varies in Clinical Isolates: Consequences For Ligand Binding and Drug Discovery. Chem Sci V. 7 4990 2016.
ISSN: ISSN 2041-6520
PubMed: 30155149
DOI: 10.1039/C6SC00696E