Calcium in PDB 5a6q: Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14

The structure of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14, PDB code: 5a6q 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)	41.42 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.948, 49.591, 75.473, 90.00, 93.37, 90.00
R / Rfree (%)	15.7 / 19.7

The binding sites of Calcium atom in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 (pdb code 5a6q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14, PDB code: 5a6q:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca199 b:12.8 occ:1.00 OD1 A:ASP101 2.3 13.8 1.0 OD2 A:ASP104 2.4 8.2 1.0 OD1 A:ASP99 2.4 20.0 1.0 OE2 A:GLU95 2.4 11.0 1.0 OE1 A:GLU95 2.5 10.9 1.0 O1 A:GOL201 2.5 17.2 1.0 O2 A:GOL201 2.5 19.0 1.0 OD1 A:ASP104 2.7 9.7 1.0 CD A:GLU95 2.8 11.0 1.0 CG A:ASP104 2.9 7.8 1.0 CG A:ASP101 3.4 14.4 1.0 C1 A:GOL201 3.4 17.2 1.0 CG A:ASP99 3.4 20.3 1.0 C2 A:GOL201 3.4 17.3 1.0 CA A:CA200 3.7 13.4 1.0 OD2 A:ASP99 3.8 20.3 1.0 OD2 A:ASP101 4.0 13.0 1.0 CG A:GLU95 4.3 9.5 1.0 N A:ASP101 4.3 13.3 1.0 OD1 A:ASP96 4.3 11.9 1.0 CB A:ASP104 4.4 7.3 1.0 N A:TYR102 4.5 9.1 1.0 N A:ASP96 4.5 9.9 1.0 N A:ASN100 4.5 16.3 1.0 CB A:ASP101 4.6 13.6 1.0 OD1 A:ASN103 4.6 8.9 1.0 CA A:GLU95 4.6 8.2 1.0 N A:SER97 4.6 13.9 1.0 C3 A:GOL201 4.7 16.5 1.0 CB A:ASP99 4.7 19.0 1.0 N A:ASP99 4.7 17.2 1.0 CA A:ASP101 4.8 13.0 1.0 CB A:SER97 4.9 18.1 1.0 O3 A:GOL201 4.9 15.1 1.0 CB A:GLU95 4.9 8.8 1.0 N A:ASP104 5.0 6.6 1.0

Calcium binding site 2 out of 8 in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca200 b:13.4 occ:1.00 OD1 A:ASN103 2.3 8.9 1.0 OD1 A:ASP104 2.4 9.7 1.0 O3 A:GOL201 2.4 15.1 1.0 O2 A:GOL201 2.4 19.0 1.0 O A:ASN21 2.4 9.2 1.0 O B:GLY114 2.5 10.3 1.0 OD2 A:ASP101 2.5 13.0 1.0 OD1 A:ASP101 3.1 13.8 1.0 CG A:ASP101 3.1 14.4 1.0 C3 A:GOL201 3.2 16.5 1.0 C2 A:GOL201 3.3 17.3 1.0 CG A:ASN103 3.4 8.6 1.0 C B:GLY114 3.5 9.3 1.0 CG A:ASP104 3.6 7.8 1.0 C A:ASN21 3.6 7.8 1.0 OXT B:GLY114 3.7 10.8 1.0 CA A:CA199 3.7 12.8 1.0 C1 A:GOL201 3.8 17.2 1.0 ND2 A:ASN103 3.8 9.2 1.0 CB A:ASN21 4.2 6.7 1.0 CA A:ASP104 4.2 6.5 1.0 N A:ASP104 4.2 6.6 1.0 O1 A:GOL201 4.3 17.2 1.0 O A:HOH2169 4.4 22.9 1.0 OD2 A:ASP104 4.4 8.2 1.0 C A:ASN103 4.4 6.8 1.0 CB A:ASP104 4.5 7.3 1.0 CA A:SER22 4.5 8.8 1.0 N A:SER22 4.5 8.6 1.0 OD2 A:ASP99 4.6 20.3 1.0 CB A:ASP101 4.6 13.6 1.0 CA A:ASN21 4.6 6.9 1.0 CB A:ASN103 4.7 7.8 1.0 CB A:SER22 4.7 8.9 1.0 O A:ASN103 4.8 6.5 1.0 CA B:GLY114 4.8 8.6 1.0 CA A:ASN103 4.9 7.0 1.0 N A:ASN103 4.9 7.4 1.0 OD1 A:ASP99 5.0 20.0 1.0

Calcium binding site 3 out of 8 in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca199 b:14.5 occ:1.00 OD1 B:ASP101 2.3 13.4 1.0 OD2 B:ASP104 2.4 8.7 1.0 OD1 B:ASP99 2.4 18.9 1.0 OE2 B:GLU95 2.4 12.8 1.0 O2 B:GOL201 2.4 16.8 1.0 OE1 B:GLU95 2.5 10.1 1.0 O1 B:GOL201 2.5 14.5 1.0 OD1 B:ASP104 2.7 9.4 1.0 CD B:GLU95 2.8 10.8 1.0 CG B:ASP104 2.9 7.7 1.0 C1 B:GOL201 3.4 13.9 1.0 CG B:ASP101 3.4 15.0 1.0 CG B:ASP99 3.4 17.5 1.0 C2 B:GOL201 3.4 15.1 1.0 OD2 B:ASP99 3.7 15.5 1.0 CA B:CA200 3.7 12.4 1.0 OD2 B:ASP101 4.0 12.4 1.0 N B:ASP101 4.2 13.7 1.0 CG B:GLU95 4.3 9.8 1.0 OD1 B:ASP96 4.3 13.7 1.0 CB B:ASP104 4.4 7.0 1.0 N B:TYR102 4.5 9.0 1.0 N B:ASN100 4.5 18.2 1.0 N B:ASP96 4.5 10.2 1.0 CB B:ASP101 4.6 12.7 1.0 OD1 B:ASN103 4.6 8.0 1.0 C3 B:GOL201 4.6 14.3 1.0 CA B:GLU95 4.7 8.2 1.0 N B:SER97 4.7 16.0 1.0 CA B:ASP101 4.7 12.4 1.0 CB B:ASP99 4.7 18.1 1.0 N B:ASP99 4.8 17.7 1.0 O3 B:GOL201 4.9 12.9 1.0 CB B:GLU95 4.9 9.2 1.0 CB B:SER97 4.9 18.7 1.0

Calcium binding site 4 out of 8 in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca200 b:12.4 occ:1.00 OD1 B:ASP104 2.3 9.4 1.0 OD1 B:ASN103 2.3 8.0 1.0 O B:ASN21 2.4 8.0 1.0 O3 B:GOL201 2.4 12.9 1.0 OD2 B:ASP101 2.5 12.4 1.0 O A:GLY114 2.6 10.8 1.0 O2 B:GOL201 2.6 16.8 1.0 OD1 B:ASP101 3.0 13.4 1.0 CG B:ASP101 3.1 15.0 1.0 C3 B:GOL201 3.3 14.3 1.0 C2 B:GOL201 3.4 15.1 1.0 CG B:ASN103 3.4 8.2 1.0 C A:GLY114 3.5 11.2 1.0 CG B:ASP104 3.6 7.7 1.0 C B:ASN21 3.6 7.8 1.0 CA B:CA199 3.7 14.5 1.0 OXT A:GLY114 3.8 13.1 1.0 ND2 B:ASN103 3.8 8.0 1.0 C1 B:GOL201 3.9 13.9 1.0 CA B:ASP104 4.2 7.0 1.0 CB B:ASN21 4.2 6.9 1.0 N B:ASP104 4.3 7.4 1.0 OD2 B:ASP104 4.4 8.7 1.0 O1 B:GOL201 4.4 14.5 1.0 O A:HOH2172 4.4 24.8 1.0 CB B:ASP104 4.4 7.0 1.0 C B:ASN103 4.5 7.5 1.0 CA B:SER22 4.5 8.2 1.0 N B:SER22 4.5 8.2 1.0 CB B:ASP101 4.6 12.7 1.0 OD2 B:ASP99 4.6 15.5 1.0 CA B:ASN21 4.6 6.8 1.0 CB B:SER22 4.7 8.5 1.0 CB B:ASN103 4.7 8.0 1.0 O B:ASN103 4.8 7.3 1.0 CA A:GLY114 4.9 10.0 1.0 N B:ASN103 4.9 7.4 1.0 CA B:ASN103 5.0 7.6 1.0

Calcium binding site 5 out of 8 in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca199 b:4.0 occ:1.00 OD1 C:ASP101 2.3 5.0 1.0 OE2 C:GLU95 2.4 3.6 1.0 OD1 C:ASP99 2.4 6.3 1.0 OD2 C:ASP104 2.4 3.5 1.0 OE1 C:GLU95 2.4 3.9 1.0 O1 C:GOL201 2.5 7.3 1.0 O2 C:GOL201 2.6 6.1 1.0 OD1 C:ASP104 2.7 3.7 1.0 CD C:GLU95 2.7 3.8 1.0 CG C:ASP104 2.9 3.6 1.0 C1 C:GOL201 3.3 6.3 1.0 C2 C:GOL201 3.4 6.4 1.0 CG C:ASP101 3.4 5.1 1.0 CG C:ASP99 3.4 6.8 1.0 CA C:CA200 3.7 4.8 1.0 OD2 C:ASP99 3.8 7.4 1.0 OD2 C:ASP101 4.0 5.4 1.0 O C:HOH2154 4.1 4.1 0.5 CG C:GLU95 4.2 3.9 1.0 N C:ASP101 4.2 5.2 1.0 OD1 C:ASP96 4.3 4.1 1.0 N C:ASP96 4.4 3.8 1.0 CB C:ASP104 4.4 3.6 1.0 N C:TYR102 4.4 5.3 1.0 N C:ASN100 4.6 6.3 1.0 CB C:ASP101 4.6 5.2 1.0 CA C:GLU95 4.6 3.6 1.0 OD1 C:ASN103 4.6 4.1 1.0 N C:SER97 4.6 4.7 1.0 N C:ASP99 4.7 6.3 1.0 CB C:ASP99 4.7 6.6 1.0 CA C:ASP101 4.7 5.4 1.0 C3 C:GOL201 4.8 6.4 1.0 CB C:GLU95 4.8 3.7 1.0 O3 C:GOL201 4.9 6.3 1.0 CA C:ASP99 5.0 6.5 1.0 CB C:SER97 5.0 6.0 1.0 C C:ASP99 5.0 6.7 1.0 CG C:ASP96 5.0 4.3 1.0

Calcium binding site 6 out of 8 in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca200 b:4.8 occ:1.00 OD1 C:ASP104 2.3 3.7 1.0 OD1 C:ASN103 2.4 4.1 1.0 O C:ASN21 2.4 3.6 1.0 O D:GLY114 2.4 4.7 1.0 O2 C:GOL201 2.4 6.1 1.0 OD2 C:ASP101 2.5 5.4 1.0 O3 C:GOL201 2.5 6.3 1.0 OD1 C:ASP101 3.1 5.0 1.0 CG C:ASP101 3.2 5.1 1.0 C2 C:GOL201 3.3 6.4 1.0 C D:GLY114 3.4 5.5 1.0 CG C:ASN103 3.4 3.9 1.0 C3 C:GOL201 3.4 6.4 1.0 CG C:ASP104 3.6 3.6 1.0 C C:ASN21 3.6 3.6 1.0 OXT D:GLY114 3.6 6.3 1.0 C1 C:GOL201 3.7 6.3 1.0 CA C:CA199 3.7 4.0 1.0 ND2 C:ASN103 3.8 4.0 1.0 CB C:ASN21 4.1 3.3 1.0 CA C:ASP104 4.2 3.6 1.0 N C:ASP104 4.2 3.6 1.0 OD2 C:ASP104 4.4 3.5 1.0 O C:HOH2165 4.4 15.4 1.0 O1 C:GOL201 4.4 7.3 1.0 C C:ASN103 4.4 3.8 1.0 CB C:ASP104 4.4 3.6 1.0 N C:SER22 4.5 3.7 1.0 CA C:SER22 4.5 3.8 1.0 CA C:ASN21 4.6 3.4 1.0 OD2 C:ASP99 4.6 7.4 1.0 CB C:ASP101 4.6 5.2 1.0 CB C:SER22 4.7 3.9 1.0 CB C:ASN103 4.7 3.9 1.0 CA D:GLY114 4.8 5.3 1.0 O C:ASN103 4.8 4.1 1.0 N C:ASN103 4.9 4.0 1.0 CA C:ASN103 4.9 3.9 1.0 OD1 C:ASP99 4.9 6.3 1.0

Calcium binding site 7 out of 8 in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca199 b:5.4 occ:1.00 OD1 D:ASP101 2.4 5.3 1.0 O2 D:GOL201 2.4 6.5 1.0 OE2 D:GLU95 2.4 3.0 1.0 OD1 D:ASP99 2.4 6.6 1.0 OD2 D:ASP104 2.4 3.2 1.0 OE1 D:GLU95 2.4 3.3 1.0 O3 D:GOL201 2.5 6.8 1.0 OD1 D:ASP104 2.7 3.7 1.0 CD D:GLU95 2.7 3.2 1.0 CG D:ASP104 2.9 3.3 1.0 C2 D:GOL201 3.3 6.6 1.0 C3 D:GOL201 3.3 6.5 1.0 CG D:ASP101 3.4 5.5 1.0 CG D:ASP99 3.4 6.6 1.0 CA D:CA200 3.8 5.0 1.0 OD2 D:ASP99 3.8 6.7 1.0 OD2 D:ASP101 4.0 5.6 1.0 N D:ASP101 4.2 6.2 1.0 CG D:GLU95 4.2 3.3 1.0 O D:HOH2141 4.2 14.3 1.0 OD1 D:ASP96 4.3 5.0 1.0 CB D:ASP104 4.4 3.4 1.0 N D:ASP96 4.4 3.9 1.0 N D:TYR102 4.5 4.8 1.0 CB D:ASP101 4.6 5.4 1.0 N D:ASN100 4.6 7.6 1.0 OD1 D:ASN103 4.6 3.5 1.0 CA D:GLU95 4.6 3.3 1.0 N D:SER97 4.7 4.8 1.0 C1 D:GOL201 4.7 6.4 1.0 CB D:ASP99 4.7 6.8 1.0 N D:ASP99 4.7 6.1 1.0 CA D:ASP101 4.7 5.6 1.0 CB D:GLU95 4.9 3.2 1.0 O1 D:GOL201 4.9 6.4 1.0 N D:ASP104 5.0 3.5 1.0 CA D:ASP99 5.0 6.7 1.0

Calcium binding site 8 out of 8 in the Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Native Structure of the Lecb Lectin From Pseudomonas Aeruginosa Strain PA14 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca200 b:5.0 occ:1.00 OD1 D:ASN103 2.3 3.5 1.0 O D:ASN21 2.4 4.3 1.0 OD1 D:ASP104 2.4 3.7 1.0 O C:GLY114 2.4 5.0 1.0 OD2 D:ASP101 2.5 5.6 1.0 O2 D:GOL201 2.5 6.5 1.0 O1 D:GOL201 2.5 6.4 1.0 OD1 D:ASP101 3.1 5.3 1.0 CG D:ASP101 3.1 5.5 1.0 C2 D:GOL201 3.4 6.6 1.0 CG D:ASN103 3.4 3.8 1.0 C C:GLY114 3.4 5.3 1.0 C1 D:GOL201 3.4 6.4 1.0 C D:ASN21 3.6 4.3 1.0 CG D:ASP104 3.6 3.3 1.0 OXT C:GLY114 3.6 5.8 1.0 CA D:CA199 3.8 5.4 1.0 ND2 D:ASN103 3.8 3.7 1.0 C3 D:GOL201 3.9 6.5 1.0 CB D:ASN21 4.1 4.0 1.0 CA D:ASP104 4.2 3.4 1.0 N D:ASP104 4.2 3.5 1.0 O C:HOH2167 4.4 19.3 1.0 OD2 D:ASP104 4.4 3.2 1.0 O3 D:GOL201 4.4 6.8 1.0 C D:ASN103 4.4 3.5 1.0 CB D:ASP104 4.5 3.4 1.0 N D:SER22 4.5 4.3 1.0 CA D:SER22 4.5 4.6 1.0 CA D:ASN21 4.5 4.0 1.0 CB D:ASP101 4.6 5.4 1.0 OD2 D:ASP99 4.6 6.7 1.0 CB D:SER22 4.7 4.6 1.0 CB D:ASN103 4.7 3.6 1.0 CA C:GLY114 4.8 5.1 1.0 O D:ASN103 4.8 4.2 1.0 N D:ASN103 4.9 3.7 1.0 CA D:ASN103 4.9 3.7 1.0 OD1 D:ASP99 5.0 6.6 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