Calcium in PDB 5mih: Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside

The structure of Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside, PDB code: 5mih was solved by S.Wagner, D.Hauk, M.Hofmann, I.Joachim, R.Sommer, R.Muller, A.Imberty, A.Varrot, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.30 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	27.343, 73.771, 101.454, 90.00, 93.36, 90.00
R / Rfree (%)	14.9 / 19.4

The binding sites of Calcium atom in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside (pdb code 5mih). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside, PDB code: 5mih:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside


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 Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca200 b:14.8 occ:1.00 O A:TYR36 2.3 14.7 1.0 O A:THR104 2.3 12.9 1.0 OD1 A:ASN108 2.4 15.5 1.0 OD2 A:ASP100 2.4 10.7 1.0 O3 A:7NU201 2.5 15.2 1.0 OD1 A:ASN107 2.5 18.8 1.0 O4 A:7NU201 2.5 17.2 1.0 C A:TYR36 3.4 16.5 1.0 C3 A:7NU201 3.4 16.3 1.0 CG A:ASP100 3.5 12.2 1.0 CG A:ASN108 3.5 14.5 1.0 C4 A:7NU201 3.5 16.2 1.0 C A:THR104 3.5 14.2 1.0 CG A:ASN107 3.5 17.1 1.0 OG1 A:THR104 3.7 14.9 1.0 OD1 A:ASP100 3.8 11.0 1.0 ND2 A:ASN107 3.9 15.0 1.0 CA A:TYR36 3.9 14.9 1.0 C2 A:7NU201 4.0 16.5 1.0 ND2 A:ASN108 4.0 13.7 1.0 CB A:THR104 4.0 16.4 1.0 CB A:TYR36 4.2 13.9 1.0 N A:TYR105 4.4 13.2 1.0 CA A:THR104 4.4 15.0 1.0 N A:GLY37 4.4 16.9 1.0 CA A:TYR105 4.4 14.6 1.0 O A:HOH304 4.5 22.8 1.0 N A:ASN108 4.6 15.9 1.0 CA A:GLY37 4.7 17.1 1.0 O2 A:7NU201 4.7 16.6 1.0 C A:TYR105 4.8 18.2 1.0 CB A:ASN108 4.8 15.3 1.0 C A:ASN107 4.8 15.8 1.0 C5 A:7NU201 4.8 16.1 1.0 N A:ASN107 4.8 15.1 1.0 CB A:ASP100 4.8 11.4 1.0 CB A:ASN107 4.9 16.2 1.0 O A:HOH419 4.9 24.0 1.0 CA A:ASN108 4.9 15.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside


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 Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca200 b:16.0 occ:1.00 O B:THR104 2.3 16.7 1.0 O B:TYR36 2.4 18.7 1.0 OD1 B:ASN108 2.4 14.3 1.0 O3 B:7NU201 2.4 14.5 1.0 OD2 B:ASP100 2.4 15.4 1.0 O4 B:7NU201 2.5 19.0 1.0 OD1 B:ASN107 2.5 17.5 1.0 C3 B:7NU201 3.2 18.7 1.0 C4 B:7NU201 3.3 20.1 1.0 C B:TYR36 3.4 14.5 1.0 C B:THR104 3.4 15.3 1.0 CG B:ASP100 3.5 16.2 1.0 CG B:ASN108 3.5 14.1 1.0 CG B:ASN107 3.6 18.3 1.0 OG1 B:THR104 3.6 18.1 1.0 OD1 B:ASP100 3.8 16.5 1.0 CB B:THR104 3.9 18.1 1.0 C2 B:7NU201 3.9 21.3 1.0 ND2 B:ASN108 3.9 14.7 1.0 ND2 B:ASN107 4.0 17.4 1.0 CA B:TYR36 4.0 12.4 1.0 CB B:TYR36 4.2 13.4 1.0 CA B:THR104 4.3 17.4 1.0 N B:TYR105 4.3 16.1 1.0 CA B:TYR105 4.4 15.0 1.0 O B:HOH305 4.4 28.2 1.0 N B:GLY37 4.5 15.7 1.0 N B:ASN108 4.6 13.5 1.0 O2 B:7NU201 4.6 22.8 1.0 C5 B:7NU201 4.7 18.0 1.0 C B:TYR105 4.7 16.4 1.0 CA B:GLY37 4.8 16.4 1.0 CB B:ASN108 4.8 13.5 1.0 C B:ASN107 4.8 14.7 1.0 CB B:ASP100 4.8 16.3 1.0 N B:ASN107 4.8 15.6 1.0 CB B:ASN107 4.9 16.6 1.0 CA B:ASN108 4.9 14.2 1.0 O B:TYR105 5.0 14.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside


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 Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca200 b:15.2 occ:1.00 O C:TYR36 2.3 13.2 1.0 O C:THR104 2.4 18.5 1.0 O4 C:7NU201 2.4 14.9 1.0 OD1 C:ASN108 2.4 13.4 1.0 OD1 C:ASN107 2.4 15.5 1.0 O3 C:7NU201 2.4 14.0 1.0 OD2 C:ASP100 2.5 12.1 1.0 C3 C:7NU201 3.3 15.4 1.0 C C:TYR36 3.3 13.8 1.0 C4 C:7NU201 3.4 16.2 1.0 CG C:ASN107 3.5 15.1 1.0 CG C:ASN108 3.5 12.7 1.0 C C:THR104 3.5 19.2 1.0 CG C:ASP100 3.5 11.2 1.0 OG1 C:THR104 3.7 17.3 1.0 OD1 C:ASP100 3.9 11.9 1.0 ND2 C:ASN107 3.9 16.2 1.0 C2 C:7NU201 3.9 15.4 1.0 CA C:TYR36 4.0 12.2 1.0 CB C:THR104 4.0 18.7 1.0 ND2 C:ASN108 4.0 13.6 1.0 CB C:TYR36 4.2 12.0 1.0 N C:GLY37 4.4 14.1 1.0 O C:HOH306 4.4 24.5 1.0 CA C:THR104 4.4 18.0 1.0 N C:TYR105 4.4 17.6 1.0 CA C:TYR105 4.5 16.3 1.0 O2 C:7NU201 4.6 13.9 1.0 N C:ASN108 4.6 14.2 1.0 CA C:GLY37 4.7 15.4 1.0 O C:HOH409 4.7 26.5 1.0 C5 C:7NU201 4.7 17.4 1.0 C C:ASN107 4.8 14.6 1.0 C C:TYR105 4.8 17.4 1.0 N C:ASN107 4.8 14.3 1.0 CB C:ASN108 4.8 13.8 1.0 CB C:ASN107 4.8 15.4 1.0 CB C:ASP100 4.9 11.9 1.0 CA C:ASN108 4.9 13.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside


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 Lectin Leca From Pseudomonas Aeruginosa in Complex with A Phenyl-Epoxy-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca200 b:11.1 occ:1.00 O D:TYR36 2.3 10.2 1.0 O D:THR104 2.3 11.4 1.0 OD1 D:ASN108 2.4 12.3 1.0 O4 D:7NU201 2.4 10.3 1.0 O3 D:7NU201 2.4 10.1 1.0 OD1 D:ASN107 2.5 12.9 1.0 OD2 D:ASP100 2.5 10.4 1.0 C3 D:7NU201 3.3 10.9 1.0 C D:TYR36 3.4 10.9 1.0 C4 D:7NU201 3.4 10.8 1.0 C D:THR104 3.5 11.0 1.0 CG D:ASP100 3.5 10.6 1.0 CG D:ASN107 3.5 13.9 1.0 CG D:ASN108 3.5 12.5 1.0 OG1 D:THR104 3.6 10.8 1.0 OD1 D:ASP100 3.8 9.9 1.0 ND2 D:ASN107 3.9 13.9 1.0 C2 D:7NU201 3.9 11.0 1.0 CB D:THR104 4.0 12.0 1.0 ND2 D:ASN108 4.0 11.9 1.0 CA D:TYR36 4.0 11.2 1.0 CB D:TYR36 4.2 11.3 1.0 CA D:THR104 4.4 11.0 1.0 N D:TYR105 4.4 9.9 1.0 N D:GLY37 4.4 11.7 1.0 CA D:TYR105 4.4 10.3 1.0 N D:ASN108 4.6 11.4 1.0 CA D:GLY37 4.7 13.3 1.0 O2 D:7NU201 4.7 11.1 1.0 C5 D:7NU201 4.7 11.3 1.0 C D:TYR105 4.8 11.0 1.0 C D:ASN107 4.8 11.6 1.0 CB D:ASN108 4.8 12.7 1.0 O D:HOH392 4.8 18.3 1.0 N D:ASN107 4.8 12.5 1.0 CB D:ASN107 4.8 12.9 1.0 CB D:ASP100 4.8 8.8 1.0 CA D:ASN108 5.0 12.1 1.0

S.Wagner, D.Hauck, M.Hoffmann, R.Sommer, I.Joachim, R.Muller, A.Imberty, A.Varrot, A.Titz. Covalent Lectin Inhibition and Application in Bacterial Biofilm Imaging. Angew. Chem. Int. Ed. Engl. V. 56 16559 2017.
ISSN: ESSN 1521-3773
PubMed: 28960731
DOI: 10.1002/ANIE.201709368