Calcium in PDB 6yo3: Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0

The structure of Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0, PDB code: 6yo3 was solved by S.Kuhaudomlarp, A.Imberty, A.Titz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.46 / 1.84
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.943, 48.63, 128.632, 90, 95.59, 90
R / Rfree (%)	17.2 / 20.8

The binding sites of Calcium atom in the Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0 (pdb code 6yo3). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0, PDB code: 6yo3:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:16.7 occ:1.00 O A:THR104 2.2 18.4 1.0 O A:TYR36 2.3 14.5 1.0 O1 A:P3K202 2.3 16.4 1.0 OD1 A:ASN107 2.4 16.9 1.0 OD1 A:ASN108 2.4 16.3 1.0 O2 A:P3K202 2.5 17.4 1.0 OD2 A:ASP100 2.5 15.8 1.0 C6 A:P3K202 3.3 18.8 1.0 C A:TYR36 3.3 18.2 1.0 C7 A:P3K202 3.3 18.3 1.0 CG A:ASN107 3.4 18.0 1.0 C A:THR104 3.5 20.0 1.0 CG A:ASN108 3.5 16.5 1.0 CG A:ASP100 3.6 15.0 1.0 ND2 A:ASN107 3.8 20.3 1.0 OG1 A:THR104 3.8 17.1 1.0 CA A:TYR36 3.8 17.3 1.0 OD1 A:ASP100 3.9 15.8 1.0 CB A:THR104 3.9 18.1 1.0 ND2 A:ASN108 4.0 14.9 1.0 CB A:TYR36 4.2 17.5 1.0 CA A:THR104 4.3 17.5 1.0 N A:GLY37 4.4 17.6 1.0 N A:TYR105 4.4 18.2 1.0 CA A:TYR105 4.5 21.0 1.0 C5 A:P3K202 4.6 20.8 1.0 N A:ASN108 4.6 19.7 1.0 C2 A:P3K202 4.7 19.3 1.0 C A:ASN107 4.7 19.2 1.0 CB A:ASN107 4.7 18.7 1.0 CA A:GLY37 4.8 17.4 1.0 C A:TYR105 4.8 21.2 1.0 CB A:ASN108 4.8 17.1 1.0 N A:ASN107 4.8 18.8 1.0 CA A:ASN108 4.9 18.9 1.0 CB A:ASP100 4.9 15.2 1.0 O A:TYR105 4.9 19.6 1.0

Calcium binding site 2 out of 4 in the Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:20.2 occ:1.00 O B:THR104 2.3 20.1 1.0 OD1 B:ASN108 2.3 14.8 1.0 O B:TYR36 2.4 22.9 1.0 O2 B:EDO203 2.4 27.5 1.0 O1 B:EDO203 2.4 21.8 1.0 OD1 B:ASN107 2.4 21.7 1.0 OD2 B:ASP100 2.5 19.5 1.0 CG B:ASN108 3.4 16.2 1.0 C B:TYR36 3.4 21.7 1.0 C1 B:EDO203 3.4 32.6 1.0 C2 B:EDO203 3.4 31.9 1.0 C B:THR104 3.5 20.7 1.0 CG B:ASN107 3.5 22.2 1.0 CG B:ASP100 3.6 19.5 1.0 OG1 B:THR104 3.8 23.0 1.0 CA B:TYR36 3.9 19.2 1.0 OD1 B:ASP100 3.9 21.1 1.0 ND2 B:ASN108 3.9 14.6 1.0 ND2 B:ASN107 3.9 21.4 1.0 CB B:THR104 4.0 23.0 1.0 CB B:TYR36 4.1 19.3 1.0 CA B:THR104 4.4 20.4 1.0 N B:TYR105 4.4 20.6 1.0 CA B:TYR105 4.4 20.2 1.0 O B:HOH349 4.4 32.6 1.0 N B:GLY37 4.5 21.6 1.0 N B:ASN108 4.6 18.2 1.0 CB B:ASN108 4.7 15.5 1.0 C B:TYR105 4.7 21.0 1.0 C B:ASN107 4.7 21.6 1.0 N B:ASN107 4.8 21.1 1.0 CB B:ASN107 4.8 23.2 1.0 CA B:GLY37 4.8 22.6 1.0 CA B:ASN108 4.9 17.0 1.0 CB B:ASP100 4.9 18.4 1.0

Calcium binding site 3 out of 4 in the Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:15.6 occ:1.00 O C:THR104 2.3 14.6 1.0 O C:TYR36 2.3 13.1 1.0 O1 C:P3K202 2.3 17.0 1.0 OD1 C:ASN108 2.4 16.7 1.0 OD1 C:ASN107 2.4 17.3 1.0 O2 C:P3K202 2.4 15.4 1.0 OD2 C:ASP100 2.5 15.9 1.0 C6 C:P3K202 3.3 16.9 1.0 C7 C:P3K202 3.3 17.2 1.0 C C:TYR36 3.3 15.8 1.0 C C:THR104 3.4 16.8 1.0 CG C:ASN108 3.5 17.3 1.0 CG C:ASP100 3.5 15.4 1.0 CG C:ASN107 3.5 19.0 1.0 OG1 C:THR104 3.6 16.6 1.0 OD1 C:ASP100 3.8 13.7 1.0 CA C:TYR36 3.9 15.7 1.0 CB C:THR104 3.9 16.2 1.0 ND2 C:ASN108 3.9 16.9 1.0 ND2 C:ASN107 3.9 17.6 1.0 CB C:TYR36 4.2 17.3 1.0 CA C:THR104 4.2 16.8 1.0 O C:HOH329 4.3 18.8 1.0 N C:GLY37 4.4 16.4 1.0 N C:TYR105 4.4 15.8 1.0 CA C:TYR105 4.5 16.7 1.0 C5 C:P3K202 4.6 18.4 1.0 N C:ASN108 4.6 17.6 1.0 C2 C:P3K202 4.7 17.7 1.0 CA C:GLY37 4.7 18.9 1.0 C C:ASN107 4.7 18.3 1.0 CB C:ASN108 4.8 17.7 1.0 N C:ASN107 4.8 19.2 1.0 C C:TYR105 4.8 16.4 1.0 CB C:ASP100 4.8 15.2 1.0 CB C:ASN107 4.8 19.1 1.0 O C:HOH382 4.9 28.2 1.0 CA C:ASN108 4.9 18.6 1.0 O C:TYR105 5.0 20.5 1.0

Calcium binding site 4 out of 4 in the Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Leca From Pseudomonas Aeruginosa in Complex with A Catechol Cas No. 67984-81-0 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:24.7 occ:1.00 O D:THR104 2.3 25.8 1.0 O D:TYR36 2.4 27.6 1.0 OD1 D:ASN108 2.4 20.5 1.0 OD1 D:ASN107 2.4 25.0 1.0 O1 D:EDO403 2.4 32.0 1.0 OD2 D:ASP100 2.5 21.5 1.0 O2 D:EDO403 2.6 34.1 1.0 C D:TYR36 3.4 25.1 1.0 C1 D:EDO403 3.5 40.7 1.0 C D:THR104 3.5 24.7 1.0 CG D:ASN108 3.5 21.1 1.0 CG D:ASN107 3.5 24.6 1.0 C2 D:EDO403 3.5 38.9 1.0 CG D:ASP100 3.5 20.2 1.0 OG1 D:THR104 3.6 22.7 1.0 OD1 D:ASP100 3.9 20.5 1.0 CA D:TYR36 3.9 24.0 1.0 CB D:THR104 3.9 25.2 1.0 ND2 D:ASN108 4.0 22.5 1.0 ND2 D:ASN107 4.0 24.4 1.0 CB D:TYR36 4.2 24.2 1.0 CA D:THR104 4.3 25.1 1.0 N D:TYR105 4.4 23.9 1.0 N D:GLY37 4.4 25.4 1.0 CA D:TYR105 4.4 23.5 1.0 N D:ASN108 4.5 25.1 1.0 C D:ASN107 4.7 24.5 1.0 C D:TYR105 4.7 23.8 1.0 CB D:ASN108 4.7 21.1 1.0 N D:ASN107 4.8 24.5 1.0 CA D:GLY37 4.8 26.2 1.0 CB D:ASN107 4.8 25.7 1.0 CB D:ASP100 4.9 20.2 1.0 CA D:ASN108 4.9 22.4 1.0 O D:TYR105 4.9 22.6 1.0 CA D:ASN107 5.0 25.1 1.0

S.Kuhaudomlarp, E.Siebs, E.Shanina, J.Topin, I.Joachim, P.Da Silva Figueiredo Celestino Gomes, A.Varrot, D.Rognan, C.Rademacher, A.Imberty, A.Titz. Non-Carbohydrate Glycomimetics As Inhibitors of Calcium(II)-Binding Lectins. Angew.Chem.Int.Ed.Engl. 2020.
ISSN: ESSN 1521-3773
PubMed: 33314528
DOI: 10.1002/ANIE.202013217