Calcium in PDB 4a6s: Structure of the Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside

The structure of Structure of the Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside, PDB code: 4a6s was solved by J.Rodrigue, G.Ganne, B.Blanchard, C.Saucier, D.Giguere, T.S.Chiao, A.Varrot, A.Imberty, R.Roy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.13 / 2.15
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	54.334, 54.334, 390.501, 90.00, 90.00, 120.00
R / Rfree (%)	21.437 / 25.881

The binding sites of Calcium atom in the Structure of the Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside (pdb code 4a6s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of the Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside, PDB code: 4a6s:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of the Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside


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 Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1122 b:39.0 occ:1.00 O A:THR104 2.3 39.9 1.0 OD1 A:ASN108 2.3 38.0 1.0 O A:TYR36 2.4 40.0 1.0 OD2 A:ASP100 2.4 37.7 1.0 O4 A:GS91123 2.4 40.7 1.0 OD1 A:ASN107 2.5 42.2 1.0 O3 A:GS91123 2.5 42.5 1.0 C A:TYR36 3.3 39.5 1.0 C3 A:GS91123 3.4 42.2 1.0 C4 A:GS91123 3.4 41.5 1.0 CG A:ASP100 3.5 37.9 1.0 CG A:ASN108 3.5 37.6 1.0 C A:THR104 3.5 42.2 1.0 CG A:ASN107 3.6 43.1 1.0 OD1 A:ASP100 3.8 39.3 1.0 OG1 A:THR104 3.8 42.1 1.0 CA A:TYR36 3.8 38.2 1.0 C2 A:GS91123 3.9 41.5 1.0 CB A:TYR36 4.0 37.3 1.0 ND2 A:ASN108 4.0 35.5 1.0 ND2 A:ASN107 4.1 42.7 1.0 CB A:THR104 4.2 43.1 1.0 N A:GLY37 4.3 41.2 1.0 O A:HOH2081 4.3 43.5 1.0 N A:TYR105 4.4 41.4 1.0 CA A:THR104 4.5 43.3 1.0 CA A:TYR105 4.5 42.2 1.0 O2 A:GS91123 4.5 42.4 1.0 N A:ASN108 4.5 41.9 1.0 CA A:GLY37 4.7 42.9 1.0 C A:ASN107 4.7 43.0 1.0 C5 A:GS91123 4.7 41.9 1.0 CB A:ASN108 4.7 38.2 1.0 CB A:ASP100 4.8 36.6 1.0 C A:TYR105 4.8 43.5 1.0 CA A:ASN108 4.9 39.7 1.0 N A:ASN107 4.9 44.5 1.0 CB A:ASN107 4.9 44.5 1.0 O A:ASN107 4.9 43.1 1.0 O5 A:GS91123 5.0 41.8 1.0

Calcium binding site 2 out of 4 in the Structure of the Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside


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 Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1122 b:51.0 occ:1.00 O3 B:GS91123 2.3 54.2 1.0 OD2 B:ASP100 2.3 46.8 1.0 OD1 B:ASN108 2.3 45.1 1.0 O B:TYR36 2.4 43.9 1.0 OD1 B:ASN107 2.5 49.4 1.0 O B:THR104 2.5 51.1 1.0 O4 B:GS91123 2.6 51.2 1.0 C3 B:GS91123 3.3 53.3 1.0 C B:TYR36 3.4 43.1 1.0 CG B:ASN108 3.4 44.4 1.0 C B:THR104 3.4 50.8 1.0 CG B:ASP100 3.4 46.2 1.0 C4 B:GS91123 3.5 51.7 1.0 CG B:ASN107 3.6 50.5 1.0 ND2 B:ASN108 3.8 43.2 1.0 CA B:TYR36 3.8 41.7 1.0 CB B:THR104 3.9 52.5 1.0 OG1 B:THR104 3.9 51.4 1.0 OD1 B:ASP100 3.9 45.9 1.0 C2 B:GS91123 4.0 52.1 1.0 CB B:TYR36 4.0 41.0 1.0 ND2 B:ASN107 4.1 51.4 1.0 CA B:THR104 4.2 53.5 1.0 N B:TYR105 4.2 50.9 1.0 CA B:TYR105 4.3 49.4 1.0 N B:ASN108 4.4 47.5 1.0 N B:GLY37 4.5 43.4 1.0 O2 B:GS91123 4.6 53.7 1.0 C B:TYR105 4.6 50.3 1.0 CB B:ASN108 4.7 44.6 1.0 CB B:ASP100 4.7 44.9 1.0 N B:ASN107 4.7 51.6 1.0 CA B:GLY37 4.8 45.3 1.0 CA B:ASN108 4.8 45.9 1.0 C B:ASN107 4.8 49.3 1.0 CB B:ASN107 4.8 52.4 1.0 C5 B:GS91123 4.9 51.5 1.0 O B:TYR105 4.9 49.2 1.0

Calcium binding site 3 out of 4 in the Structure of the Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside


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 Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1122 b:64.6 occ:1.00 O C:THR104 2.2 63.6 1.0 O C:TYR36 2.3 58.4 1.0 OD1 C:ASN108 2.4 59.5 1.0 O3 C:GS91123 2.5 62.4 1.0 ND2 C:ASN107 2.6 66.8 1.0 OD2 C:ASP100 2.6 56.0 1.0 O4 C:GS91123 2.6 58.5 1.0 C C:TYR36 3.3 57.0 1.0 C C:THR104 3.4 64.1 1.0 CG C:ASN107 3.5 68.0 1.0 C4 C:GS91123 3.5 61.2 1.0 C3 C:GS91123 3.5 62.6 1.0 CG C:ASN108 3.6 59.1 1.0 CG C:ASP100 3.6 55.5 1.0 OD1 C:ASN107 3.7 68.9 1.0 CA C:TYR36 3.8 54.7 1.0 CB C:THR104 3.8 64.0 1.0 C2 C:GS91123 3.9 62.2 1.0 OG1 C:THR104 4.0 62.0 1.0 CB C:TYR36 4.0 53.3 1.0 OD1 C:ASP100 4.0 55.9 1.0 ND2 C:ASN108 4.1 58.4 1.0 CA C:THR104 4.3 65.3 1.0 CA C:TYR105 4.3 63.6 1.0 N C:TYR105 4.3 64.6 1.0 N C:GLY37 4.3 57.9 1.0 N C:ASN108 4.4 63.0 1.0 O2 C:GS91123 4.5 63.7 1.0 C C:TYR105 4.6 65.2 1.0 CA C:GLY37 4.7 59.8 1.0 O C:TYR105 4.7 64.1 1.0 C C:ASN107 4.7 64.7 1.0 CB C:ASN108 4.8 59.5 1.0 CA C:ASN108 4.8 60.9 1.0 CB C:ASN107 4.9 69.1 1.0 N C:ASN107 4.9 68.4 1.0 C5 C:GS91123 4.9 61.2 1.0 CB C:ASP100 4.9 53.9 1.0

Calcium binding site 4 out of 4 in the Structure of the Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside


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 Pail Lectin From Pseudomonas Aeruginosa in Complex with 2-Naphtyl-1-Thio-Beta-D-Galactopyranoside within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1122 b:47.5 occ:1.00 O D:THR104 2.2 47.8 1.0 OD1 D:ASN108 2.3 45.9 1.0 O D:TYR36 2.4 43.8 1.0 OD1 D:ASN107 2.4 49.1 1.0 O4 D:GS91123 2.4 46.6 1.0 O3 D:GS91123 2.6 48.8 1.0 OD2 D:ASP100 2.6 44.8 1.0 C D:TYR36 3.3 43.0 1.0 C4 D:GS91123 3.3 48.1 1.0 C D:THR104 3.4 49.0 1.0 CG D:ASN108 3.4 44.7 1.0 C3 D:GS91123 3.4 48.8 1.0 CG D:ASN107 3.5 49.7 1.0 CG D:ASP100 3.6 44.3 1.0 OG1 D:THR104 3.7 48.6 1.0 ND2 D:ASN108 3.9 43.6 1.0 CA D:TYR36 3.9 41.7 1.0 C2 D:GS91123 3.9 48.0 1.0 ND2 D:ASN107 3.9 49.4 1.0 CB D:THR104 3.9 49.8 1.0 OD1 D:ASP100 3.9 44.3 1.0 CB D:TYR36 4.1 41.2 1.0 O D:HOH2050 4.1 46.3 1.0 CA D:THR104 4.2 50.6 1.0 N D:TYR105 4.3 48.9 1.0 N D:GLY37 4.3 43.7 1.0 CA D:TYR105 4.4 48.4 1.0 O2 D:GS91123 4.4 48.7 1.0 N D:ASN108 4.5 46.8 1.0 CA D:GLY37 4.6 44.5 1.0 CB D:ASN108 4.6 44.6 1.0 C D:ASN107 4.7 48.5 1.0 C5 D:GS91123 4.7 48.1 1.0 C D:TYR105 4.7 49.4 1.0 CA D:ASN108 4.8 45.6 1.0 N D:ASN107 4.8 49.9 1.0 CB D:ASN107 4.8 50.3 1.0 CB D:ASP100 4.9 43.7 1.0 O D:TYR105 5.0 48.5 1.0 CA D:ASN107 5.0 49.9 1.0

J.Rodrigue, G.Ganne, B.Blanchard, C.Saucier, D.Giguere, T.C.Shiao, A.Varrot, A.Imberty, R.Roy. Aromatic Thioglycoside Inhibitors Against the Virulence Factor Leca From Pseudomonas Aeruginosa. Org.Biomol.Chem. V. 11 6906 2013.
ISSN: ISSN 1477-0520
PubMed: 24057051
DOI: 10.1039/C3OB41422A