Calcium in PDB 4cp9: Crystal Structure of Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom

The structure of Crystal Structure of Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom, PDB code: 4cp9 was solved by J.Topin, A.Varrot, A.Imberty, N.Wissinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.47 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.876, 66.259, 159.427, 90.00, 90.00, 90.00
R / Rfree (%)	15.525 / 18.362

The binding sites of Calcium atom in the Crystal Structure of Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom (pdb code 4cp9). 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 Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom, PDB code: 4cp9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom


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 Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1122 b:17.4 occ:1.00 O A:THR104 2.3 22.2 1.0 OD2 A:ASP100 2.3 18.6 1.0 OD1 A:ASN108 2.4 20.3 1.0 O3 A:GAL1123 2.4 17.4 1.0 O A:TYR36 2.4 19.4 1.0 O4 A:GAL1123 2.5 17.9 1.0 OD1 A:ASN107 2.5 20.7 1.0 C3 A:GAL1123 3.3 15.4 1.0 C4 A:GAL1123 3.4 18.0 1.0 C A:TYR36 3.4 18.8 1.0 CG A:ASP100 3.4 18.7 1.0 C A:THR104 3.4 22.3 1.0 CG A:ASN108 3.5 19.4 1.0 OG1 A:THR104 3.5 24.3 1.0 CG A:ASN107 3.5 21.9 1.0 OD1 A:ASP100 3.8 17.9 1.0 CB A:THR104 3.9 24.2 1.0 C2 A:GAL1123 3.9 18.8 1.0 ND2 A:ASN108 3.9 18.8 1.0 CA A:TYR36 3.9 18.1 1.0 ND2 A:ASN107 4.0 21.7 1.0 CB A:TYR36 4.1 19.1 1.0 CA A:THR104 4.3 23.1 1.0 N A:TYR105 4.4 23.6 1.0 CA A:TYR105 4.4 22.4 1.0 N A:GLY37 4.5 18.8 1.0 N A:ASN108 4.6 20.5 1.0 C A:TYR105 4.7 22.9 1.0 C5 A:GAL1123 4.7 18.9 1.0 O2 A:GAL1123 4.8 19.4 1.0 CB A:ASN108 4.8 19.6 1.0 CB A:ASP100 4.8 18.3 1.0 CA A:GLY37 4.8 20.4 1.0 C A:ASN107 4.8 20.8 1.0 N A:ASN107 4.8 23.2 1.0 CB A:ASN107 4.8 21.4 1.0 CA A:ASN108 5.0 20.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom


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 Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1123 b:20.2 occ:1.00 O B:TYR36 2.3 22.0 1.0 O B:THR104 2.4 21.7 1.0 OD1 B:ASN108 2.4 20.3 1.0 OD1 B:ASN107 2.5 23.1 1.0 O3 B:GAL1124 2.5 23.9 1.0 OD2 B:ASP100 2.5 20.1 1.0 O4 B:GAL1124 2.5 23.3 1.0 C3 B:GAL1124 3.4 24.3 1.0 C B:TYR36 3.4 22.1 1.0 C4 B:GAL1124 3.4 25.3 1.0 C B:THR104 3.5 22.1 1.0 CG B:ASN108 3.5 20.5 1.0 CG B:ASP100 3.5 20.9 1.0 CG B:ASN107 3.5 24.7 1.0 OG1 B:THR104 3.6 23.6 1.0 OD1 B:ASP100 3.8 20.2 1.0 CA B:TYR36 4.0 20.1 1.0 ND2 B:ASN108 4.0 19.6 1.0 C2 B:GAL1124 4.0 25.9 1.0 CB B:THR104 4.0 24.6 1.0 ND2 B:ASN107 4.0 24.6 1.0 CB B:TYR36 4.2 20.5 1.0 CA B:TYR105 4.3 21.7 1.0 N B:TYR105 4.3 22.1 1.0 CA B:THR104 4.4 23.3 1.0 N B:GLY37 4.4 22.9 1.0 O B:HOH2108 4.5 17.9 0.5 O B:HOH2105 4.5 24.0 0.5 N B:ASN108 4.6 19.8 1.0 O2 B:GAL1124 4.7 27.2 1.0 C B:TYR105 4.7 22.9 1.0 CA B:GLY37 4.7 24.6 1.0 N B:ASN107 4.7 22.1 1.0 C B:ASN107 4.8 20.8 1.0 CB B:ASN108 4.8 19.2 1.0 C5 B:GAL1124 4.8 25.3 1.0 CB B:ASN107 4.8 24.0 1.0 CB B:ASP100 4.9 19.9 1.0 CA B:ASN108 4.9 19.8 1.0 CA B:ASN107 5.0 22.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom


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 Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1123 b:32.5 occ:1.00 O4 C:GAL1124 1.8 29.8 1.0 O C:THR104 2.3 43.7 1.0 O C:TYR36 2.3 41.3 1.0 OD2 C:ASP100 2.4 34.9 1.0 O3 C:GAL1124 2.4 32.0 1.0 OD1 C:ASN108 2.5 42.5 1.0 OD1 C:ASN107 2.6 45.0 1.0 C4 C:GAL1124 3.1 36.0 1.0 C3 C:GAL1124 3.2 31.0 1.0 C C:TYR36 3.4 39.0 1.0 CG C:ASP100 3.4 36.5 1.0 C C:THR104 3.4 45.7 1.0 CG C:ASN108 3.5 39.5 1.0 OG1 C:THR104 3.6 44.3 1.0 CG C:ASN107 3.6 47.8 1.0 OD1 C:ASP100 3.7 35.1 1.0 C2 C:GAL1124 3.9 40.3 1.0 CB C:THR104 3.9 49.4 1.0 CA C:TYR36 4.0 36.3 1.0 ND2 C:ASN108 4.0 37.4 1.0 ND2 C:ASN107 4.1 48.9 1.0 CB C:TYR36 4.1 35.8 1.0 CA C:THR104 4.3 46.9 1.0 N C:TYR105 4.4 44.0 1.0 CA C:TYR105 4.4 41.9 1.0 N C:GLY37 4.4 41.3 1.0 C5 C:GAL1124 4.5 36.2 1.0 O C:HOH2075 4.5 45.3 1.0 O2 C:GAL1124 4.6 41.9 1.0 N C:ASN108 4.6 42.9 1.0 CA C:GLY37 4.7 44.8 1.0 CB C:ASP100 4.7 33.4 1.0 C C:TYR105 4.8 44.7 1.0 C C:ASN107 4.8 43.5 1.0 CB C:ASN108 4.8 39.2 1.0 N C:ASN107 4.9 45.4 1.0 CB C:ASN107 5.0 47.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom


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 Leca Lectin Complexed with A Divalent Galactoside at 1.65 Anstrom within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1123 b:19.6 occ:1.00 O D:THR104 2.2 24.1 1.0 OD2 D:ASP100 2.4 19.3 1.0 O D:TYR36 2.4 20.6 1.0 O3 D:GAL1124 2.4 18.0 1.0 OD1 D:ASN108 2.4 20.5 1.0 O4 D:GAL1124 2.5 23.3 1.0 OD1 D:ASN107 2.5 21.6 1.0 C3 D:GAL1124 3.3 19.3 1.0 C D:TYR36 3.4 20.7 1.0 C D:THR104 3.4 25.0 1.0 C4 D:GAL1124 3.4 22.3 1.0 CG D:ASP100 3.4 21.8 1.0 CG D:ASN108 3.5 20.8 1.0 OG1 D:THR104 3.6 26.7 1.0 CG D:ASN107 3.6 22.7 1.0 OD1 D:ASP100 3.8 22.9 1.0 CB D:THR104 3.9 26.0 1.0 ND2 D:ASN108 3.9 19.6 1.0 CA D:TYR36 4.0 20.2 1.0 ND2 D:ASN107 4.0 22.3 1.0 C2 D:GAL1124 4.0 21.9 1.0 CB D:TYR36 4.1 20.8 1.0 CA D:THR104 4.3 26.4 1.0 N D:TYR105 4.3 24.3 1.0 CA D:TYR105 4.3 23.8 1.0 N D:GLY37 4.4 21.8 1.0 N D:ASN108 4.6 21.3 1.0 C D:TYR105 4.7 23.4 1.0 O2 D:GAL1124 4.8 23.3 1.0 CA D:GLY37 4.8 21.5 1.0 CB D:ASN108 4.8 20.2 1.0 C5 D:GAL1124 4.8 22.1 1.0 C D:ASN107 4.8 21.6 1.0 CB D:ASP100 4.8 22.4 1.0 N D:ASN107 4.8 23.0 1.0 CB D:ASN107 4.9 22.2 1.0 CA D:ASN108 4.9 21.0 1.0 O D:TYR105 5.0 22.8 1.0

A.Novoa, T.Eierhoff, J.Topin, A.Varrot, S.Barluenga, A.Imberty, W.Romer, N.Winssinger. A Leca Ligand Identified From A Galactoside-Conjugate Array Inhibits Host Cell Invasion By Pseudomonas Aeruginosa. Angew.Chem.Int.Ed.Engl. V. 53 8885 2014.
ISSN: ISSN 1433-7851
PubMed: 25044671
DOI: 10.1002/ANIE.201402831