Calcium in PDB 5d21: Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca

The structure of Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca, PDB code: 5d21 was solved by M.Bergmann, G.Michaud, R.Visini, X.Jin, A.Stocker, T.Darbre, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.90 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.539, 72.940, 79.008, 117.51, 104.90, 89.91
R / Rfree (%)	21 / 22.5

The binding sites of Calcium atom in the Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca (pdb code 5d21). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca, PDB code: 5d21:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:9.4 occ:1.00 O A:TYR36 2.3 9.4 1.0 O A:THR104 2.3 9.4 1.0 O4 A:56N902 2.4 6.0 1.0 OD1 A:ASN108 2.4 8.4 1.0 O3 A:56N902 2.4 14.2 1.0 OD2 A:ASP100 2.5 9.6 1.0 OD1 A:ASN107 2.6 9.7 1.0 C A:TYR36 3.3 9.2 1.0 C4 A:56N902 3.4 12.6 1.0 C3 A:56N902 3.4 11.4 1.0 C A:THR104 3.5 7.8 1.0 CG A:ASP100 3.5 11.7 1.0 CG A:ASN108 3.5 10.9 1.0 CG A:ASN107 3.6 11.8 1.0 OG1 A:THR104 3.7 9.0 1.0 OD1 A:ASP100 3.8 8.8 1.0 CB A:THR104 3.9 13.3 1.0 CA A:TYR36 3.9 7.1 1.0 C2 A:56N902 4.0 14.5 1.0 ND2 A:ASN108 4.0 8.5 1.0 CB A:TYR36 4.1 12.4 1.0 ND2 A:ASN107 4.1 8.7 1.0 CA A:THR104 4.3 12.2 1.0 N A:TYR105 4.4 10.4 1.0 N A:GLY37 4.4 10.2 1.0 CA A:TYR105 4.4 9.2 1.0 N A:ASN108 4.6 12.8 1.0 O2 A:56N902 4.7 12.4 1.0 O A:HOH1043 4.7 23.5 1.0 CA A:GLY37 4.7 9.7 1.0 C5 A:56N902 4.7 17.9 1.0 C A:ASN107 4.8 11.4 1.0 C A:TYR105 4.8 11.6 1.0 N A:ASN107 4.8 10.5 1.0 CB A:ASN108 4.8 9.5 1.0 CB A:ASP100 4.9 5.8 1.0 CB A:ASN107 4.9 12.7 1.0 CA A:ASN108 5.0 10.0 1.0

Calcium binding site 2 out of 4 in the Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:10.0 occ:1.00 O B:TYR36 2.3 12.1 1.0 O B:THR104 2.3 9.0 1.0 OD1 B:ASN108 2.4 6.5 1.0 O4 B:56N202 2.4 6.8 1.0 O3 B:56N202 2.4 13.2 1.0 OD2 B:ASP100 2.5 10.7 1.0 OD1 B:ASN107 2.5 8.8 1.0 C B:TYR36 3.3 11.2 1.0 C4 B:56N202 3.3 14.3 1.0 C3 B:56N202 3.4 13.0 1.0 C B:THR104 3.4 11.1 1.0 CG B:ASN108 3.5 9.1 1.0 CG B:ASP100 3.5 9.6 1.0 CG B:ASN107 3.6 8.6 1.0 OG1 B:THR104 3.7 9.9 1.0 OD1 B:ASP100 3.9 8.7 1.0 CB B:THR104 3.9 16.9 1.0 C2 B:56N202 3.9 14.5 1.0 CA B:TYR36 3.9 8.8 1.0 ND2 B:ASN108 4.0 8.0 1.0 ND2 B:ASN107 4.0 9.6 1.0 CB B:TYR36 4.1 12.1 1.0 CA B:THR104 4.3 11.2 1.0 N B:TYR105 4.4 11.5 1.0 N B:GLY37 4.4 10.1 1.0 CA B:TYR105 4.4 9.3 1.0 N B:ASN108 4.6 9.9 1.0 O2 B:56N202 4.6 11.6 1.0 O B:HOH315 4.6 19.6 1.0 CA B:GLY37 4.7 15.0 1.0 C5 B:56N202 4.7 19.1 1.0 C B:TYR105 4.8 9.9 1.0 N B:ASN107 4.8 8.3 1.0 C B:ASN107 4.8 10.7 1.0 CB B:ASN108 4.8 9.2 1.0 CB B:ASP100 4.9 5.6 1.0 CB B:ASN107 4.9 11.2 1.0 CA B:ASN108 5.0 9.0 1.0

Calcium binding site 3 out of 4 in the Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:9.1 occ:1.00 O C:TYR36 2.3 10.5 1.0 O C:THR104 2.3 9.4 1.0 O4 C:56N202 2.4 7.4 1.0 O3 C:56N202 2.4 13.0 1.0 OD1 C:ASN108 2.4 7.5 1.0 OD1 C:ASN107 2.5 10.7 1.0 OD2 C:ASP100 2.5 10.2 1.0 C C:TYR36 3.3 10.0 1.0 C4 C:56N202 3.3 12.5 1.0 C3 C:56N202 3.4 14.6 1.0 C C:THR104 3.4 10.2 1.0 CG C:ASN108 3.5 9.4 1.0 CG C:ASP100 3.5 10.8 1.0 CG C:ASN107 3.6 9.0 1.0 OG1 C:THR104 3.6 8.0 1.0 OD1 C:ASP100 3.8 9.3 1.0 CB C:THR104 3.9 17.1 1.0 CA C:TYR36 3.9 8.4 1.0 C2 C:56N202 4.0 19.4 1.0 ND2 C:ASN107 4.0 10.0 1.0 ND2 C:ASN108 4.0 8.7 1.0 CB C:TYR36 4.1 12.5 1.0 CA C:THR104 4.3 10.7 1.0 N C:TYR105 4.3 11.4 1.0 N C:GLY37 4.4 10.1 1.0 CA C:TYR105 4.4 11.5 1.0 N C:ASN108 4.6 11.4 1.0 O2 C:56N202 4.7 14.6 1.0 O C:HOH363 4.7 25.5 1.0 CA C:GLY37 4.7 15.6 1.0 C5 C:56N202 4.7 17.3 1.0 C C:ASN107 4.8 10.3 1.0 N C:ASN107 4.8 9.3 1.0 C C:TYR105 4.8 11.4 1.0 CB C:ASN108 4.8 9.5 1.0 CB C:ASN107 4.9 10.7 1.0 CB C:ASP100 4.9 5.0 1.0 CA C:ASN108 4.9 7.8 1.0

Calcium binding site 4 out of 4 in the Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Multivalency Effects in Glycopeptide Dendrimer Inhibitors of Pseudomonas Aeruginosa Biofilms Targeting Lectin Leca within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:9.6 occ:1.00 O D:TYR36 2.3 12.2 1.0 O D:THR104 2.3 8.1 1.0 O3 D:56N202 2.4 12.4 1.0 OD1 D:ASN108 2.4 7.2 1.0 O4 D:56N202 2.5 7.3 1.0 OD2 D:ASP100 2.5 9.8 1.0 OD1 D:ASN107 2.5 11.3 1.0 C D:TYR36 3.3 9.8 1.0 C3 D:56N202 3.4 12.2 1.0 C4 D:56N202 3.4 11.1 1.0 C D:THR104 3.4 8.7 1.0 CG D:ASP100 3.5 10.6 1.0 CG D:ASN108 3.5 10.1 1.0 CG D:ASN107 3.6 9.7 1.0 OG1 D:THR104 3.7 8.4 1.0 OD1 D:ASP100 3.8 7.1 1.0 CB D:THR104 3.9 15.6 1.0 CA D:TYR36 3.9 8.8 1.0 C2 D:56N202 4.0 15.2 1.0 ND2 D:ASN107 4.0 7.9 1.0 ND2 D:ASN108 4.0 8.5 1.0 CB D:TYR36 4.1 11.5 1.0 CA D:THR104 4.3 13.6 1.0 N D:TYR105 4.4 11.0 1.0 N D:GLY37 4.4 12.0 1.0 CA D:TYR105 4.4 9.7 1.0 N D:ASN108 4.6 11.5 1.0 O2 D:56N202 4.7 13.2 1.0 O D:HOH367 4.7 22.8 1.0 CA D:GLY37 4.7 13.4 1.0 C5 D:56N202 4.7 16.2 1.0 C D:ASN107 4.8 11.8 1.0 CB D:ASN108 4.8 11.1 1.0 C D:TYR105 4.8 11.3 1.0 N D:ASN107 4.8 9.6 1.0 CB D:ASP100 4.8 5.2 1.0 CB D:ASN107 4.9 11.1 1.0 CA D:ASN108 5.0 8.5 1.0

M.Bergmann, G.Michaud, R.Visini, X.Jin, E.Gillon, A.Stocker, A.Imberty, T.Darbre, J.L.Reymond. Multivalency Effects on Pseudomonas Aeruginosa Biofilm Inhibition and Dispersal By Glycopeptide Dendrimers Targeting Lectin Leca. Org.Biomol.Chem. V. 14 138 2016.
ISSN: ESSN 1477-0539
PubMed: 26416170
DOI: 10.1039/C5OB01682G