Calcium in PDB 6s5s: Cfucosylated Second Generation Peptide Dendrimer SBD8 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.43 Angstrom Resolution

The structure of Cfucosylated Second Generation Peptide Dendrimer SBD8 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.43 Angstrom Resolution, PDB code: 6s5s was solved by S.Baeriswyl, A.Stocker, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.52 / 1.43
Space group	P 6 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.297, 106.297, 57.090, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 17.9

The binding sites of Calcium atom in the Cfucosylated Second Generation Peptide Dendrimer SBD8 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.43 Angstrom Resolution (pdb code 6s5s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Cfucosylated Second Generation Peptide Dendrimer SBD8 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.43 Angstrom Resolution, PDB code: 6s5s:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Cfucosylated Second Generation Peptide Dendrimer SBD8 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.43 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cfucosylated Second Generation Peptide Dendrimer SBD8 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.43 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:11.4 occ:1.00 OD1 A:ASP101 2.4 12.7 1.0 OD1 A:ASP99 2.4 14.9 1.0 OD2 A:ASP104 2.4 10.8 1.0 OE2 A:GLU95 2.4 12.9 1.0 OE1 A:GLU95 2.4 12.3 1.0 O3 C:ZDC101 2.5 12.2 1.0 H4O C:ZDC101 2.5 14.4 1.0 O4 C:ZDC101 2.6 12.0 1.0 OD1 A:ASP104 2.6 10.8 1.0 CD A:GLU95 2.7 12.4 1.0 CG A:ASP104 2.9 11.1 1.0 H3O C:ZDC101 3.0 14.5 1.0 H A:ASP101 3.3 15.9 1.0 C4 C:ZDC101 3.4 11.1 1.0 C3 C:ZDC101 3.4 11.8 1.0 CG A:ASP99 3.4 16.5 1.0 CG A:ASP101 3.4 12.8 1.0 H4 C:ZDC101 3.5 13.3 1.0 H3 C:ZDC101 3.6 14.1 1.0 OD2 A:ASP99 3.7 14.2 1.0 CA A:CA302 3.7 10.8 1.0 H A:TYR102 3.7 14.1 1.0 H A:ASP96 3.8 14.0 1.0 HA A:GLU95 3.9 13.9 1.0 OD2 A:ASP101 4.0 11.4 1.0 H A:GLY97 4.1 15.8 1.0 H A:ASN100 4.1 18.5 1.0 H A:ASP99 4.1 19.1 1.0 N A:ASP101 4.1 13.3 1.0 OD1 A:ASP96 4.2 13.6 1.0 CG A:GLU95 4.2 12.8 1.0 O A:HOH454 4.3 31.1 1.0 CB A:ASP104 4.4 10.0 1.0 N A:TYR102 4.4 11.8 1.0 N A:ASN100 4.5 15.5 1.0 H A:ASN103 4.5 12.3 1.0 N A:ASP96 4.5 11.7 1.0 CB A:ASP101 4.6 12.0 1.0 HG3 A:GLU95 4.6 15.4 1.0 N A:GLY97 4.6 13.2 1.0 HA3 A:GLY97 4.6 18.2 1.0 HB2 A:ASP104 4.7 12.0 1.0 C2 C:ZDC101 4.7 11.6 1.0 CA A:GLU95 4.7 11.6 1.0 H A:ASP104 4.7 11.5 1.0 CA A:ASP101 4.7 13.6 1.0 CB A:ASP99 4.7 15.3 1.0 OD1 A:ASN103 4.7 10.0 1.0 HG2 A:GLU95 4.7 15.4 1.0 C5 C:ZDC101 4.8 11.7 1.0 N A:ASP99 4.8 16.0 1.0 O2 C:ZDC101 4.8 11.2 1.0 HB3 A:ASP104 4.8 12.0 1.0 H2O C:ZDC101 4.8 13.4 1.0 HB3 A:ASP101 4.9 14.3 1.0 CB A:GLU95 4.9 13.3 1.0 HA A:ASN100 4.9 18.3 1.0 CG A:ASP96 4.9 12.7 1.0 HB2 A:GLU95 5.0 15.9 1.0 C A:ASP99 5.0 15.8 1.0

Calcium binding site 2 out of 2 in the Cfucosylated Second Generation Peptide Dendrimer SBD8 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.43 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cfucosylated Second Generation Peptide Dendrimer SBD8 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 1.43 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:10.8 occ:1.00 H2O C:ZDC101 2.0 13.4 1.0 OD1 A:ASN103 2.3 10.0 1.0 O A:ASN21 2.3 12.0 1.0 OD1 A:ASP104 2.4 10.8 1.0 O3 C:ZDC101 2.4 12.2 1.0 OD2 A:ASP101 2.5 11.4 1.0 O2 C:ZDC101 2.5 11.2 1.0 H3O C:ZDC101 2.6 14.5 1.0 OD1 A:ASP101 3.1 12.7 1.0 CG A:ASP101 3.1 12.8 1.0 H4 C:ZDC101 3.4 13.3 1.0 CG A:ASN103 3.4 10.0 1.0 HD21 A:ASN103 3.4 14.0 1.0 C3 C:ZDC101 3.4 11.8 1.0 C2 C:ZDC101 3.4 11.6 1.0 HA A:ASP104 3.5 12.2 1.0 C A:ASN21 3.5 11.6 1.0 CG A:ASP104 3.6 11.1 1.0 HA A:SER22 3.7 13.3 1.0 HB3 A:ASN21 3.7 13.3 1.0 H2 C:ZDC101 3.7 13.8 1.0 CA A:CA301 3.7 11.4 1.0 ND2 A:ASN103 3.8 11.7 1.0 C4 C:ZDC101 3.8 11.1 1.0 HB2 A:ASN21 3.9 13.3 1.0 HB2 A:SER22 3.9 14.5 1.0 H A:ASN103 4.1 12.3 1.0 CB A:ASN21 4.2 11.1 1.0 CA A:ASP104 4.2 10.2 1.0 H3 C:ZDC101 4.3 14.1 1.0 N A:ASP104 4.3 9.6 1.0 CA A:SER22 4.4 11.1 1.0 N A:SER22 4.4 11.0 1.0 OD2 A:ASP104 4.4 10.8 1.0 CB A:ASP104 4.5 10.0 1.0 O4 C:ZDC101 4.5 12.0 1.0 C A:ASN103 4.5 9.8 1.0 H4O C:ZDC101 4.5 14.4 1.0 OD2 A:ASP99 4.5 14.2 1.0 CA A:ASN21 4.5 10.7 1.0 CB A:ASP101 4.5 12.0 1.0 O A:HOH444 4.6 28.3 1.0 H A:ASP104 4.6 11.5 1.0 CB A:SER22 4.6 12.1 1.0 HD22 A:ASN103 4.6 14.0 1.0 HB2 A:ASP101 4.7 14.3 1.0 CB A:ASN103 4.7 10.4 1.0 C1 C:ZDC101 4.8 12.6 1.0 HB3 A:ASP104 4.8 12.0 1.0 O A:ASN103 4.8 10.5 1.0 N A:ASN103 4.8 10.3 1.0 CA A:ASN103 4.9 9.7 1.0 HB3 A:ASP101 5.0 14.3 1.0

S.Baeriswyl, S.Javor, A.Stocker, T.Darbre, J.-L.Reymond. X-Ray Crystal Structure of A Second Generation Peptide Dendrimer in Complex with Pseudomonas Aeruginosa Lectin Lecb Helv.Chim.Acta 2019.
ISSN: ISSN 0018-019X
DOI: 10.1002/HLCA.201900178