Calcium in PDB 6s5r: Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure

The structure of Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure, PDB code: 6s5r 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)	45.04 / 2.08
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	91.003, 91.003, 315.583, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 23.7

The binding sites of Calcium atom in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure (pdb code 6s5r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure, PDB code: 6s5r:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure


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 SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:44.6 occ:1.00 OD1 A:ASP99 2.3 48.2 1.0 OD1 A:ASP101 2.4 40.1 1.0 OE2 A:GLU95 2.4 38.6 1.0 OD2 A:ASP104 2.4 37.7 1.0 OE1 A:GLU95 2.5 45.0 1.0 O4 A:ZDC303 2.5 62.5 1.0 O3 A:ZDC303 2.5 62.3 1.0 OD1 A:ASP104 2.6 48.5 1.0 CD A:GLU95 2.7 40.3 1.0 CG A:ASP104 2.9 49.2 1.0 CG A:ASP99 3.2 35.7 1.0 C4 A:ZDC303 3.3 63.1 1.0 C3 A:ZDC303 3.3 63.0 1.0 OD2 A:ASP99 3.4 50.8 1.0 CG A:ASP101 3.4 46.8 1.0 CA A:CA302 3.7 46.4 1.0 OD2 A:ASP101 3.9 45.8 1.0 N A:ASP101 4.1 31.5 1.0 O A:HOH406 4.2 56.0 1.0 CG A:GLU95 4.2 42.3 1.0 OD1 A:ASP96 4.2 35.6 1.0 N A:ASN100 4.4 45.5 1.0 CB A:ASP104 4.4 41.3 1.0 N A:TYR102 4.5 41.9 1.0 N A:ASP96 4.5 32.2 1.0 OD1 A:ASN103 4.6 48.2 1.0 CB A:ASP99 4.6 40.5 1.0 N A:GLY97 4.6 41.1 1.0 CB A:ASP101 4.6 47.1 1.0 C2 A:ZDC303 4.7 62.5 1.0 CA A:GLU95 4.7 34.7 1.0 C5 A:ZDC303 4.7 63.9 1.0 N A:ASP99 4.8 49.3 1.0 CA A:ASP101 4.8 36.2 1.0 O2 A:ZDC303 4.8 62.5 1.0 CB A:GLU95 4.9 39.7 1.0 C A:ASP99 4.9 49.9 1.0 CA A:ASN100 4.9 44.9 1.0 CA A:ASP99 5.0 59.4 1.0

Calcium binding site 2 out of 8 in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure


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 SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:46.4 occ:1.00 O A:ASN21 2.3 67.8 1.0 OD1 A:ASN103 2.3 48.2 1.0 O B:GLY114 2.4 42.6 1.0 OD2 A:ASP101 2.4 45.8 1.0 O3 A:ZDC303 2.4 62.3 1.0 O2 A:ZDC303 2.7 62.5 1.0 OD2 A:ASP104 2.7 37.7 1.0 CG A:ASP101 3.1 46.8 1.0 OD1 A:ASP101 3.1 40.1 1.0 CG A:ASN103 3.3 43.8 1.0 C B:GLY114 3.3 57.9 1.0 C3 A:ZDC303 3.4 63.0 1.0 C2 A:ZDC303 3.5 62.5 1.0 OXT B:GLY114 3.5 51.4 1.0 C A:ASN21 3.5 60.1 1.0 ND2 A:ASN103 3.6 43.8 1.0 CA A:CA301 3.7 44.6 1.0 C4 A:ZDC303 3.8 63.1 1.0 CG A:ASP104 3.9 49.2 1.0 CB A:ASN21 4.2 39.2 1.0 N A:ASP104 4.2 35.6 1.0 CA A:ASP104 4.2 59.6 1.0 OD2 A:ASP99 4.3 50.8 1.0 CA A:SER22 4.4 42.7 1.0 N A:SER22 4.5 49.1 1.0 C A:ASN103 4.5 38.2 1.0 CA A:ASN21 4.5 46.5 1.0 O4 A:ZDC303 4.5 62.5 1.0 CB A:ASP101 4.5 47.1 1.0 CB A:SER22 4.6 48.4 1.0 CB A:ASP104 4.6 41.3 1.0 CB A:ASN103 4.7 40.7 1.0 CA B:GLY114 4.7 47.4 1.0 OD1 A:ASP104 4.8 48.5 1.0 C1 A:ZDC303 4.8 62.7 1.0 O A:ASN103 4.8 41.0 1.0 N A:ASN103 4.9 34.3 1.0 CA A:ASN103 4.9 32.7 1.0

Calcium binding site 3 out of 8 in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:50.4 occ:1.00 OD1 B:ASN103 2.3 46.0 1.0 O B:ASN21 2.3 54.7 1.0 OD2 B:ASP101 2.4 49.0 1.0 O2 A:ZDC305 2.4 63.0 1.0 OD1 B:ASP104 2.5 49.6 1.0 O A:GLY114 2.5 53.0 1.0 O3 A:ZDC305 2.6 64.5 1.0 CG B:ASP101 3.1 36.3 1.0 OD1 B:ASP101 3.1 39.9 1.0 CG B:ASN103 3.3 42.6 1.0 C A:GLY114 3.5 59.6 1.0 C B:ASN21 3.5 62.5 1.0 C2 A:ZDC305 3.5 63.2 1.0 C3 A:ZDC305 3.5 64.1 1.0 OXT A:GLY114 3.7 57.1 1.0 CA B:CA301 3.7 46.2 1.0 ND2 B:ASN103 3.7 53.1 1.0 CG B:ASP104 3.7 46.0 1.0 C4 A:ZDC305 3.8 65.5 1.0 CB B:ASN21 4.1 46.5 1.0 N B:ASP104 4.1 54.2 1.0 CA B:ASP104 4.1 51.5 1.0 OD2 B:ASP99 4.3 57.7 1.0 N B:SER22 4.4 53.0 1.0 C B:ASN103 4.4 57.3 1.0 CA B:ASN21 4.4 48.5 1.0 CA B:SER22 4.5 56.0 1.0 CB B:ASP104 4.5 55.5 1.0 O4 A:ZDC305 4.5 64.5 1.0 CB B:ASP101 4.5 46.7 1.0 OD2 B:ASP104 4.6 52.6 1.0 CB B:ASN103 4.7 37.8 1.0 CB B:SER22 4.7 47.5 1.0 C1 A:ZDC305 4.8 64.0 1.0 O B:ASN103 4.8 36.8 1.0 N B:ASN103 4.9 46.9 1.0 CA A:GLY114 4.9 44.5 1.0 CA B:ASN103 4.9 46.7 1.0

Calcium binding site 4 out of 8 in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:46.2 occ:1.00 O3 A:ZDC305 2.4 64.5 1.0 OD1 B:ASP99 2.4 55.0 1.0 OD1 B:ASP101 2.4 39.9 1.0 OD1 B:ASP104 2.4 49.6 1.0 OD2 B:ASP104 2.4 52.6 1.0 OE2 B:GLU95 2.5 47.6 1.0 OE1 B:GLU95 2.5 41.8 1.0 O4 A:ZDC305 2.7 64.5 1.0 CG B:ASP104 2.8 46.0 1.0 CD B:GLU95 2.8 45.2 1.0 C3 A:ZDC305 3.3 64.1 1.0 CG B:ASP99 3.3 50.0 1.0 C4 A:ZDC305 3.4 65.5 1.0 CG B:ASP101 3.4 36.3 1.0 OD2 B:ASP99 3.5 57.7 1.0 CA A:CA304 3.7 50.4 1.0 OD2 B:ASP101 3.8 49.0 1.0 OD1 B:ASP96 4.0 58.2 1.0 O B:HOH436 4.1 54.2 1.0 N B:ASP101 4.2 40.4 1.0 CB B:ASP104 4.3 55.5 1.0 CG B:GLU95 4.3 39.6 1.0 N B:ASP96 4.4 37.7 1.0 N B:TYR102 4.5 36.1 1.0 N B:ASN100 4.5 42.0 1.0 N B:GLY97 4.6 45.7 1.0 O2 A:ZDC305 4.6 63.0 1.0 C2 A:ZDC305 4.6 63.2 1.0 OD1 B:ASN103 4.6 46.0 1.0 CB B:ASP101 4.6 46.7 1.0 CA B:GLU95 4.6 39.8 1.0 CB B:ASP99 4.7 39.6 1.0 CA B:ASP101 4.8 38.8 1.0 C5 A:ZDC305 4.8 66.3 1.0 CG B:ASP96 4.8 40.9 1.0 N B:ASP104 4.8 54.2 1.0 N B:ASP99 4.9 53.5 1.0 CB B:GLU95 4.9 43.1 1.0 CA B:ASP104 5.0 51.5 1.0

Calcium binding site 5 out of 8 in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:50.9 occ:1.00 OD1 C:ASP99 2.3 52.1 1.0 OD1 C:ASP101 2.5 60.8 1.0 OD1 C:ASP104 2.5 45.2 1.0 OD2 C:ASP104 2.6 51.7 1.0 OE2 C:GLU95 2.6 54.2 1.0 O3 C:ZDC303 2.6 66.7 1.0 OE1 C:GLU95 2.6 56.5 1.0 O4 C:ZDC303 2.7 67.0 1.0 CG C:ASP104 2.9 67.2 1.0 CD C:GLU95 2.9 61.5 1.0 CG C:ASP99 3.3 62.7 1.0 CG C:ASP101 3.4 57.4 1.0 C3 C:ZDC303 3.5 67.6 1.0 C4 C:ZDC303 3.5 68.4 1.0 OD2 C:ASP99 3.5 61.4 1.0 CA C:CA302 3.6 52.4 1.0 OD2 C:ASP101 3.8 50.6 1.0 OD1 C:ASP96 4.1 58.0 1.0 N C:ASP101 4.2 54.2 1.0 CG C:GLU95 4.3 53.5 1.0 CB C:ASP104 4.4 55.7 1.0 N C:ASN100 4.4 55.0 1.0 N C:TYR102 4.5 51.7 1.0 N C:ASP96 4.5 54.5 1.0 CB C:ASP101 4.6 48.6 1.0 N C:GLY97 4.6 57.4 1.0 CB C:ASP99 4.7 55.7 1.0 N C:ASP99 4.7 71.3 1.0 CA C:GLU95 4.7 64.0 1.0 OD1 C:ASN103 4.8 46.6 1.0 C2 C:ZDC303 4.8 66.1 1.0 CA C:ASP101 4.9 55.5 1.0 CB C:GLU95 4.9 63.0 1.0 C5 C:ZDC303 4.9 68.5 1.0 O2 C:ZDC303 4.9 66.3 1.0 C C:ASP99 4.9 55.2 1.0 CG C:ASP96 5.0 74.2 1.0 CA C:ASP99 5.0 57.7 1.0

Calcium binding site 6 out of 8 in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:52.4 occ:1.00 O C:ASN21 2.3 44.8 1.0 OD1 C:ASP104 2.3 45.2 1.0 OD2 C:ASP101 2.4 50.6 1.0 OD1 C:ASN103 2.4 46.6 1.0 O3 C:ZDC303 2.5 66.7 1.0 O D:GLY114 2.6 52.1 1.0 O2 C:ZDC303 2.7 66.3 1.0 CG C:ASP101 3.2 57.4 1.0 OD1 C:ASP101 3.3 60.8 1.0 C3 C:ZDC303 3.4 67.6 1.0 C D:GLY114 3.4 60.3 1.0 C2 C:ZDC303 3.5 66.1 1.0 CG C:ASN103 3.5 57.6 1.0 OXT D:GLY114 3.5 49.4 1.0 C C:ASN21 3.5 56.9 1.0 CG C:ASP104 3.6 67.2 1.0 CA C:CA301 3.6 50.9 1.0 C4 C:ZDC303 3.8 68.4 1.0 ND2 C:ASN103 3.9 40.3 1.0 CA C:ASP104 4.1 52.5 1.0 N C:ASP104 4.1 46.6 1.0 CB C:ASN21 4.2 42.5 1.0 OD2 C:ASP99 4.3 61.4 1.0 CB C:ASP104 4.4 55.7 1.0 O4 C:ZDC303 4.4 67.0 1.0 CA C:SER22 4.4 46.1 1.0 N C:SER22 4.4 45.9 1.0 C C:ASN103 4.5 43.0 1.0 OD2 C:ASP104 4.5 51.7 1.0 CA C:ASN21 4.5 44.0 1.0 CB C:SER22 4.5 45.5 1.0 CB C:ASP101 4.6 48.6 1.0 CB C:ASN103 4.8 47.5 1.0 C1 C:ZDC303 4.8 66.5 1.0 O C:ASN103 4.8 43.0 1.0 CA D:GLY114 4.9 47.5 1.0 N C:ASN103 4.9 50.2 1.0 CA C:ASN103 5.0 47.2 1.0

Calcium binding site 7 out of 8 in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:49.6 occ:1.00 OD1 D:ASN103 2.3 48.9 1.0 O D:ASN21 2.4 55.6 1.0 OD2 D:ASP101 2.4 43.5 1.0 O3 H:ZDC201 2.4 65.6 1.0 O2 H:ZDC201 2.5 65.5 1.0 OD1 D:ASP104 2.5 41.8 1.0 O C:GLY114 2.5 49.8 1.0 OD1 D:ASP101 3.0 45.0 1.0 CG D:ASP101 3.1 50.0 1.0 C3 H:ZDC201 3.3 66.7 1.0 C2 H:ZDC201 3.4 66.0 1.0 CG D:ASN103 3.4 51.8 1.0 C C:GLY114 3.5 60.2 1.0 C D:ASN21 3.5 45.8 1.0 OXT C:GLY114 3.6 64.1 1.0 CA D:CA301 3.7 52.2 1.0 C4 H:ZDC201 3.7 67.3 1.0 CG D:ASP104 3.7 61.4 1.0 ND2 D:ASN103 3.8 44.6 1.0 O D:HOH404 4.1 49.9 1.0 CB D:ASN21 4.2 46.0 1.0 CA D:ASP104 4.2 45.1 1.0 N D:ASP104 4.2 37.9 1.0 OD2 D:ASP99 4.3 50.3 1.0 CA D:SER22 4.4 50.6 1.0 N D:SER22 4.4 59.2 1.0 O4 H:ZDC201 4.5 66.9 1.0 C D:ASN103 4.5 45.6 1.0 CA D:ASN21 4.5 56.0 1.0 CB D:ASP101 4.5 50.1 1.0 CB D:ASP104 4.5 38.5 1.0 OD2 D:ASP104 4.6 41.5 1.0 CB D:SER22 4.7 55.3 1.0 CB D:ASN103 4.7 45.6 1.0 C1 H:ZDC201 4.7 66.7 1.0 O D:ASN103 4.8 45.4 1.0 CA C:GLY114 4.9 53.7 1.0 N D:ASN103 4.9 49.5 1.0 CA D:ASN103 4.9 48.7 1.0 O5 H:ZDC201 5.0 67.1 1.0 C5 H:ZDC201 5.0 68.5 1.0

Calcium binding site 8 out of 8 in the Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Cfucosylated Second Generation Peptide Dendrimer SBD6 Bound to Fucose Binding Lectin Lecb (Pa-Iil) From Pseudomonas Aeruginosa at 2.08 Angstrom Resolution, Incomplete Structure within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:52.2 occ:1.00 OE2 D:GLU95 2.3 57.3 1.0 OD1 D:ASP99 2.4 62.4 1.0 OD1 D:ASP101 2.4 45.0 1.0 OD1 D:ASP104 2.5 41.8 1.0 O3 H:ZDC201 2.5 65.6 1.0 O4 H:ZDC201 2.5 66.9 1.0 OE1 D:GLU95 2.6 64.2 1.0 OD2 D:ASP104 2.6 41.5 1.0 CD D:GLU95 2.7 62.0 1.0 CG D:ASP104 2.9 61.4 1.0 C4 H:ZDC201 3.2 67.3 1.0 CG D:ASP99 3.3 49.2 1.0 C3 H:ZDC201 3.3 66.7 1.0 CG D:ASP101 3.4 50.0 1.0 OD2 D:ASP99 3.5 50.3 1.0 CA C:CA304 3.7 49.6 1.0 O D:HOH427 3.7 47.5 1.0 OD2 D:ASP101 3.9 43.5 1.0 N D:ASP101 4.1 55.5 1.0 OD1 D:ASP96 4.1 51.1 1.0 CG D:GLU95 4.1 52.6 1.0 CB D:ASP104 4.4 38.5 1.0 N D:ASP96 4.5 41.5 1.0 N D:ASN100 4.5 45.9 1.0 N D:TYR102 4.5 36.5 1.0 N D:GLY97 4.6 55.3 1.0 CB D:ASP101 4.6 50.1 1.0 CA D:GLU95 4.6 57.7 1.0 CB D:GLU95 4.6 53.0 1.0 C2 H:ZDC201 4.7 66.0 1.0 CB D:ASP99 4.7 56.1 1.0 OD1 D:ASN103 4.7 48.9 1.0 C5 H:ZDC201 4.7 68.5 1.0 CA D:ASP101 4.8 50.0 1.0 O2 H:ZDC201 4.8 65.5 1.0 N D:ASP99 4.9 57.8 1.0 CG D:ASP96 4.9 54.6 1.0 CA D:ASN100 5.0 55.6 1.0 N D:ASP104 5.0 37.9 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