Calcium in PDB 6q8d: Structure of Fucosylated D-Antimicrobial Peptide SB15 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.630 Angstrom Resolution

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB15 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.630 Angstrom Resolution, PDB code: 6q8d 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)	49.00 / 1.63
Space group	P 42 2 2
Cell size a, b, c (Å), α, β, γ (°)	51.445, 51.445, 98.006, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 23.8

The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB15 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.630 Angstrom Resolution (pdb code 6q8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Fucosylated D-Antimicrobial Peptide SB15 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.630 Angstrom Resolution, PDB code: 6q8d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Fucosylated D-Antimicrobial Peptide SB15 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.630 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Fucosylated D-Antimicrobial Peptide SB15 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.630 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:41.0 occ:1.00 OE2 A:GLU95 2.4 34.9 1.0 OD1 A:ASP99 2.4 36.9 1.0 O4 B:ZDC1 2.5 36.9 1.0 OD1 A:ASP101 2.5 31.3 1.0 OE1 A:GLU95 2.5 36.0 1.0 OD2 A:ASP104 2.6 35.4 1.0 O3 B:ZDC1 2.6 33.7 1.0 OD1 A:ASP104 2.6 34.2 1.0 CD A:GLU95 2.7 35.7 1.0 CG A:ASP104 2.9 47.9 1.0 C4 B:ZDC1 3.3 34.2 1.0 CG A:ASP99 3.4 63.6 1.0 C3 B:ZDC1 3.5 33.0 1.0 CG A:ASP101 3.5 51.9 1.0 OD2 A:ASP99 3.7 39.2 1.0 CA A:CA302 3.7 38.7 1.0 N A:ASP101 4.0 31.3 1.0 OD2 A:ASP101 4.1 39.4 1.0 O A:HOH439 4.1 38.3 1.0 OD1 A:ASP96 4.2 38.3 1.0 CG A:GLU95 4.2 33.5 1.0 N A:ASP96 4.4 38.5 1.0 N A:ASN100 4.4 41.4 1.0 N A:TYR102 4.4 29.0 1.0 CB A:ASP104 4.5 31.2 1.0 N A:GLY97 4.5 39.7 1.0 CA A:GLU95 4.6 31.1 1.0 CB A:ASP101 4.7 43.8 1.0 C5 B:ZDC1 4.7 35.6 1.0 CA A:ASP101 4.7 30.6 1.0 OD1 A:ASN103 4.8 29.0 1.0 CB A:GLU95 4.8 31.3 1.0 CB A:ASP99 4.8 57.2 1.0 C2 B:ZDC1 4.8 32.7 1.0 CG A:ASP96 4.8 41.8 1.0 N A:ASP99 4.9 41.6 1.0 O2 B:ZDC1 4.9 33.6 1.0 CA A:ASN100 4.9 46.6 1.0 C A:ASP99 5.0 37.1 1.0 C A:ASP101 5.0 35.4 1.0 C A:GLU95 5.0 36.3 1.0 C A:ASN100 5.0 41.6 1.0

Calcium binding site 2 out of 2 in the Structure of Fucosylated D-Antimicrobial Peptide SB15 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.630 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Fucosylated D-Antimicrobial Peptide SB15 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.630 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:38.7 occ:1.00 O A:ASN21 2.4 37.4 1.0 OD1 A:ASN103 2.4 29.0 1.0 O2 B:ZDC1 2.4 33.6 1.0 OD1 A:ASP104 2.5 34.2 1.0 O3 B:ZDC1 2.5 33.7 1.0 OD2 A:ASP101 2.5 39.4 1.0 OD1 A:ASP101 3.1 31.3 1.0 CG A:ASP101 3.1 51.9 1.0 C3 B:ZDC1 3.3 33.0 1.0 C2 B:ZDC1 3.4 32.7 1.0 CG A:ASN103 3.5 32.5 1.0 C A:ASN21 3.6 50.0 1.0 C4 B:ZDC1 3.7 34.2 1.0 CA A:CA301 3.7 41.0 1.0 CG A:ASP104 3.7 47.9 1.0 ND2 A:ASN103 4.0 33.2 1.0 CA A:ASP104 4.2 29.7 1.0 CB A:ASN21 4.2 31.2 1.0 N A:ASP104 4.2 28.2 1.0 O4 B:ZDC1 4.3 36.9 1.0 CA A:SER22 4.3 37.4 1.0 N A:SER22 4.4 39.3 1.0 O A:HOH416 4.4 42.3 1.0 C A:ASN103 4.5 29.1 1.0 OD2 A:ASP99 4.5 39.2 1.0 CA A:ASN21 4.5 40.0 1.0 CB A:SER22 4.5 36.4 1.0 CB A:ASP104 4.6 31.2 1.0 OD2 A:ASP104 4.6 35.4 1.0 CB A:ASP101 4.6 43.8 1.0 C1 B:ZDC1 4.7 33.5 1.0 O A:ASN103 4.8 33.5 1.0 CB A:ASN103 4.8 27.2 1.0 N A:ASN103 4.9 28.7 1.0 O5 B:ZDC1 5.0 35.6 1.0 C5 B:ZDC1 5.0 35.6 1.0 CA A:ASN103 5.0 35.5 1.0

S.Baeriswyl, B.H.Gan, T.N.Siriwardena, R.Visini, M.Robadey, S.Javor, A.Stocker, T.Darbre, J.L.Reymond. X-Ray Crystal Structures of Short Antimicrobial Peptides As Pseudomonas Aeruginosa Lectin B Complexes. Acs Chem.Biol. V. 14 758 2019.
ISSN: ESSN 1554-8937
PubMed: 30830745
DOI: 10.1021/ACSCHEMBIO.9B00047