Calcium in PDB 6q87: Structure of Fucosylated D-Antimicrobial Peptide SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.541 Angstrom Resolution

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.541 Angstrom Resolution, PDB code: 6q87 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)	45.42 / 2.54
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	130.200, 130.200, 49.623, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 25.7

The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.541 Angstrom Resolution (pdb code 6q87). 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 SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.541 Angstrom Resolution, PDB code: 6q87:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Fucosylated D-Antimicrobial Peptide SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.541 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 SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.541 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:67.8 occ:1.00 OD2 A:ASP101 2.2 74.9 1.0 OE1 A:GLU95 2.3 70.2 1.0 O4 B:ZDC1 2.3 86.6 1.0 OD1 A:ASP99 2.4 82.9 1.0 OE2 A:GLU95 2.5 67.2 1.0 OD1 A:ASP104 2.5 56.7 1.0 O3 B:ZDC1 2.6 83.0 1.0 OD2 A:ASP104 2.6 64.2 1.0 CD A:GLU95 2.7 71.4 1.0 CG A:ASP104 2.9 64.6 1.0 C4 B:ZDC1 3.2 81.2 1.0 CG A:ASP101 3.3 71.9 1.0 C3 B:ZDC1 3.3 74.1 1.0 CG A:ASP99 3.4 77.9 1.0 OD2 A:ASP99 3.7 78.7 1.0 OD1 A:ASP101 3.7 75.9 1.0 CA A:CA302 4.0 67.4 1.0 N A:ASP101 4.0 76.6 1.0 CG A:GLU95 4.1 74.7 1.0 N A:TYR102 4.3 63.5 1.0 N A:ASN100 4.3 69.9 1.0 OD2 A:ASP96 4.3 74.8 1.0 CB A:ASP104 4.4 58.4 1.0 N A:ASP96 4.4 60.5 1.0 N A:GLY97 4.5 66.3 1.0 CB A:ASP101 4.5 67.1 1.0 CA A:GLU95 4.5 71.8 1.0 C5 B:ZDC1 4.6 73.1 1.0 CB A:GLU95 4.6 64.5 1.0 N A:ASP99 4.6 70.8 1.0 C2 B:ZDC1 4.7 70.7 1.0 CA A:ASP101 4.7 72.2 1.0 OD1 A:ASN103 4.7 63.1 1.0 CB A:ASP99 4.7 68.7 1.0 O2 B:ZDC1 4.8 66.9 1.0 CG A:ASP96 4.9 73.7 1.0 C A:ASP99 4.9 71.1 1.0 CA A:ASN100 4.9 76.8 1.0 C A:ASP101 5.0 66.0 1.0 C A:ASN100 5.0 76.0 1.0 C A:GLU95 5.0 79.3 1.0 CA A:ASP99 5.0 68.3 1.0

Calcium binding site 2 out of 2 in the Structure of Fucosylated D-Antimicrobial Peptide SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.541 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 SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.541 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:67.4 occ:1.00 OD1 A:ASN103 2.4 63.1 1.0 O A:ASN21 2.4 86.1 1.0 OD1 A:ASP101 2.4 75.9 1.0 O2 B:ZDC1 2.5 66.9 1.0 O3 B:ZDC1 2.5 83.0 1.0 OD2 A:ASP104 2.6 64.2 1.0 CG A:ASP101 3.2 71.9 1.0 CG A:ASN103 3.3 61.2 1.0 OD2 A:ASP101 3.4 74.9 1.0 C2 B:ZDC1 3.5 70.7 1.0 C3 B:ZDC1 3.5 74.1 1.0 C A:ASN21 3.5 78.2 1.0 ND2 A:ASN103 3.7 57.7 1.0 CG A:ASP104 3.8 64.6 1.0 CB A:ASN21 3.8 64.5 1.0 C4 B:ZDC1 3.9 81.2 1.0 CA A:CA301 4.0 67.8 1.0 CA A:ASP104 4.1 57.3 1.0 N A:ASP104 4.2 53.5 1.0 C A:ASN103 4.3 62.1 1.0 CA A:ASN21 4.3 68.6 1.0 OD2 A:ASP99 4.4 78.7 1.0 N A:SER22 4.5 72.4 1.0 CB A:ASP101 4.5 67.1 1.0 O A:ASN103 4.5 59.8 1.0 O4 B:ZDC1 4.6 86.6 1.0 CA A:SER22 4.6 76.3 1.0 CB A:ASP104 4.6 58.4 1.0 CB A:ASN103 4.6 69.5 1.0 OD1 A:ASP104 4.7 56.7 1.0 N A:ASN103 4.8 63.5 1.0 CA A:ASN103 4.8 65.7 1.0 C1 B:ZDC1 4.8 74.5 1.0 CB A:SER22 4.9 77.5 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