Calcium in PDB 6q6w: Structure of Fucosylated D-Antimicrobial Peptide SB5 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.438 Angstrom Resolution

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB5 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.438 Angstrom Resolution, PDB code: 6q6w 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)	47.46 / 1.44
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	56.977, 56.977, 173.543, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 19.7

The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB5 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.438 Angstrom Resolution (pdb code 6q6w). 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 SB5 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.438 Angstrom Resolution, PDB code: 6q6w:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Fucosylated D-Antimicrobial Peptide SB5 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.438 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 SB5 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.438 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:28.1 occ:1.00 OD1 A:ASP101 2.4 24.3 1.0 OE2 A:GLU95 2.4 25.3 1.0 OD1 A:ASP99 2.4 28.6 1.0 OD2 A:ASP104 2.4 24.6 1.0 OE1 A:GLU95 2.4 22.5 1.0 O4 B:ZDC1 2.4 24.6 1.0 O3 B:ZDC1 2.5 25.0 1.0 OD1 A:ASP104 2.6 24.7 1.0 CD A:GLU95 2.7 24.1 1.0 CG A:ASP104 2.9 24.8 1.0 C4 B:ZDC1 3.3 22.5 1.0 C3 B:ZDC1 3.4 22.6 1.0 CG A:ASP101 3.4 24.5 1.0 CG A:ASP99 3.4 28.5 1.0 CA A:CA302 3.7 28.0 1.0 OD2 A:ASP99 3.8 28.0 1.0 O A:HOH451 4.0 34.8 1.0 OD2 A:ASP101 4.0 23.8 1.0 OD1 A:ASP96 4.1 26.8 1.0 N A:ASP101 4.2 25.4 1.0 CG A:GLU95 4.2 23.9 1.0 CB A:ASP104 4.4 22.1 1.0 N A:TYR102 4.5 23.2 1.0 N A:ASN100 4.5 27.7 1.0 N A:ASP96 4.5 23.2 1.0 CB A:ASP101 4.6 27.2 1.0 N A:GLY97 4.7 25.1 1.0 CA A:GLU95 4.7 23.6 1.0 OD1 A:ASN103 4.7 23.3 1.0 C2 B:ZDC1 4.7 21.6 1.0 C5 B:ZDC1 4.7 22.1 1.0 O2 B:ZDC1 4.7 24.6 1.0 CA A:ASP101 4.8 25.5 1.0 CB A:ASP99 4.8 27.7 1.0 N A:ASP99 4.8 28.4 1.0 CB A:GLU95 4.9 21.9 1.0 CG A:ASP96 4.9 27.4 1.0

Calcium binding site 2 out of 2 in the Structure of Fucosylated D-Antimicrobial Peptide SB5 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.438 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 SB5 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.438 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:28.0 occ:1.00 OD1 A:ASN103 2.3 23.3 1.0 O A:ASN21 2.4 21.0 1.0 OD1 A:ASP104 2.4 24.7 1.0 O2 B:ZDC1 2.4 24.6 1.0 OD2 A:ASP101 2.4 23.8 1.0 O3 B:ZDC1 2.5 25.0 1.0 CG A:ASP101 3.1 24.5 1.0 OD1 A:ASP101 3.1 24.3 1.0 C2 B:ZDC1 3.4 21.6 1.0 CG A:ASN103 3.4 21.3 1.0 C3 B:ZDC1 3.4 22.6 1.0 C A:ASN21 3.6 20.6 1.0 CG A:ASP104 3.6 24.8 1.0 CA A:CA301 3.7 28.1 1.0 ND2 A:ASN103 3.8 22.4 1.0 C4 B:ZDC1 3.8 22.5 1.0 CB A:ASN21 4.2 22.2 1.0 CA A:ASP104 4.2 21.9 1.0 N A:ASP104 4.2 20.6 1.0 O4 B:ZDC1 4.4 24.6 1.0 N A:SER22 4.4 24.5 1.0 C A:ASN103 4.4 21.8 1.0 CA A:SER22 4.5 23.7 1.0 OD2 A:ASP104 4.5 24.6 1.0 O A:HOH431 4.5 36.7 1.0 CB A:ASP104 4.5 22.1 1.0 CA A:ASN21 4.5 21.1 1.0 CB A:ASP101 4.6 27.2 1.0 OD2 A:ASP99 4.6 28.0 1.0 CB A:ASN103 4.7 20.7 1.0 CB A:SER22 4.7 24.9 1.0 C1 B:ZDC1 4.7 24.6 1.0 O A:ASN103 4.8 22.6 1.0 N A:ASN103 4.9 21.9 1.0 CA A:ASN103 4.9 19.8 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