Calcium in PDB 6q8h: Structure of Fucosylated D-Antimicrobial Peptide SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.707 Angstrom Resolution

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB10 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.707 Angstrom Resolution, PDB code: 6q8h 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)	45.72 / 1.71
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.522, 131.522, 49.920, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 18.9

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 1.707 Angstrom Resolution (pdb code 6q8h). 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 1.707 Angstrom Resolution, PDB code: 6q8h:
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 1.707 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 1.707 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:29.6 occ:1.00 OE1 A:GLU95 2.4 31.3 1.0 OD2 A:ASP104 2.4 27.5 1.0 OD1 A:ASP101 2.4 29.3 1.0 OD1 A:ASP99 2.4 31.8 1.0 OE2 A:GLU95 2.4 29.7 1.0 O4 A:ZDC303 2.5 30.4 1.0 O3 A:ZDC303 2.5 30.1 1.0 OD1 A:ASP104 2.7 31.1 1.0 CD A:GLU95 2.7 35.7 1.0 CG A:ASP104 2.9 30.7 1.0 C4 A:ZDC303 3.3 35.1 1.0 C3 A:ZDC303 3.4 32.2 1.0 CG A:ASP99 3.5 32.3 1.0 CG A:ASP101 3.5 30.6 1.0 OD2 A:ASP99 3.8 33.1 1.0 CA A:CA302 3.8 29.1 1.0 OD2 A:ASP101 3.9 28.4 1.0 N A:ASP101 4.1 27.4 1.0 CG A:GLU95 4.2 27.4 1.0 O A:HOH473 4.3 46.2 1.0 OD1 A:ASP96 4.3 34.7 1.0 CB A:ASP104 4.4 26.6 1.0 N A:TYR102 4.4 27.6 1.0 N A:ASN100 4.4 32.0 1.0 N A:ASP96 4.5 31.1 1.0 N A:GLY97 4.6 31.7 1.0 CA A:GLU95 4.6 29.3 1.0 CB A:ASP101 4.7 28.0 1.0 C5 A:ZDC303 4.7 34.3 1.0 C2 A:ZDC303 4.8 29.9 1.0 CB A:ASP99 4.8 30.4 1.0 CA A:ASP101 4.8 26.8 1.0 CB A:GLU95 4.8 26.2 1.0 N A:ASP99 4.8 33.7 1.0 OD1 A:ASN103 4.8 26.3 1.0 O2 A:ZDC303 4.9 29.1 1.0 CG A:ASP96 5.0 33.2 1.0 C A:ASP99 5.0 36.2 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 1.707 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 1.707 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:29.1 occ:1.00 O A:ASN21 2.3 27.9 1.0 OD2 A:ASP101 2.4 28.4 1.0 OD1 A:ASN103 2.4 26.3 1.0 OD1 A:ASP104 2.4 31.1 1.0 O3 A:ZDC303 2.5 30.1 1.0 O2 A:ZDC303 2.5 29.1 1.0 CG A:ASP101 3.1 30.6 1.0 OD1 A:ASP101 3.2 29.3 1.0 C3 A:ZDC303 3.4 32.2 1.0 C2 A:ZDC303 3.4 29.9 1.0 CG A:ASN103 3.4 34.3 1.0 C A:ASN21 3.5 27.0 1.0 CG A:ASP104 3.7 30.7 1.0 CA A:CA301 3.8 29.6 1.0 C4 A:ZDC303 3.8 35.1 1.0 ND2 A:ASN103 3.9 28.5 1.0 CB A:ASN21 4.2 25.8 1.0 CA A:ASP104 4.2 25.8 1.0 N A:ASP104 4.3 25.0 1.0 O A:HOH452 4.3 36.6 1.0 CA A:SER22 4.3 30.3 1.0 N A:SER22 4.4 31.0 1.0 O4 A:ZDC303 4.4 30.4 1.0 CA A:ASN21 4.5 29.0 1.0 C A:ASN103 4.5 28.5 1.0 OD2 A:ASP104 4.5 27.5 1.0 CB A:ASP104 4.5 26.6 1.0 OD2 A:ASP99 4.5 33.1 1.0 CB A:ASP101 4.5 28.0 1.0 CB A:SER22 4.5 30.8 1.0 CB A:ASN103 4.8 26.1 1.0 C1 A:ZDC303 4.8 29.8 1.0 O A:ASN103 4.8 25.9 1.0 N A:ASN103 4.9 26.9 1.0 CA A:ASN103 5.0 28.2 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