Calcium in PDB 6q86: Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution, PDB code: 6q86 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)	48.15 / 2.01
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	55.600, 55.600, 150.621, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 19

The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution (pdb code 6q86). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution, PDB code: 6q86:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 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 SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:41.0 occ:1.00 OD2 A:ASP101 2.1 44.1 1.0 O A:ASN21 2.2 39.6 1.0 OD1 A:ASP104 2.3 43.7 1.0 OD1 A:ASN103 2.4 41.6 1.0 O2 C:ZDC1 2.5 42.4 1.0 O3 C:ZDC1 2.6 43.8 1.0 CG A:ASP101 2.9 42.2 1.0 OD1 A:ASP101 3.0 43.1 1.0 C2 C:ZDC1 3.4 39.5 1.0 C3 C:ZDC1 3.4 36.2 1.0 C A:ASN21 3.5 34.5 1.0 CG A:ASN103 3.5 37.0 1.0 CG A:ASP104 3.6 41.6 1.0 CA A:CA203 3.7 42.0 1.0 C4 C:ZDC1 3.7 33.4 1.0 ND2 A:ASN103 4.0 32.7 1.0 N A:ASP104 4.0 34.5 1.0 CB A:ASN21 4.1 31.3 1.0 CA A:ASP104 4.1 31.7 1.0 CA A:SER22 4.3 38.2 1.0 CB A:ASP101 4.3 43.7 1.0 C A:ASN103 4.3 33.5 1.0 N A:SER22 4.3 36.2 1.0 CB A:ASP104 4.4 32.4 1.0 CA A:ASN21 4.4 40.5 1.0 O4 C:ZDC1 4.4 35.0 1.0 OD2 A:ASP104 4.4 42.5 1.0 OD2 A:ASP99 4.5 48.1 1.0 CB A:SER22 4.6 40.5 1.0 O A:ASN103 4.7 36.8 1.0 C1 C:ZDC1 4.7 34.0 1.0 CB A:ASN103 4.7 34.1 1.0 N A:ASN103 4.8 29.6 1.0 CA A:ASN103 4.9 29.4 1.0 O5 C:ZDC1 5.0 41.0 1.0

Calcium binding site 2 out of 4 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 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 SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:42.0 occ:1.00 OE2 A:GLU95 2.2 48.6 1.0 OD1 A:ASP101 2.4 43.1 1.0 OE1 A:GLU95 2.4 42.0 1.0 OD2 A:ASP104 2.4 42.5 1.0 O3 C:ZDC1 2.4 43.8 1.0 OD1 A:ASP99 2.4 49.9 1.0 O4 C:ZDC1 2.5 35.0 1.0 CD A:GLU95 2.6 38.7 1.0 OD1 A:ASP104 2.6 43.7 1.0 CG A:ASP104 2.9 41.6 1.0 C4 C:ZDC1 3.2 33.4 1.0 CG A:ASP101 3.3 42.2 1.0 C3 C:ZDC1 3.3 36.2 1.0 CG A:ASP99 3.4 49.2 1.0 OD2 A:ASP99 3.6 48.1 1.0 CA A:CA202 3.7 41.0 1.0 OD2 A:ASP101 3.8 44.1 1.0 OD1 A:ASP96 4.0 49.5 1.0 N A:ASP101 4.0 46.2 1.0 CG A:GLU95 4.1 39.6 1.0 CB A:ASP104 4.4 32.4 1.0 N A:TYR102 4.4 36.3 1.0 N A:ASN100 4.4 41.6 1.0 CB A:ASP101 4.4 43.7 1.0 N A:ASP96 4.5 39.9 1.0 N A:GLY97 4.5 36.5 1.0 CA A:GLU95 4.6 38.2 1.0 C2 C:ZDC1 4.6 39.5 1.0 C5 C:ZDC1 4.6 42.7 1.0 CA A:ASP101 4.7 44.0 1.0 O2 C:ZDC1 4.7 42.4 1.0 CG A:ASP96 4.8 44.7 1.0 CB A:GLU95 4.8 35.6 1.0 CB A:ASP99 4.8 51.1 1.0 N A:ASP99 4.9 52.7 1.0 OD1 A:ASN103 4.9 41.6 1.0 C A:ASP101 4.9 42.0 1.0 N A:ASP104 5.0 34.5 1.0 CA A:GLY97 5.0 38.2 1.0

Calcium binding site 3 out of 4 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:43.7 occ:1.00 OD2 B:ASP104 2.2 57.5 1.0 OE2 B:GLU95 2.3 40.5 1.0 OD1 B:ASP101 2.3 48.8 1.0 OD1 B:ASP99 2.4 51.7 1.0 O3 D:ZDC1 2.4 53.3 1.0 OE1 B:GLU95 2.4 35.8 1.0 OD1 B:ASP104 2.5 42.8 1.0 CG B:ASP104 2.7 50.5 1.0 CD B:GLU95 2.7 34.6 1.0 O4 D:ZDC1 2.8 46.8 1.0 CG B:ASP99 3.3 48.9 1.0 CG B:ASP101 3.3 39.0 1.0 C3 D:ZDC1 3.4 46.9 1.0 OD2 B:ASP99 3.5 50.0 1.0 C4 D:ZDC1 3.5 46.4 1.0 CA B:CA203 3.7 47.4 1.0 OD2 B:ASP101 3.8 43.8 1.0 CG B:GLU95 4.2 34.7 1.0 N B:ASP101 4.2 48.5 1.0 CB B:ASP104 4.2 42.7 1.0 OD1 B:ASP96 4.2 49.0 1.0 N B:TYR102 4.3 36.3 1.0 N B:ASP96 4.5 50.5 1.0 N B:ASN100 4.5 42.5 1.0 N B:GLY97 4.5 44.0 1.0 CB B:ASP101 4.5 40.9 1.0 CA B:GLU95 4.6 35.5 1.0 CB B:ASP99 4.7 48.3 1.0 C2 D:ZDC1 4.7 46.0 1.0 CA B:ASP101 4.8 36.1 1.0 OD1 B:ASN103 4.8 40.2 1.0 N B:ASP104 4.8 41.6 1.0 CG B:ASP96 4.8 52.3 1.0 O2 D:ZDC1 4.8 46.5 1.0 CB B:GLU95 4.8 33.8 1.0 N B:ASP99 4.9 51.6 1.0 C5 D:ZDC1 4.9 46.5 1.0 C B:ASP101 4.9 42.8 1.0 CA B:ASP104 5.0 44.9 1.0

Calcium binding site 4 out of 4 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.008 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:47.4 occ:1.00 OD1 B:ASP104 2.3 42.8 1.0 OD1 B:ASN103 2.3 40.2 1.0 OD2 B:ASP101 2.3 43.8 1.0 O B:ASN21 2.3 45.1 1.0 O2 D:ZDC1 2.5 46.5 1.0 O3 D:ZDC1 2.5 53.3 1.0 CG B:ASP101 3.1 39.0 1.0 OD1 B:ASP101 3.2 48.8 1.0 CG B:ASN103 3.4 40.1 1.0 C3 D:ZDC1 3.4 46.9 1.0 C2 D:ZDC1 3.4 46.0 1.0 CG B:ASP104 3.5 50.5 1.0 C B:ASN21 3.5 46.3 1.0 CA B:CA202 3.7 43.7 1.0 C4 D:ZDC1 3.8 46.4 1.0 ND2 B:ASN103 3.8 42.1 1.0 O B:HOH309 4.0 40.6 1.0 CB B:ASN21 4.1 53.9 1.0 N B:ASP104 4.1 41.6 1.0 CA B:ASP104 4.1 44.9 1.0 OD2 B:ASP99 4.2 50.0 1.0 OD2 B:ASP104 4.3 57.5 1.0 CB B:ASP104 4.4 42.7 1.0 C B:ASN103 4.4 40.3 1.0 N B:SER22 4.4 48.6 1.0 CA B:ASN21 4.4 50.0 1.0 CA B:SER22 4.4 49.7 1.0 CB B:ASP101 4.5 40.9 1.0 O4 D:ZDC1 4.5 46.8 1.0 CB B:ASN103 4.7 37.8 1.0 CB B:SER22 4.7 49.1 1.0 C1 D:ZDC1 4.7 46.5 1.0 O B:ASN103 4.7 46.9 1.0 N B:ASN103 4.8 46.4 1.0 CA B:ASN103 4.9 37.9 1.0 O5 D:ZDC1 5.0 44.7 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