Calcium in PDB 6q85: Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution, PDB code: 6q85 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)	45.90 / 1.99
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	132.785, 132.785, 190.554, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 21.9

The binding sites of Calcium atom in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution (pdb code 6q85). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution, PDB code: 6q85:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 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 SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:40.1 occ:1.00 OD1 A:ASP99 2.4 41.0 1.0 O4 E:ZDC1 2.4 40.7 1.0 OD1 A:ASP101 2.4 39.7 1.0 OE1 A:GLU95 2.5 44.9 1.0 OD1 A:ASP104 2.5 40.8 1.0 OD2 A:ASP104 2.5 40.6 1.0 O3 E:ZDC1 2.5 39.9 1.0 OE2 A:GLU95 2.6 41.0 1.0 CD A:GLU95 2.8 42.0 1.0 CG A:ASP104 2.8 39.5 1.0 C4 E:ZDC1 3.1 41.2 1.0 C3 E:ZDC1 3.3 38.6 1.0 CG A:ASP99 3.4 40.5 1.0 CG A:ASP101 3.4 38.8 1.0 OD2 A:ASP99 3.6 40.2 1.0 CA A:CA302 3.7 39.8 1.0 OD2 A:ASP101 3.9 39.2 1.0 O A:HOH410 4.1 38.6 1.0 OD1 A:ASP96 4.1 39.3 1.0 N A:ASP101 4.2 36.3 1.0 CG A:GLU95 4.3 39.4 1.0 CB A:ASP104 4.4 38.6 1.0 N A:TYR102 4.4 36.7 1.0 N A:ASP96 4.5 41.5 1.0 N A:ASN100 4.5 37.2 1.0 C5 E:ZDC1 4.6 42.2 1.0 CB A:ASP101 4.6 39.7 1.0 N A:GLY97 4.6 40.5 1.0 C2 E:ZDC1 4.7 40.0 1.0 CA A:GLU95 4.7 37.3 1.0 CB A:ASP99 4.7 37.9 1.0 OD1 A:ASN103 4.7 40.0 1.0 CA A:ASP101 4.8 36.4 1.0 CG A:ASP96 4.9 42.3 1.0 O2 E:ZDC1 4.9 40.9 1.0 N A:ASP99 4.9 42.5 1.0 CB A:GLU95 4.9 38.7 1.0

Calcium binding site 2 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 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 SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:39.8 occ:1.00 OD1 A:ASN103 2.3 40.0 1.0 O A:ASN21 2.3 39.2 1.0 O3 E:ZDC1 2.4 39.9 1.0 OD2 A:ASP104 2.4 40.6 1.0 OD2 A:ASP101 2.5 39.2 1.0 O B:GLY114 2.6 36.9 1.0 O2 E:ZDC1 2.6 40.9 1.0 OD1 A:ASP101 3.1 39.7 1.0 CG A:ASP101 3.1 38.8 1.0 C3 E:ZDC1 3.3 38.6 1.0 CG A:ASN103 3.4 39.2 1.0 C2 E:ZDC1 3.5 40.0 1.0 C B:GLY114 3.5 36.9 1.0 C A:ASN21 3.5 41.2 1.0 OXT B:GLY114 3.6 36.9 1.0 CG A:ASP104 3.6 39.5 1.0 CA A:CA301 3.7 40.1 1.0 C4 E:ZDC1 3.7 41.2 1.0 ND2 A:ASN103 3.9 38.6 1.0 CA A:ASP104 4.1 38.2 1.0 N A:ASP104 4.2 36.8 1.0 CB A:ASN21 4.2 39.5 1.0 CA A:SER22 4.4 40.2 1.0 N A:SER22 4.4 40.3 1.0 OD2 A:ASP99 4.4 40.2 1.0 C A:ASN103 4.4 41.7 1.0 O4 E:ZDC1 4.4 40.7 1.0 CB A:ASP104 4.4 38.6 1.0 CA A:ASN21 4.5 39.2 1.0 OD1 A:ASP104 4.5 40.8 1.0 CB A:SER22 4.5 37.2 1.0 CB A:ASP101 4.6 39.7 1.0 O A:HOH431 4.6 43.3 1.0 CB A:ASN103 4.7 37.6 1.0 C1 E:ZDC1 4.8 37.1 1.0 N A:ASN103 4.8 39.5 1.0 O A:ASN103 4.8 41.6 1.0 CA A:ASN103 4.9 40.7 1.0 CA B:GLY114 4.9 32.0 1.0 O5 E:ZDC1 5.0 42.6 1.0

Calcium binding site 3 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 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 SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:54.7 occ:1.00 O B:ASN21 2.3 45.6 1.0 OD1 B:ASN103 2.4 41.4 1.0 OD2 B:ASP101 2.4 44.0 1.0 O3 F:ZDC1 2.4 45.2 1.0 OD1 B:ASP104 2.5 52.0 1.0 O2 F:ZDC1 2.5 45.3 1.0 O A:GLY114 2.6 60.4 1.0 CG B:ASP101 3.1 45.1 1.0 OD1 B:ASP101 3.2 47.1 1.0 C3 F:ZDC1 3.4 44.9 1.0 C2 F:ZDC1 3.4 45.6 1.0 CG B:ASN103 3.4 42.2 1.0 C A:GLY114 3.5 58.0 1.0 C B:ASN21 3.5 46.5 1.0 OXT A:GLY114 3.5 54.1 1.0 CA B:CA301 3.7 47.2 1.0 CG B:ASP104 3.7 47.5 1.0 C4 F:ZDC1 3.8 46.0 1.0 ND2 B:ASN103 3.9 46.5 1.0 CB B:ASN21 4.1 37.8 1.0 CA B:ASP104 4.1 43.8 1.0 N B:ASP104 4.2 42.8 1.0 CA B:SER22 4.4 47.8 1.0 N B:SER22 4.4 49.2 1.0 C B:ASN103 4.4 42.7 1.0 CB B:SER22 4.5 48.5 1.0 OD2 B:ASP99 4.5 45.6 1.0 CB B:ASP104 4.5 45.2 1.0 CA B:ASN21 4.5 42.0 1.0 O4 F:ZDC1 4.5 45.4 1.0 CB B:ASP101 4.6 42.4 1.0 OD2 B:ASP104 4.6 46.3 1.0 O A:HOH433 4.7 46.9 1.0 CB B:ASN103 4.8 43.1 1.0 C1 F:ZDC1 4.8 49.8 1.0 O B:ASN103 4.8 44.2 1.0 N B:ASN103 4.8 40.7 1.0 CA A:GLY114 4.9 52.9 1.0 CA B:ASN103 4.9 40.8 1.0

Calcium binding site 4 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 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 SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:47.2 occ:1.00 OD1 B:ASP101 2.3 47.1 1.0 OD1 B:ASP99 2.4 50.2 1.0 OE2 B:GLU95 2.5 46.8 1.0 OD1 B:ASP104 2.5 52.0 1.0 O3 F:ZDC1 2.5 45.2 1.0 O4 F:ZDC1 2.5 45.4 1.0 OE1 B:GLU95 2.6 45.8 1.0 OD2 B:ASP104 2.6 46.3 1.0 CD B:GLU95 2.8 45.0 1.0 CG B:ASP104 2.9 47.5 1.0 C4 F:ZDC1 3.3 46.0 1.0 CG B:ASP99 3.3 48.4 1.0 C3 F:ZDC1 3.4 44.9 1.0 CG B:ASP101 3.4 45.1 1.0 OD2 B:ASP99 3.5 45.6 1.0 CA A:CA303 3.7 54.7 1.0 OD2 B:ASP101 3.9 44.0 1.0 O B:HOH441 4.0 51.7 1.0 N B:ASP101 4.1 44.8 1.0 OD1 B:ASP96 4.2 45.8 1.0 CG B:GLU95 4.3 41.8 1.0 N B:TYR102 4.4 44.7 1.0 CB B:ASP104 4.4 45.2 1.0 N B:ASN100 4.4 49.9 1.0 N B:ASP96 4.5 45.3 1.0 CB B:ASP101 4.6 42.4 1.0 CB B:ASP99 4.7 46.6 1.0 CA B:GLU95 4.7 41.7 1.0 C5 F:ZDC1 4.7 48.6 1.0 C2 F:ZDC1 4.7 45.6 1.0 N B:GLY97 4.7 50.3 1.0 OD1 B:ASN103 4.7 41.4 1.0 CA B:ASP101 4.7 42.7 1.0 N B:ASP99 4.8 49.0 1.0 O2 F:ZDC1 4.9 45.3 1.0 CB B:GLU95 4.9 43.4 1.0 CG B:ASP96 4.9 48.8 1.0 C B:ASP101 5.0 46.2 1.0 C B:ASP99 5.0 50.4 1.0

Calcium binding site 5 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:41.3 occ:1.00 OD1 C:ASP101 2.3 36.7 1.0 OE2 C:GLU95 2.4 41.0 1.0 O4 G:ZDC1 2.5 40.3 1.0 OD2 C:ASP104 2.5 39.3 1.0 O3 G:ZDC1 2.5 38.6 1.0 OD1 C:ASP99 2.5 44.1 1.0 OE1 C:GLU95 2.6 34.1 1.0 OD1 C:ASP104 2.7 43.0 1.0 CD C:GLU95 2.8 39.2 1.0 CG C:ASP104 2.9 40.2 1.0 C4 G:ZDC1 3.3 40.6 1.0 CG C:ASP101 3.3 36.3 1.0 C3 G:ZDC1 3.4 42.0 1.0 CG C:ASP99 3.4 40.1 1.0 OD2 C:ASP99 3.6 40.9 1.0 CA C:CA302 3.7 39.8 1.0 OD2 C:ASP101 3.8 38.7 1.0 N C:ASP101 4.1 37.0 1.0 OD1 C:ASP96 4.3 42.8 1.0 CG C:GLU95 4.3 37.1 1.0 N C:TYR102 4.3 34.4 1.0 CB C:ASP104 4.4 37.3 1.0 N C:ASN100 4.4 39.3 1.0 N C:ASP96 4.5 38.5 1.0 N C:GLY97 4.5 44.2 1.0 CB C:ASP101 4.6 35.3 1.0 O C:HOH455 4.6 45.0 1.0 CA C:GLU95 4.6 37.0 1.0 C5 G:ZDC1 4.7 42.0 1.0 OD1 C:ASN103 4.7 37.9 1.0 C2 G:ZDC1 4.7 40.6 1.0 CA C:ASP101 4.7 36.5 1.0 CB C:ASP99 4.8 39.1 1.0 CB C:GLU95 4.9 36.2 1.0 N C:ASP99 4.9 37.9 1.0 CG C:ASP96 4.9 44.9 1.0 O2 G:ZDC1 4.9 39.0 1.0 C C:ASP101 4.9 39.9 1.0 CA C:GLY97 5.0 42.7 1.0

Calcium binding site 6 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:39.8 occ:1.00 OD1 C:ASN103 2.3 37.9 1.0 O C:ASN21 2.3 36.5 1.0 OD2 C:ASP101 2.4 38.7 1.0 O3 G:ZDC1 2.4 38.6 1.0 OD1 C:ASP104 2.5 43.0 1.0 O2 G:ZDC1 2.6 39.0 1.0 O D:GLY114 2.6 38.1 1.0 CG C:ASP101 3.1 36.3 1.0 OD1 C:ASP101 3.2 36.7 1.0 C3 G:ZDC1 3.3 42.0 1.0 CG C:ASN103 3.4 34.0 1.0 C D:GLY114 3.4 40.2 1.0 C2 G:ZDC1 3.4 40.6 1.0 OXT D:GLY114 3.5 35.9 1.0 C C:ASN21 3.5 38.6 1.0 CG C:ASP104 3.7 40.2 1.0 CA C:CA301 3.7 41.3 1.0 C4 G:ZDC1 3.7 40.6 1.0 ND2 C:ASN103 3.8 32.3 1.0 CB C:ASN21 4.1 39.7 1.0 CA C:ASP104 4.2 36.3 1.0 N C:ASP104 4.3 32.6 1.0 CA C:SER22 4.4 38.8 1.0 O4 G:ZDC1 4.4 40.3 1.0 N C:SER22 4.4 38.3 1.0 C C:ASN103 4.4 32.2 1.0 CA C:ASN21 4.5 39.7 1.0 OD2 C:ASP99 4.5 40.9 1.0 OD2 C:ASP104 4.5 39.3 1.0 O D:HOH431 4.5 47.3 1.0 CB C:ASP104 4.5 37.3 1.0 CB C:ASP101 4.6 35.3 1.0 CB C:SER22 4.6 41.7 1.0 CB C:ASN103 4.7 30.7 1.0 C1 G:ZDC1 4.7 37.7 1.0 O C:ASN103 4.8 31.4 1.0 CA D:GLY114 4.8 37.8 1.0 N C:ASN103 4.8 33.3 1.0 CA C:ASN103 4.9 30.4 1.0 O5 G:ZDC1 5.0 42.7 1.0

Calcium binding site 7 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:47.2 occ:1.00 O D:ASN21 2.3 45.4 1.0 OD1 D:ASN103 2.4 43.3 1.0 OD2 D:ASP101 2.4 42.7 1.0 O3 H:ZDC1 2.5 38.1 1.0 OD1 D:ASP104 2.5 44.2 1.0 O C:GLY114 2.5 50.8 1.0 O2 H:ZDC1 2.5 41.3 1.0 CG D:ASP101 3.1 45.2 1.0 OD1 D:ASP101 3.1 44.8 1.0 C3 H:ZDC1 3.3 39.2 1.0 CG D:ASN103 3.4 40.3 1.0 C2 H:ZDC1 3.4 41.3 1.0 C C:GLY114 3.4 47.7 1.0 C D:ASN21 3.5 47.6 1.0 OXT C:GLY114 3.5 44.1 1.0 CA D:CA301 3.7 48.8 1.0 CG D:ASP104 3.7 43.2 1.0 C4 H:ZDC1 3.7 44.3 1.0 ND2 D:ASN103 3.8 41.7 1.0 CB D:ASN21 4.1 41.4 1.0 CA D:ASP104 4.2 42.9 1.0 N D:ASP104 4.2 41.1 1.0 N D:SER22 4.3 47.4 1.0 CA D:SER22 4.3 45.4 1.0 O4 H:ZDC1 4.3 48.0 1.0 CA D:ASN21 4.4 45.1 1.0 C D:ASN103 4.4 43.1 1.0 OD2 D:ASP99 4.5 41.7 1.0 CB D:ASP104 4.5 42.7 1.0 CB D:SER22 4.5 44.1 1.0 CB D:ASP101 4.6 40.9 1.0 O C:HOH421 4.6 49.5 1.0 OD2 D:ASP104 4.6 44.0 1.0 CB D:ASN103 4.8 36.3 1.0 C1 H:ZDC1 4.8 43.7 1.0 O D:ASN103 4.8 44.5 1.0 CA C:GLY114 4.8 45.4 1.0 N D:ASN103 4.9 37.3 1.0 CA D:ASN103 4.9 38.5 1.0 O5 H:ZDC1 5.0 50.3 1.0 C5 H:ZDC1 5.0 49.0 1.0

Calcium binding site 8 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Fucosylated D-Antimicrobial Peptide SB11 in Complex with the Fucose-Binding Lectin Pa-Iil at 1.990 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:48.8 occ:1.00 OE2 D:GLU95 2.3 44.0 1.0 OD1 D:ASP101 2.3 44.8 1.0 O4 H:ZDC1 2.5 48.0 1.0 O3 H:ZDC1 2.5 38.1 1.0 OD1 D:ASP99 2.5 50.5 1.0 OD1 D:ASP104 2.5 44.2 1.0 OD2 D:ASP104 2.6 44.0 1.0 OE1 D:GLU95 2.6 46.4 1.0 CD D:GLU95 2.8 44.3 1.0 CG D:ASP104 2.9 43.2 1.0 C4 H:ZDC1 3.3 44.3 1.0 C3 H:ZDC1 3.3 39.2 1.0 CG D:ASP99 3.4 45.9 1.0 CG D:ASP101 3.4 45.2 1.0 OD2 D:ASP99 3.5 41.7 1.0 CA C:CA303 3.7 47.2 1.0 OD2 D:ASP101 3.9 42.7 1.0 OD1 D:ASP96 4.1 58.7 1.0 N D:ASP101 4.2 38.4 1.0 CG D:GLU95 4.3 40.6 1.0 O D:HOH435 4.3 51.5 1.0 CB D:ASP104 4.4 42.7 1.0 N D:GLY97 4.5 50.7 1.0 N D:TYR102 4.5 40.0 1.0 N D:ASN100 4.5 45.0 1.0 N D:ASP96 4.5 43.4 1.0 CB D:ASP101 4.6 40.9 1.0 C2 H:ZDC1 4.7 41.3 1.0 C5 H:ZDC1 4.7 49.0 1.0 OD1 D:ASN103 4.7 43.3 1.0 CA D:GLU95 4.7 39.0 1.0 CA D:ASP101 4.8 39.5 1.0 CB D:ASP99 4.8 45.3 1.0 O2 H:ZDC1 4.8 41.3 1.0 CG D:ASP96 4.9 54.2 1.0 CB D:GLU95 4.9 39.1 1.0 CA D:GLY97 4.9 52.1 1.0 N D:ASP99 4.9 52.0 1.0 C D:ASP101 5.0 42.6 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