Calcium in PDB 6q79: Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution

The structure of Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution, PDB code: 6q79 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)	41.63 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.422, 64.124, 68.960, 90.00, 104.06, 90.00
R / Rfree (%)	15.4 / 23.2

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 2.009 Angstrom Resolution (pdb code 6q79). 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 SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution, PDB code: 6q79:
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 SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 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 2.009 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:35.4 occ:1.00 OD1 A:ASN103 2.3 29.6 1.0 O A:ASN21 2.3 34.1 1.0 OD2 A:ASP101 2.3 33.8 1.0 O3 E:ZDC1 2.3 31.6 1.0 O D:GLY114 2.5 34.8 1.0 OD1 A:ASP104 2.6 33.0 1.0 O2 E:ZDC1 2.6 34.1 1.0 CG A:ASP101 3.1 34.3 1.0 OD1 A:ASP101 3.1 36.9 1.0 C3 E:ZDC1 3.3 31.4 1.0 CG A:ASN103 3.4 30.1 1.0 C2 E:ZDC1 3.5 33.7 1.0 C D:GLY114 3.5 36.5 1.0 C A:ASN21 3.5 34.8 1.0 CA A:CA302 3.6 36.0 1.0 OXT D:GLY114 3.7 38.8 1.0 C4 E:ZDC1 3.8 33.2 1.0 CG A:ASP104 3.8 35.2 1.0 ND2 A:ASN103 3.9 28.4 1.0 N A:ASP104 4.1 30.8 1.0 CB A:ASN21 4.1 29.3 1.0 CA A:ASP104 4.1 33.7 1.0 OD2 A:ASP99 4.3 38.2 1.0 N A:SER22 4.4 36.5 1.0 CA A:SER22 4.4 36.6 1.0 C A:ASN103 4.4 31.7 1.0 O4 E:ZDC1 4.4 32.6 1.0 CA A:ASN21 4.5 33.2 1.0 CB A:ASP101 4.5 31.4 1.0 O A:HOH436 4.5 45.7 1.0 CB A:ASP104 4.6 34.3 1.0 CB A:SER22 4.6 37.6 1.0 CB A:ASN103 4.7 28.1 1.0 OD2 A:ASP104 4.7 37.7 1.0 O A:ASN103 4.8 32.9 1.0 N A:ASN103 4.8 29.7 1.0 C1 E:ZDC1 4.8 37.6 1.0 CA D:GLY114 4.8 36.4 1.0 CA A:ASN103 4.9 29.6 1.0 OD1 A:ASP99 4.9 40.9 1.0

Calcium binding site 2 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 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 2.009 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:36.0 occ:1.00 OD1 A:ASP99 2.3 40.9 1.0 O3 E:ZDC1 2.4 31.6 1.0 O4 E:ZDC1 2.4 32.6 1.0 OD1 A:ASP101 2.4 36.9 1.0 OD1 A:ASP104 2.5 33.0 1.0 OE2 A:GLU95 2.5 31.1 1.0 OE1 A:GLU95 2.6 32.9 1.0 OD2 A:ASP104 2.7 37.7 1.0 CD A:GLU95 2.8 33.6 1.0 CG A:ASP104 3.0 35.2 1.0 C4 E:ZDC1 3.2 33.2 1.0 C3 E:ZDC1 3.2 31.4 1.0 CG A:ASP99 3.3 40.6 1.0 CG A:ASP101 3.5 34.3 1.0 OD2 A:ASP99 3.6 38.2 1.0 CA A:CA301 3.6 35.4 1.0 OD2 A:ASP101 3.9 33.8 1.0 O A:HOH422 4.0 36.3 1.0 N A:ASP101 4.2 34.1 1.0 OD1 A:ASP96 4.2 32.2 1.0 CG A:GLU95 4.3 33.7 1.0 N A:ASN100 4.4 41.2 1.0 CB A:ASP104 4.5 34.3 1.0 N A:TYR102 4.5 31.8 1.0 N A:ASP96 4.5 35.9 1.0 N A:GLY97 4.6 39.2 1.0 C2 E:ZDC1 4.6 33.7 1.0 CB A:ASP99 4.6 39.1 1.0 C5 E:ZDC1 4.6 37.6 1.0 CB A:ASP101 4.7 31.4 1.0 CA A:GLU95 4.7 30.5 1.0 N A:ASP99 4.8 35.1 1.0 O2 E:ZDC1 4.8 34.1 1.0 CA A:ASP101 4.8 32.0 1.0 OD1 A:ASN103 4.9 29.6 1.0 CG A:ASP96 4.9 34.3 1.0 C A:ASP99 4.9 39.5 1.0 CB A:GLU95 4.9 30.2 1.0 N A:ASP104 5.0 30.8 1.0

Calcium binding site 3 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 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 2.009 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:37.3 occ:1.00 OD1 D:ASN103 2.3 31.9 1.0 O D:ASN21 2.3 38.5 1.0 OD2 D:ASP101 2.3 33.2 1.0 O3 H:ZDC1 2.4 37.8 1.0 O2 H:ZDC1 2.4 39.9 1.0 OD1 D:ASP104 2.5 38.2 1.0 O A:GLY114 2.6 44.6 1.0 CG D:ASP101 3.1 34.9 1.0 OD1 D:ASP101 3.1 35.2 1.0 C3 H:ZDC1 3.3 38.8 1.0 C2 H:ZDC1 3.4 38.1 1.0 CG D:ASN103 3.4 32.2 1.0 C A:GLY114 3.4 44.9 1.0 C D:ASN21 3.5 38.7 1.0 OXT A:GLY114 3.5 47.8 1.0 CA D:CA301 3.6 35.3 1.0 C4 H:ZDC1 3.7 38.0 1.0 CG D:ASP104 3.7 36.8 1.0 ND2 D:ASN103 3.8 29.1 1.0 N D:ASP104 4.1 34.3 1.0 CB D:ASN21 4.2 35.9 1.0 CA D:ASP104 4.2 35.8 1.0 O4 H:ZDC1 4.3 36.4 1.0 CA D:SER22 4.3 43.4 1.0 CB D:SER22 4.3 43.5 1.0 N D:SER22 4.4 41.3 1.0 OD2 D:ASP99 4.4 44.4 1.0 C D:ASN103 4.5 33.8 1.0 CB D:ASP104 4.5 36.5 1.0 CA D:ASN21 4.5 38.4 1.0 CB D:ASP101 4.5 33.1 1.0 OD2 D:ASP104 4.6 34.7 1.0 CB D:ASN103 4.7 31.4 1.0 C1 H:ZDC1 4.7 38.6 1.0 CA A:GLY114 4.8 43.6 1.0 N D:ASN103 4.9 34.4 1.0 O D:ASN103 4.9 33.7 1.0 CA D:ASN103 4.9 32.8 1.0 O5 H:ZDC1 5.0 38.9 1.0 C5 H:ZDC1 5.0 39.0 1.0 OD1 D:ASP99 5.0 39.8 1.0

Calcium binding site 4 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 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 2.009 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:0.2 occ:1.00 OD2 B:ASP101 2.2 38.2 1.0 O3 F:ZDC1 2.4 29.9 1.0 OD1 B:ASP104 2.4 32.4 1.0 O B:ASN21 2.4 38.2 1.0 O C:GLY114 2.4 37.1 1.0 O2 F:ZDC1 2.5 29.5 1.0 OD1 B:ASN103 2.6 30.5 1.0 CG B:ASP101 3.1 35.5 1.0 OD1 B:ASP101 3.2 36.8 1.0 C3 F:ZDC1 3.2 29.2 1.0 C2 F:ZDC1 3.3 27.6 1.0 C C:GLY114 3.3 36.0 1.0 OXT C:GLY114 3.5 34.2 1.0 CA B:CA302 3.6 27.0 1.0 C B:ASN21 3.6 34.8 1.0 CG B:ASP104 3.6 32.3 1.0 CG B:ASN103 3.6 27.5 1.0 C4 F:ZDC1 3.7 29.4 1.0 ND2 B:ASN103 4.1 25.4 1.0 CA B:ASP104 4.2 28.5 1.0 N B:ASP104 4.2 26.8 1.0 CB B:ASN21 4.3 28.6 1.0 OD2 B:ASP99 4.3 31.7 1.0 CA B:SER22 4.4 30.9 1.0 O4 F:ZDC1 4.4 29.3 1.0 N B:SER22 4.4 32.3 1.0 CB B:ASP104 4.4 29.9 1.0 OD2 B:ASP104 4.5 32.9 1.0 CB B:ASP101 4.5 34.0 1.0 C B:ASN103 4.6 26.1 1.0 CB B:SER22 4.6 29.4 1.0 CA B:ASN21 4.6 29.4 1.0 C1 F:ZDC1 4.6 30.5 1.0 NZ F:DLY5 4.6 54.6 1.0 CA C:GLY114 4.8 34.8 1.0 O5 F:ZDC1 4.8 30.7 1.0 O B:ASN103 4.9 24.9 1.0 C5 F:ZDC1 4.9 31.2 1.0 CB B:ASN103 4.9 23.8 1.0 N B:ASN103 4.9 23.9 1.0

Calcium binding site 5 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 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 SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:27.0 occ:1.00 O3 F:ZDC1 2.4 29.9 1.0 OD1 B:ASP101 2.4 36.8 1.0 OD1 B:ASP99 2.4 34.4 1.0 OE1 B:GLU95 2.4 30.0 1.0 OE2 B:GLU95 2.5 23.0 1.0 OD2 B:ASP104 2.5 32.9 1.0 OD1 B:ASP104 2.5 32.4 1.0 O4 F:ZDC1 2.5 29.3 1.0 CD B:GLU95 2.8 25.8 1.0 CG B:ASP104 2.8 32.3 1.0 C4 F:ZDC1 3.2 29.4 1.0 C3 F:ZDC1 3.3 29.2 1.0 CG B:ASP99 3.3 32.5 1.0 CG B:ASP101 3.4 35.5 1.0 OD2 B:ASP99 3.5 31.7 1.0 CA B:CA301 3.6 0.2 1.0 OD2 B:ASP101 3.8 38.2 1.0 N B:ASP101 4.2 32.2 1.0 O B:HOH438 4.2 32.1 1.0 OD1 B:ASP96 4.3 35.7 1.0 CG B:GLU95 4.3 26.1 1.0 CB B:ASP104 4.4 29.9 1.0 N B:ASN100 4.4 34.4 1.0 N B:TYR102 4.5 26.4 1.0 N B:ASP96 4.5 28.0 1.0 N B:GLY97 4.6 34.4 1.0 CB B:ASP101 4.6 34.0 1.0 C2 F:ZDC1 4.6 27.6 1.0 C5 F:ZDC1 4.7 31.2 1.0 CA B:GLU95 4.7 27.2 1.0 CB B:ASP99 4.7 32.4 1.0 OD1 B:ASN103 4.8 30.5 1.0 CA B:ASP101 4.8 29.8 1.0 O2 F:ZDC1 4.8 29.5 1.0 N B:ASP99 4.9 34.5 1.0 CB B:GLU95 4.9 26.6 1.0 CG B:ASP96 4.9 35.7 1.0 N B:ASP104 5.0 26.8 1.0

Calcium binding site 6 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 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 SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:26.2 occ:1.00 OD2 C:ASP101 2.3 23.2 1.0 OD1 C:ASN103 2.3 22.4 1.0 O C:ASN21 2.4 28.1 1.0 OD1 C:ASP104 2.5 27.4 1.0 O3 G:ZDC1 2.5 28.7 1.0 O B:GLY114 2.5 29.1 1.0 O2 G:ZDC1 2.5 29.8 1.0 CG C:ASP101 3.0 25.1 1.0 OD1 C:ASP101 3.1 25.9 1.0 CG C:ASN103 3.3 25.1 1.0 C3 G:ZDC1 3.4 30.8 1.0 C2 G:ZDC1 3.4 31.6 1.0 C B:GLY114 3.4 29.1 1.0 OXT B:GLY114 3.6 29.8 1.0 C C:ASN21 3.6 28.9 1.0 CG C:ASP104 3.7 28.4 1.0 CA C:CA201 3.7 29.4 1.0 ND2 C:ASN103 3.8 26.9 1.0 C4 G:ZDC1 3.8 31.8 1.0 CB C:ASN21 4.2 28.7 1.0 N C:ASP104 4.2 28.6 1.0 CA C:ASP104 4.2 27.8 1.0 NZ G:DLY5 4.2 54.3 1.0 O4 G:ZDC1 4.4 30.3 1.0 C C:ASN103 4.4 25.6 1.0 CB C:ASP101 4.5 25.0 1.0 OD2 C:ASP99 4.5 28.8 1.0 CE G:DLY5 4.5 57.1 1.0 CA C:SER22 4.5 28.4 1.0 CB C:ASP104 4.5 27.4 1.0 N C:SER22 4.5 28.6 1.0 OD2 C:ASP104 4.5 28.9 1.0 CA C:ASN21 4.6 28.7 1.0 CB C:SER22 4.6 27.2 1.0 CB C:ASN103 4.7 22.7 1.0 C1 G:ZDC1 4.8 34.1 1.0 CA B:GLY114 4.8 27.9 1.0 O C:ASN103 4.8 23.0 1.0 N C:ASN103 4.8 24.1 1.0 CA C:ASN103 4.9 23.1 1.0

Calcium binding site 7 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 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 SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:29.4 occ:1.00 O4 G:ZDC1 2.4 30.3 1.0 OD1 C:ASP99 2.4 31.9 1.0 OD1 C:ASP101 2.4 25.9 1.0 OE1 C:GLU95 2.5 32.4 1.0 OE2 C:GLU95 2.5 32.1 1.0 O3 G:ZDC1 2.5 28.7 1.0 OD2 C:ASP104 2.5 28.9 1.0 OD1 C:ASP104 2.6 27.4 1.0 CD C:GLU95 2.8 31.3 1.0 CG C:ASP104 2.9 28.4 1.0 C4 G:ZDC1 3.2 31.8 1.0 C3 G:ZDC1 3.3 30.8 1.0 CG C:ASP99 3.4 29.7 1.0 CG C:ASP101 3.4 25.1 1.0 OD2 C:ASP99 3.6 28.8 1.0 CA B:CA303 3.7 26.2 1.0 OD2 C:ASP101 3.9 23.2 1.0 O C:HOH423 4.1 31.6 1.0 N C:ASP101 4.1 28.4 1.0 OD1 C:ASP96 4.2 31.2 1.0 CG C:GLU95 4.3 28.6 1.0 N C:ASN100 4.4 28.9 1.0 N C:TYR102 4.4 27.8 1.0 CB C:ASP104 4.4 27.4 1.0 N C:GLY97 4.5 31.6 1.0 N C:ASP96 4.5 26.9 1.0 CB C:ASP101 4.6 25.0 1.0 C5 G:ZDC1 4.6 32.2 1.0 C2 G:ZDC1 4.7 31.6 1.0 CA C:GLU95 4.7 25.2 1.0 CA C:ASP101 4.8 26.4 1.0 CB C:ASP99 4.8 27.1 1.0 O2 G:ZDC1 4.8 29.8 1.0 N C:ASP99 4.8 32.3 1.0 OD1 C:ASN103 4.8 22.4 1.0 CG C:ASP96 4.9 32.6 1.0 CB C:GLU95 4.9 26.9 1.0 CA C:GLY97 5.0 33.3 1.0 C C:ASP99 5.0 30.6 1.0

Calcium binding site 8 out of 8 in the Structure of Fucosylated D-Antimicrobial Peptide SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 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 SB4 in Complex with the Fucose-Binding Lectin Pa-Iil at 2.009 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:35.3 occ:1.00 O4 H:ZDC1 2.3 36.4 1.0 OD1 D:ASP99 2.3 39.8 1.0 OD1 D:ASP101 2.4 35.2 1.0 O3 H:ZDC1 2.5 37.8 1.0 OE2 D:GLU95 2.5 30.9 1.0 OD1 D:ASP104 2.6 38.2 1.0 OE1 D:GLU95 2.6 33.5 1.0 OD2 D:ASP104 2.7 34.7 1.0 CD D:GLU95 2.9 33.9 1.0 CG D:ASP104 3.0 36.8 1.0 C4 H:ZDC1 3.2 38.0 1.0 CG D:ASP99 3.3 42.1 1.0 CG D:ASP101 3.3 34.9 1.0 C3 H:ZDC1 3.3 38.8 1.0 OD2 D:ASP99 3.5 44.4 1.0 CA A:CA303 3.6 37.3 1.0 OD2 D:ASP101 3.7 33.2 1.0 O D:HOH430 3.8 42.6 1.0 N D:ASP101 4.1 37.0 1.0 OD1 D:ASP96 4.1 45.0 1.0 CG D:GLU95 4.4 34.0 1.0 N D:TYR102 4.4 33.6 1.0 CB D:ASP101 4.5 33.1 1.0 CB D:ASP104 4.5 36.5 1.0 N D:ASN100 4.5 39.6 1.0 C5 H:ZDC1 4.6 39.0 1.0 N D:ASP96 4.6 37.7 1.0 C2 H:ZDC1 4.7 38.1 1.0 CB D:ASP99 4.7 41.1 1.0 N D:GLY97 4.7 38.3 1.0 CA D:ASP101 4.7 33.5 1.0 OD1 D:ASN103 4.7 31.9 1.0 O2 H:ZDC1 4.7 39.9 1.0 N D:ASP99 4.8 43.7 1.0 CA D:GLU95 4.8 36.0 1.0 C D:ASP101 4.9 35.0 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