Calcium in PDB 7new: Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution

The structure of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution, PDB code: 7new was solved by H.Personne, 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)	40.03 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.586, 64.786, 73.632, 90, 113.33, 90
R / Rfree (%)	20.7 / 22.8

The binding sites of Calcium atom in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution (pdb code 7new). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution, PDB code: 7new:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:37.9 occ:1.00 O A:ASN21 2.4 36.2 1.0 OD1 A:ASN103 2.5 33.7 1.0 OD2 A:ASP101 2.5 36.0 1.0 O3 G:ZDC1 2.5 38.2 1.0 OD1 A:ASP104 2.5 37.7 1.0 O B:GLY114 2.5 39.6 1.0 O2 G:ZDC1 2.5 37.4 1.0 CG A:ASP101 3.2 37.0 1.0 OD1 A:ASP101 3.3 40.4 1.0 C3 G:ZDC1 3.4 40.2 1.0 C B:GLY114 3.4 40.2 1.0 C2 G:ZDC1 3.5 39.2 1.0 OXT B:GLY114 3.5 41.3 1.0 CG A:ASN103 3.5 34.9 1.0 C A:ASN21 3.6 37.0 1.0 C4 G:ZDC1 3.7 41.4 1.0 CG A:ASP104 3.7 37.2 1.0 CA A:CA302 3.8 37.5 1.0 ND2 A:ASN103 4.0 39.6 1.0 N A:ASP104 4.1 34.6 1.0 CA A:ASP104 4.2 33.7 1.0 CB A:ASN21 4.3 32.0 1.0 CA A:SER22 4.4 36.4 1.0 O4 G:ZDC1 4.4 39.5 1.0 OD2 A:ASP99 4.4 46.2 1.0 N A:SER22 4.4 37.4 1.0 C A:ASN103 4.5 33.5 1.0 CB A:ASP104 4.5 33.8 1.0 CA A:ASN21 4.6 34.1 1.0 CB A:SER22 4.6 33.5 1.0 CB A:ASP101 4.6 33.5 1.0 OD2 A:ASP104 4.6 36.7 1.0 C1 G:ZDC1 4.8 40.4 1.0 CA B:GLY114 4.8 38.1 1.0 CB A:ASN103 4.8 34.2 1.0 N A:ASN103 4.9 34.5 1.0 O A:ASN103 5.0 32.4 1.0 CA A:ASN103 5.0 32.2 1.0

Calcium binding site 2 out of 8 in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:37.5 occ:1.00 OD1 A:ASP99 2.4 47.5 1.0 OE2 A:GLU95 2.4 36.1 1.0 OD1 A:ASP101 2.4 40.4 1.0 OE1 A:GLU95 2.5 32.0 1.0 O4 G:ZDC1 2.6 39.5 1.0 OD2 A:ASP104 2.7 36.7 1.0 O3 G:ZDC1 2.7 38.2 1.0 OD1 A:ASP104 2.7 37.7 1.0 CD A:GLU95 2.8 34.2 1.0 CG A:ASP104 3.0 37.2 1.0 CG A:ASP99 3.3 47.5 1.0 CG A:ASP101 3.4 37.0 1.0 C4 G:ZDC1 3.5 41.4 1.0 OD2 A:ASP99 3.5 46.2 1.0 C3 G:ZDC1 3.5 40.2 1.0 CA A:CA301 3.8 37.9 1.0 OD2 A:ASP101 3.8 36.0 1.0 OD1 A:ASP96 4.1 34.6 1.0 N A:ASP101 4.1 37.5 1.0 CG A:GLU95 4.3 32.7 1.0 O A:HOH424 4.3 40.9 1.0 N A:ASN100 4.4 42.3 1.0 N A:TYR102 4.4 36.2 1.0 N A:GLY97 4.5 42.1 1.0 N A:ASP96 4.5 38.8 1.0 CB A:ASP104 4.5 33.8 1.0 CB A:ASP101 4.6 33.5 1.0 CA A:GLU95 4.7 34.4 1.0 CB A:ASP99 4.7 45.7 1.0 CA A:ASP101 4.8 36.8 1.0 N A:ASP99 4.8 46.6 1.0 OD1 A:ASN103 4.8 33.7 1.0 C5 G:ZDC1 4.9 44.4 1.0 C2 G:ZDC1 4.9 39.2 1.0 CB A:GLU95 4.9 31.4 1.0 CG A:ASP96 4.9 36.8 1.0 CA A:GLY97 5.0 43.5 1.0 CA A:ASN100 5.0 42.7 1.0

Calcium binding site 3 out of 8 in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:43.4 occ:1.00 OD1 B:ASP101 2.4 36.6 1.0 OE2 B:GLU95 2.4 41.4 1.0 OD1 B:ASP99 2.5 44.6 1.0 O3 F:ZDC1 2.5 38.6 1.0 O4 F:ZDC1 2.5 46.9 1.0 OD1 B:ASP104 2.5 36.5 1.0 OD2 B:ASP104 2.6 37.0 1.0 OE1 B:GLU95 2.6 38.4 1.0 CD B:GLU95 2.8 39.5 1.0 CG B:ASP104 2.9 37.1 1.0 C4 F:ZDC1 3.3 45.8 1.0 CG B:ASP99 3.3 46.4 1.0 C3 F:ZDC1 3.4 41.3 1.0 CG B:ASP101 3.4 36.1 1.0 OD2 B:ASP99 3.5 46.0 1.0 CA B:CA302 3.7 39.4 1.0 OD2 B:ASP101 3.8 36.2 1.0 OD1 B:ASP96 3.9 41.7 1.0 N B:ASP101 4.2 37.8 1.0 CG B:GLU95 4.3 38.6 1.0 CB B:ASP104 4.4 36.8 1.0 O B:HOH426 4.4 50.6 1.0 N B:TYR102 4.4 36.1 1.0 N B:GLY97 4.5 44.3 1.0 N B:ASP96 4.5 38.2 1.0 N B:ASN100 4.5 42.5 1.0 CB B:ASP101 4.6 34.0 1.0 C2 F:ZDC1 4.7 41.0 1.0 C5 F:ZDC1 4.7 49.7 1.0 CA B:GLU95 4.7 36.8 1.0 CB B:ASP99 4.8 47.2 1.0 OD1 B:ASN103 4.8 29.0 1.0 O2 F:ZDC1 4.8 39.5 1.0 CA B:ASP101 4.8 35.7 1.0 CG B:ASP96 4.9 42.2 1.0 N B:ASP99 4.9 47.8 1.0 N B:ASP104 4.9 35.6 1.0 CB B:GLU95 4.9 37.0 1.0 CA B:GLY97 4.9 44.8 1.0

Calcium binding site 4 out of 8 in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:39.4 occ:1.00 O B:ASN21 2.4 36.0 1.0 OD1 B:ASN103 2.4 29.0 1.0 OD2 B:ASP101 2.4 36.2 1.0 O A:GLY114 2.5 37.6 1.0 O3 F:ZDC1 2.5 38.6 1.0 O2 F:ZDC1 2.5 39.5 1.0 OD1 B:ASP104 2.6 36.5 1.0 CG B:ASP101 3.2 36.1 1.0 OD1 B:ASP101 3.3 36.6 1.0 C A:GLY114 3.4 37.4 1.0 C3 F:ZDC1 3.4 41.3 1.0 C2 F:ZDC1 3.4 41.0 1.0 OXT A:GLY114 3.5 38.3 1.0 CG B:ASN103 3.5 35.7 1.0 C B:ASN21 3.6 37.0 1.0 CA B:CA301 3.7 43.4 1.0 CG B:ASP104 3.8 37.1 1.0 C4 F:ZDC1 3.8 45.8 1.0 ND2 B:ASN103 4.0 34.6 1.0 CB B:ASN21 4.1 29.2 1.0 N B:ASP104 4.1 35.6 1.0 CA B:ASP104 4.2 37.7 1.0 OD2 B:ASP99 4.3 46.0 1.0 C B:ASN103 4.4 35.5 1.0 N B:SER22 4.5 37.7 1.0 O4 F:ZDC1 4.5 46.9 1.0 CA B:ASN21 4.5 37.7 1.0 CA B:SER22 4.5 37.7 1.0 CB B:ASP104 4.6 36.8 1.0 CB B:ASP101 4.6 34.0 1.0 OD2 B:ASP104 4.7 37.0 1.0 CB B:SER22 4.8 37.4 1.0 O B:ASN103 4.8 35.1 1.0 CA A:GLY114 4.8 36.4 1.0 CB B:ASN103 4.8 36.0 1.0 C1 F:ZDC1 4.8 44.0 1.0 N B:ASN103 4.9 36.1 1.0 CA B:ASN103 4.9 35.6 1.0

Calcium binding site 5 out of 8 in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:41.1 occ:1.00 O C:ASN21 2.3 33.8 1.0 OD1 C:ASN103 2.5 34.2 1.0 O2 E:ZDC1 2.5 38.5 1.0 OD2 C:ASP101 2.5 38.6 1.0 OD1 C:ASP104 2.5 41.0 1.0 O3 E:ZDC1 2.6 38.1 1.0 O D:GLY114 2.6 42.7 1.0 CG C:ASP101 3.2 36.3 1.0 OD1 C:ASP101 3.3 38.2 1.0 C3 E:ZDC1 3.4 40.5 1.0 OXT D:GLY114 3.4 42.1 1.0 C D:GLY114 3.4 44.3 1.0 C2 E:ZDC1 3.4 39.5 1.0 C C:ASN21 3.6 36.7 1.0 CG C:ASN103 3.6 33.2 1.0 C4 E:ZDC1 3.7 41.9 1.0 CG C:ASP104 3.7 40.6 1.0 CA C:CA302 3.8 38.1 1.0 ND2 C:ASN103 4.1 33.9 1.0 N C:ASP104 4.1 35.1 1.0 CA C:ASP104 4.2 37.3 1.0 CA C:SER22 4.2 39.1 1.0 CB C:SER22 4.3 41.5 1.0 CB C:ASN21 4.3 37.0 1.0 O4 E:ZDC1 4.3 40.3 1.0 N C:SER22 4.4 37.0 1.0 OD2 C:ASP99 4.4 43.4 1.0 C C:ASN103 4.5 32.9 1.0 CB C:ASP104 4.5 38.3 1.0 CA C:ASN21 4.6 37.2 1.0 OD2 C:ASP104 4.6 42.5 1.0 CB C:ASP101 4.7 32.1 1.0 C1 E:ZDC1 4.7 41.6 1.0 CB C:ASN103 4.8 31.5 1.0 N C:ASN103 4.9 34.6 1.0 CA D:GLY114 4.9 45.5 1.0 O C:ASN103 4.9 30.1 1.0 C5 E:ZDC1 5.0 46.9 1.0 O5 E:ZDC1 5.0 44.3 1.0 CA C:ASN103 5.0 31.7 1.0 O D:HOH428 5.0 44.9 1.0

Calcium binding site 6 out of 8 in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:38.1 occ:1.00 OD1 C:ASP101 2.4 38.2 1.0 OE2 C:GLU95 2.4 36.7 1.0 OE1 C:GLU95 2.4 35.8 1.0 OD1 C:ASP99 2.4 42.1 1.0 O3 E:ZDC1 2.6 38.1 1.0 O4 E:ZDC1 2.6 40.3 1.0 OD1 C:ASP104 2.6 41.0 1.0 OD2 C:ASP104 2.7 42.5 1.0 CD C:GLU95 2.7 36.2 1.0 CG C:ASP104 3.0 40.6 1.0 CG C:ASP99 3.4 44.2 1.0 C4 E:ZDC1 3.4 41.9 1.0 CG C:ASP101 3.4 36.3 1.0 C3 E:ZDC1 3.5 40.5 1.0 OD2 C:ASP99 3.6 43.4 1.0 CA C:CA301 3.8 41.1 1.0 OD2 C:ASP101 3.9 38.6 1.0 OD1 C:ASP96 4.0 43.9 1.0 O C:HOH412 4.2 39.6 1.0 CG C:GLU95 4.2 34.6 1.0 N C:ASP101 4.2 33.9 1.0 N C:TYR102 4.4 34.1 1.0 N C:ASN100 4.4 43.1 1.0 N C:GLY97 4.4 43.6 1.0 N C:ASP96 4.4 36.6 1.0 CB C:ASP104 4.5 38.3 1.0 CA C:GLU95 4.6 34.3 1.0 CB C:ASP101 4.7 32.1 1.0 CB C:ASP99 4.8 41.9 1.0 C2 E:ZDC1 4.8 39.5 1.0 CB C:GLU95 4.8 31.4 1.0 N C:ASP99 4.8 45.4 1.0 CA C:ASP101 4.8 33.1 1.0 C5 E:ZDC1 4.8 46.9 1.0 CG C:ASP96 4.9 43.1 1.0 OD1 C:ASN103 4.9 34.2 1.0 O2 E:ZDC1 4.9 38.5 1.0 CA C:GLY97 4.9 44.6 1.0

Calcium binding site 7 out of 8 in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:37.2 occ:1.00 OD1 D:ASP101 2.4 36.1 1.0 O4 H:ZDC1 2.4 44.5 1.0 O3 H:ZDC1 2.4 44.9 1.0 OE2 D:GLU95 2.4 36.0 1.0 OD1 D:ASP99 2.4 44.6 1.0 OE1 D:GLU95 2.5 34.7 1.0 OD1 D:ASP104 2.6 38.1 1.0 OD2 D:ASP104 2.7 38.6 1.0 CD D:GLU95 2.7 34.6 1.0 CG D:ASP104 3.0 38.4 1.0 C4 H:ZDC1 3.2 43.8 1.0 C3 H:ZDC1 3.2 43.9 1.0 CG D:ASP101 3.3 37.0 1.0 CG D:ASP99 3.4 44.5 1.0 OD2 D:ASP99 3.6 43.6 1.0 CA D:CA302 3.6 38.8 1.0 OD2 D:ASP101 3.7 36.3 1.0 N D:ASP101 4.1 35.7 1.0 OD1 D:ASP96 4.2 45.0 1.0 CG D:GLU95 4.2 33.0 1.0 N D:ASN100 4.4 43.6 1.0 N D:TYR102 4.4 35.8 1.0 O D:HOH426 4.4 51.3 1.0 CB D:ASP104 4.5 35.5 1.0 CB D:ASP101 4.5 35.3 1.0 N D:GLY97 4.6 44.0 1.0 C2 H:ZDC1 4.6 41.7 1.0 C5 H:ZDC1 4.6 46.9 1.0 N D:ASP96 4.6 41.2 1.0 OD1 D:ASN103 4.7 32.5 1.0 O2 H:ZDC1 4.7 40.3 1.0 CA D:GLU95 4.7 36.2 1.0 CA D:ASP101 4.7 36.6 1.0 CB D:ASP99 4.8 42.5 1.0 N D:ASP99 4.8 46.8 1.0 CB D:GLU95 4.9 35.2 1.0 CA D:ASN100 5.0 40.7 1.0 C D:ASP101 5.0 34.8 1.0 C D:ASP99 5.0 43.6 1.0

Calcium binding site 8 out of 8 in the Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Fucosylated Heterochiral Linear Peptide FDLN69 Bound to the Fucose Binding Lectin Lecb Pa-Iil From Pseudomonas Aeruginosa at 2.0 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:38.8 occ:1.00 O D:ASN21 2.4 37.5 1.0 OD2 D:ASP101 2.4 36.3 1.0 OD1 D:ASN103 2.4 32.5 1.0 O3 H:ZDC1 2.4 44.9 1.0 OD1 D:ASP104 2.5 38.1 1.0 O2 H:ZDC1 2.5 40.3 1.0 O C:GLY114 2.5 38.2 1.0 CG D:ASP101 3.1 37.0 1.0 OD1 D:ASP101 3.2 36.1 1.0 C3 H:ZDC1 3.3 43.9 1.0 C C:GLY114 3.4 40.0 1.0 C2 H:ZDC1 3.4 41.7 1.0 OXT C:GLY114 3.4 39.2 1.0 CG D:ASN103 3.5 35.2 1.0 C D:ASN21 3.5 35.7 1.0 CA D:CA301 3.6 37.2 1.0 C4 H:ZDC1 3.7 43.8 1.0 CG D:ASP104 3.7 38.4 1.0 ND2 D:ASN103 4.0 33.0 1.0 N D:ASP104 4.1 34.5 1.0 CB D:ASN21 4.2 31.7 1.0 CA D:ASP104 4.2 34.2 1.0 O4 H:ZDC1 4.3 44.5 1.0 CA D:SER22 4.4 38.4 1.0 N D:SER22 4.4 35.4 1.0 OD2 D:ASP99 4.4 43.6 1.0 CB D:ASP104 4.5 35.5 1.0 CA D:ASN21 4.5 35.6 1.0 C D:ASN103 4.5 34.2 1.0 O D:HOH431 4.5 47.8 1.0 CB D:ASP101 4.6 35.3 1.0 CB D:SER22 4.6 36.2 1.0 OD2 D:ASP104 4.6 38.6 1.0 C1 H:ZDC1 4.7 42.7 1.0 CA C:GLY114 4.8 40.9 1.0 CB D:ASN103 4.8 35.4 1.0 N D:ASN103 4.9 36.1 1.0 C5 H:ZDC1 4.9 46.9 1.0 O5 H:ZDC1 5.0 46.0 1.0 CA D:ASN103 5.0 35.4 1.0 O D:ASN103 5.0 33.1 1.0

H.Personne, S.Baeriswyl, I.Di Bonaventura, T.Kohler, C.Van Delden, A.Stocker, S.Javor, J.-L.Reymond. Mixed Chirality Alpha-Helix in A Stapled Bicyclic and A Linear Antimicrobial Peptide Revealed By X-Ray Crystallography Chemrxiv 2021.
DOI: 10.26434/CHEMRXIV.14052293.V1