Calcium in PDB 5i8m: Bicyclic Antimibrocial Peptides

The structure of Bicyclic Antimibrocial Peptides, PDB code: 5i8m was solved by I.Di Bonaventura, X.Jin, R.Visini, G.Michaud, M.Robadey, T.Koehler, C.Vandelden, A.Stocker, T.Darbre, J.-L.Reymond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.16 / 2.13
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.309, 79.365, 52.584, 90.00, 94.46, 90.00
R / Rfree (%)	17.9 / 22.5

The binding sites of Calcium atom in the Bicyclic Antimibrocial Peptides (pdb code 5i8m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Bicyclic Antimibrocial Peptides, PDB code: 5i8m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Bicyclic Antimibrocial Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bicyclic Antimibrocial Peptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:16.0 occ:1.00 OD1 A:ASP99 2.4 21.2 1.0 OE2 A:GLU95 2.4 16.7 1.0 O3 E:ZDC201 2.4 16.1 1.0 OE1 A:GLU95 2.4 17.3 1.0 OD1 A:ASP101 2.5 14.2 1.0 OD2 A:ASP104 2.6 16.0 1.0 O4 E:ZDC201 2.6 15.4 1.0 OD1 A:ASP104 2.6 13.6 1.0 CD A:GLU95 2.7 17.2 1.0 CG A:ASP104 3.0 16.1 1.0 CG A:ASP99 3.3 21.8 1.0 C4 E:ZDC201 3.4 16.3 1.0 C3 E:ZDC201 3.4 15.6 1.0 CG A:ASP101 3.4 15.2 1.0 OD2 A:ASP99 3.6 20.9 1.0 CA A:CA302 3.8 14.9 1.0 OD2 A:ASP101 3.8 14.2 1.0 O A:HOH408 4.0 22.7 1.0 OD1 A:ASP96 4.1 15.5 1.0 N A:ASP101 4.2 17.8 1.0 CG A:GLU95 4.2 15.5 1.0 N A:ASN100 4.5 23.6 1.0 CB A:ASP104 4.5 13.0 1.0 N A:TYR102 4.5 13.8 1.0 N A:ASP96 4.5 15.5 1.0 N A:GLY97 4.5 17.5 1.0 CB A:ASP101 4.6 15.5 1.0 CA A:GLU95 4.7 14.3 1.0 CB A:ASP99 4.7 23.1 1.0 C2 E:ZDC201 4.7 14.7 1.0 C5 E:ZDC201 4.8 17.3 1.0 OD1 A:ASN103 4.8 13.3 1.0 N A:ASP99 4.8 22.4 1.0 CA A:ASP101 4.8 15.9 1.0 CG A:ASP96 4.9 15.6 1.0 O2 E:ZDC201 4.9 14.3 1.0 CB A:GLU95 4.9 15.9 1.0

Calcium binding site 2 out of 8 in the Bicyclic Antimibrocial Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bicyclic Antimibrocial Peptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:14.9 occ:1.00 OD1 A:ASN103 2.4 13.3 1.0 O A:ASN21 2.4 16.4 1.0 OD2 A:ASP101 2.4 14.2 1.0 O3 E:ZDC201 2.5 16.1 1.0 O D:GLY114 2.5 18.2 1.0 OD1 A:ASP104 2.6 13.6 1.0 O2 E:ZDC201 2.6 14.3 1.0 CG A:ASP101 3.2 15.2 1.0 OD1 A:ASP101 3.2 14.2 1.0 C3 E:ZDC201 3.4 15.6 1.0 CG A:ASN103 3.4 13.0 1.0 C2 E:ZDC201 3.4 14.7 1.0 C D:GLY114 3.5 17.7 1.0 C A:ASN21 3.6 16.2 1.0 OXT D:GLY114 3.6 18.1 1.0 CG A:ASP104 3.8 16.1 1.0 CA A:CA301 3.8 16.0 1.0 ND2 A:ASN103 3.8 12.8 1.0 C4 E:ZDC201 3.9 16.3 1.0 CB A:ASN21 4.2 12.6 1.0 N A:ASP104 4.2 14.9 1.0 CA A:ASP104 4.3 12.5 1.0 OD2 A:ASP99 4.4 20.9 1.0 N A:SER22 4.4 13.8 1.0 CA A:SER22 4.4 16.4 1.0 O4 E:ZDC201 4.5 15.4 1.0 CA A:ASN21 4.5 12.9 1.0 C A:ASN103 4.5 14.1 1.0 CB A:ASP101 4.6 15.5 1.0 CB A:ASP104 4.6 13.0 1.0 O A:HOH442 4.6 26.1 1.0 OD2 A:ASP104 4.7 16.0 1.0 CB A:SER22 4.7 14.0 1.0 CB A:ASN103 4.8 12.7 1.0 C1 E:ZDC201 4.8 15.0 1.0 CA D:GLY114 4.9 16.5 1.0 N A:ASN103 4.9 14.4 1.0 O A:ASN103 5.0 14.9 1.0 CA A:ASN103 5.0 13.5 1.0

Calcium binding site 3 out of 8 in the Bicyclic Antimibrocial Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Bicyclic Antimibrocial Peptides within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:15.9 occ:1.00 OD1 D:ASN103 2.3 17.5 1.0 OD2 D:ASP101 2.4 15.3 1.0 O D:ASN21 2.4 18.8 1.0 O3 A:ZDC304 2.4 19.1 1.0 OD1 D:ASP104 2.4 15.1 1.0 O A:GLY114 2.6 18.2 1.0 O2 A:ZDC304 2.6 19.7 1.0 CG D:ASP101 3.2 15.7 1.0 OD1 D:ASP101 3.2 17.1 1.0 C3 A:ZDC304 3.4 18.4 1.0 CG D:ASN103 3.4 16.8 1.0 C A:GLY114 3.5 17.9 1.0 C2 A:ZDC304 3.5 18.3 1.0 OXT A:GLY114 3.6 17.2 1.0 C D:ASN21 3.6 18.6 1.0 CA D:CA201 3.6 15.8 1.0 CG D:ASP104 3.7 15.1 1.0 ND2 D:ASN103 3.9 17.4 1.0 C4 A:ZDC304 3.9 18.2 1.0 N D:ASP104 4.1 16.2 1.0 CA D:ASP104 4.2 15.2 1.0 CB D:ASN21 4.2 13.3 1.0 OD2 D:ASP99 4.4 16.7 1.0 C D:ASN103 4.5 16.2 1.0 CA D:SER22 4.5 16.2 1.0 N D:SER22 4.5 16.3 1.0 O4 A:ZDC304 4.5 17.7 1.0 CB D:ASP104 4.5 14.5 1.0 OD2 D:ASP104 4.5 14.8 1.0 O D:HOH347 4.5 26.7 1.0 CA D:ASN21 4.6 14.9 1.0 CB D:SER22 4.6 15.1 1.0 CB D:ASP101 4.6 14.9 1.0 CB D:ASN103 4.7 15.5 1.0 C1 A:ZDC304 4.8 17.7 1.0 N D:ASN103 4.8 15.9 1.0 CA A:GLY114 4.9 16.4 1.0 O D:ASN103 4.9 17.4 1.0 CA D:ASN103 4.9 15.7 1.0

Calcium binding site 4 out of 8 in the Bicyclic Antimibrocial Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Bicyclic Antimibrocial Peptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:18.7 occ:1.00 OD1 B:ASP99 2.2 31.4 1.0 O4 B:ZDC201 2.4 18.4 1.0 OD1 B:ASP101 2.4 24.1 1.0 OE2 B:GLU95 2.5 21.7 1.0 OD2 B:ASP104 2.5 17.0 1.0 OE1 B:GLU95 2.5 19.9 1.0 O3 B:ZDC201 2.5 16.3 1.0 OD1 B:ASP104 2.6 15.8 1.0 CD B:GLU95 2.8 20.9 1.0 CG B:ASP104 2.9 17.3 1.0 CG B:ASP99 2.9 32.0 1.0 OD2 B:ASP99 2.9 34.7 1.0 C4 B:ZDC201 3.2 17.9 1.0 C3 B:ZDC201 3.4 17.2 1.0 CG B:ASP101 3.4 23.1 1.0 CA B:CA203 3.7 19.9 1.0 OD2 B:ASP101 3.9 22.3 1.0 OD1 B:ASP96 4.1 18.9 1.0 N B:ASP101 4.2 24.4 1.0 CG B:GLU95 4.2 21.4 1.0 N B:TYR102 4.4 19.6 1.0 CB B:ASP104 4.4 14.7 1.0 CB B:ASP99 4.4 33.0 1.0 N B:ASN100 4.4 28.7 1.0 N B:ASP96 4.5 18.4 1.0 N B:GLY97 4.5 24.8 1.0 CA B:GLU95 4.6 17.8 1.0 CB B:ASP101 4.7 22.9 1.0 C5 B:ZDC201 4.7 19.4 1.0 C2 B:ZDC201 4.7 17.2 1.0 O2 B:ZDC201 4.7 17.8 1.0 N B:ASP99 4.7 32.9 1.0 OD1 B:ASN103 4.8 16.2 1.0 CB B:GLU95 4.8 19.8 1.0 CA B:ASP101 4.8 22.5 1.0 CG B:ASP96 4.9 17.5 1.0 CA B:ASP99 4.9 32.8 1.0 C B:ASP99 4.9 30.5 1.0 N B:ASP104 4.9 14.9 1.0 CA B:GLY97 5.0 29.1 1.0

Calcium binding site 5 out of 8 in the Bicyclic Antimibrocial Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Bicyclic Antimibrocial Peptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:19.9 occ:1.00 OD1 B:ASN103 2.4 16.2 1.0 O B:ASN21 2.4 19.7 1.0 OD1 B:ASP104 2.4 15.8 1.0 OD2 B:ASP101 2.5 22.3 1.0 O2 B:ZDC201 2.5 17.8 1.0 O C:GLY114 2.5 17.6 1.0 O3 B:ZDC201 2.9 16.3 1.0 CG B:ASP101 3.2 23.1 1.0 OD1 B:ASP101 3.3 24.1 1.0 C C:GLY114 3.4 17.1 1.0 C2 B:ZDC201 3.4 17.2 1.0 OXT C:GLY114 3.4 16.9 1.0 CG B:ASN103 3.5 16.4 1.0 C3 B:ZDC201 3.5 17.2 1.0 C B:ASN21 3.6 21.0 1.0 CG B:ASP104 3.7 17.3 1.0 CA B:CA202 3.7 18.7 1.0 C4 B:ZDC201 3.8 17.9 1.0 OD2 B:ASP99 3.9 34.7 1.0 ND2 B:ASN103 3.9 14.0 1.0 N B:ASP104 4.1 14.9 1.0 CA B:ASP104 4.2 13.8 1.0 CB B:ASN21 4.2 15.7 1.0 CA B:SER22 4.4 18.8 1.0 N B:SER22 4.4 19.0 1.0 O4 B:ZDC201 4.4 18.4 1.0 C B:ASN103 4.4 14.1 1.0 CA B:ASN21 4.5 17.6 1.0 OD2 B:ASP104 4.5 17.0 1.0 CB B:ASP104 4.5 14.7 1.0 CB B:SER22 4.6 17.8 1.0 CB B:ASP101 4.7 22.9 1.0 C1 B:ZDC201 4.7 16.4 1.0 CB B:ASN103 4.8 14.8 1.0 CA C:GLY114 4.8 16.2 1.0 N B:ASN103 4.8 16.6 1.0 O B:ASN103 4.8 12.4 1.0 CG B:ASP99 4.9 32.0 1.0 CA B:ASN103 4.9 14.3 1.0

Calcium binding site 6 out of 8 in the Bicyclic Antimibrocial Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Bicyclic Antimibrocial Peptides within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:15.8 occ:1.00 O3 B:ZDC205 2.3 22.0 1.0 O C:ASN21 2.3 14.4 1.0 OD1 C:ASN103 2.4 16.4 1.0 OD1 C:ASP104 2.4 16.6 1.0 OD2 C:ASP101 2.5 14.9 1.0 O B:GLY114 2.6 17.9 1.0 O2 B:ZDC205 2.6 21.7 1.0 CG C:ASP101 3.2 16.1 1.0 C3 B:ZDC205 3.3 20.6 1.0 OD1 C:ASP101 3.3 17.1 1.0 C2 B:ZDC205 3.4 21.2 1.0 C B:GLY114 3.5 16.4 1.0 CG C:ASN103 3.5 16.0 1.0 OXT B:GLY114 3.5 17.1 1.0 C C:ASN21 3.5 15.2 1.0 CG C:ASP104 3.7 16.2 1.0 CA C:CA201 3.7 17.7 1.0 C4 B:ZDC205 3.8 19.7 1.0 ND2 C:ASN103 4.0 15.9 1.0 N C:ASP104 4.1 14.2 1.0 CA C:ASP104 4.1 14.6 1.0 CB C:ASN21 4.2 13.0 1.0 C C:ASN103 4.4 15.3 1.0 OD2 C:ASP99 4.4 24.8 1.0 N C:SER22 4.4 16.1 1.0 CA C:SER22 4.4 17.7 1.0 O C:HOH333 4.4 30.6 1.0 CB C:ASP104 4.5 14.5 1.0 CA C:ASN21 4.5 14.0 1.0 O4 B:ZDC205 4.5 18.6 1.0 OD2 C:ASP104 4.5 16.4 1.0 CB C:SER22 4.6 15.8 1.0 CB C:ASP101 4.7 16.3 1.0 CB C:ASN103 4.8 15.1 1.0 C1 B:ZDC205 4.8 20.6 1.0 O C:ASN103 4.8 15.0 1.0 N C:ASN103 4.8 14.9 1.0 CA B:GLY114 4.9 15.7 1.0 CA C:ASN103 4.9 15.1 1.0 O5 B:ZDC205 4.9 20.4 1.0

Calcium binding site 7 out of 8 in the Bicyclic Antimibrocial Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Bicyclic Antimibrocial Peptides within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:17.7 occ:1.00 OD1 C:ASP99 2.3 25.2 1.0 O3 B:ZDC205 2.4 22.0 1.0 OD1 C:ASP101 2.4 17.1 1.0 OE1 C:GLU95 2.5 17.9 1.0 OE2 C:GLU95 2.5 19.6 1.0 O4 B:ZDC205 2.5 18.6 1.0 OD2 C:ASP104 2.5 16.4 1.0 OD1 C:ASP104 2.6 16.6 1.0 CD C:GLU95 2.8 18.0 1.0 CG C:ASP104 2.9 16.2 1.0 C4 B:ZDC205 3.3 19.7 1.0 CG C:ASP99 3.3 24.5 1.0 C3 B:ZDC205 3.3 20.6 1.0 CG C:ASP101 3.4 16.1 1.0 OD2 C:ASP99 3.5 24.8 1.0 CA B:CA204 3.7 15.8 1.0 OD2 C:ASP101 3.8 14.9 1.0 OD1 C:ASP96 4.1 14.1 1.0 O C:HOH348 4.2 21.9 1.0 N C:ASP101 4.2 18.3 1.0 CG C:GLU95 4.3 16.1 1.0 CB C:ASP104 4.4 14.5 1.0 N C:TYR102 4.4 14.4 1.0 N C:ASN100 4.4 21.2 1.0 N C:ASP96 4.5 14.3 1.0 N C:GLY97 4.6 17.0 1.0 CB C:ASP101 4.6 16.3 1.0 C2 B:ZDC205 4.7 21.2 1.0 CA C:GLU95 4.7 13.5 1.0 CB C:ASP99 4.7 24.1 1.0 C5 B:ZDC205 4.7 20.8 1.0 OD1 C:ASN103 4.8 16.4 1.0 N C:ASP99 4.8 23.1 1.0 CA C:ASP101 4.8 16.5 1.0 CB C:GLU95 4.9 13.9 1.0 O2 B:ZDC205 4.9 21.7 1.0 CG C:ASP96 4.9 13.6 1.0 N C:ASP104 5.0 14.2 1.0

Calcium binding site 8 out of 8 in the Bicyclic Antimibrocial Peptides


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Bicyclic Antimibrocial Peptides within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:15.8 occ:1.00 O3 A:ZDC304 2.4 19.1 1.0 OD1 D:ASP99 2.4 16.4 1.0 OD1 D:ASP101 2.4 17.1 1.0 OD2 D:ASP104 2.5 14.8 1.0 OE2 D:GLU95 2.5 17.0 1.0 OE1 D:GLU95 2.6 17.0 1.0 OD1 D:ASP104 2.6 15.1 1.0 O4 A:ZDC304 2.6 17.7 1.0 CD D:GLU95 2.9 17.1 1.0 CG D:ASP104 2.9 15.1 1.0 CG D:ASP99 3.3 16.6 1.0 CG D:ASP101 3.3 15.7 1.0 C4 A:ZDC304 3.4 18.2 1.0 C3 A:ZDC304 3.4 18.4 1.0 OD2 D:ASP99 3.5 16.7 1.0 CA A:CA303 3.6 15.9 1.0 OD2 D:ASP101 3.7 15.3 1.0 OD1 D:ASP96 4.0 17.9 1.0 O A:HOH443 4.1 28.5 1.0 N D:ASP101 4.2 17.1 1.0 CG D:GLU95 4.4 17.2 1.0 CB D:ASP104 4.4 14.5 1.0 N D:TYR102 4.4 14.2 1.0 CB D:ASP101 4.5 14.9 1.0 N D:ASP96 4.6 16.0 1.0 N D:ASN100 4.6 21.8 1.0 N D:GLY97 4.6 16.3 1.0 CB D:ASP99 4.7 18.2 1.0 OD1 D:ASN103 4.7 17.5 1.0 C2 A:ZDC304 4.7 18.3 1.0 CA D:GLU95 4.8 16.6 1.0 CA D:ASP101 4.8 15.3 1.0 O2 A:ZDC304 4.8 19.7 1.0 C5 A:ZDC304 4.8 19.8 1.0 CG D:ASP96 4.9 16.9 1.0 N D:ASP99 4.9 21.4 1.0 N D:ASP104 4.9 16.2 1.0 C D:ASP101 5.0 14.7 1.0 CB D:GLU95 5.0 16.5 1.0

I.Di Bonaventura, X.Jin, R.Visini, D.Probst, S.Javor, B.H.Gan, G.Michaud, A.Natalello, S.M.Doglia, T.Kohler, C.Van Delden, A.Stocker, T.Darbre, J.L.Reymond. Chemical Space Guided Discovery of Antimicrobial Bridged Bicyclic Peptides Against Pseudomonas Aeruginosa and Its Biofilms. Chem Sci V. 8 6784 2017.
ISSN: ISSN 2041-6520
PubMed: 29147502
DOI: 10.1039/C7SC01314K