Calcium in PDB 5ney: Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa

The structure of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa, PDB code: 5ney was solved by J.-L.Reymond, T.Darbre, A.Stocker, W.Hong, C.Van Delden, T.Koehler, A.Luscher, R.Visini, Y.Fu, I.Di Bonaventura, R.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.43 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.925, 45.748, 103.850, 90.00, 114.98, 90.00
R / Rfree (%)	18.5 / 21.7

The binding sites of Calcium atom in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa (pdb code 5ney). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa, PDB code: 5ney:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:13.5 occ:1.00 OD1 A:ASP101 2.3 11.4 1.0 OD2 A:ASP104 2.4 13.7 1.0 OD1 A:ASP99 2.4 15.1 1.0 O4 A:ZDC201 2.4 17.3 1.0 OE2 A:GLU95 2.4 13.8 1.0 O3 A:ZDC201 2.5 15.3 1.0 OE1 A:GLU95 2.5 13.3 1.0 OD1 A:ASP104 2.6 12.3 1.0 CD A:GLU95 2.8 12.3 1.0 CG A:ASP104 2.9 12.8 1.0 C4 A:ZDC201 3.2 15.8 1.0 C3 A:ZDC201 3.3 13.8 1.0 CG A:ASP101 3.4 13.8 1.0 CG A:ASP99 3.4 18.8 1.0 CA A:CA203 3.7 14.1 1.0 OD2 A:ASP99 3.7 20.6 1.0 OD2 A:ASP101 3.9 16.2 1.0 O A:HOH341 4.0 24.4 1.0 N A:ASP101 4.1 15.7 1.0 OD1 A:ASP96 4.2 15.2 1.0 CG A:GLU95 4.3 13.2 1.0 CB A:ASP104 4.4 13.8 1.0 N A:ASN100 4.4 17.7 1.0 N A:TYR102 4.5 12.1 1.0 N A:ASP96 4.5 12.7 1.0 CB A:ASP101 4.6 18.2 1.0 N A:GLY97 4.6 16.4 1.0 C5 A:ZDC201 4.7 33.0 1.0 C2 A:ZDC201 4.7 19.1 1.0 OD1 A:ASN103 4.7 13.4 1.0 CA A:GLU95 4.7 14.1 1.0 CA A:ASP101 4.7 15.0 1.0 CB A:ASP99 4.8 17.6 1.0 O2 A:ZDC201 4.8 16.4 1.0 N A:ASP99 4.8 16.6 1.0 CB A:GLU95 4.9 9.9 1.0 CG A:ASP96 4.9 13.6 1.0 C A:ASP99 5.0 16.4 1.0 C A:ASP101 5.0 17.2 1.0 CA A:ASN100 5.0 19.0 1.0

Calcium binding site 2 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:14.1 occ:1.00 OD1 A:ASN103 2.3 13.4 1.0 OD1 A:ASP104 2.3 12.3 1.0 O A:ASN21 2.4 14.6 1.0 OD2 A:ASP101 2.4 16.2 1.0 O2 A:ZDC201 2.4 16.4 1.0 O3 A:ZDC201 2.4 15.3 1.0 O D:GLY114 2.5 14.8 1.0 OD1 A:ASP101 3.0 11.4 1.0 CG A:ASP101 3.0 13.8 1.0 C3 A:ZDC201 3.3 13.8 1.0 C2 A:ZDC201 3.3 19.1 1.0 CG A:ASN103 3.4 14.7 1.0 C D:GLY114 3.5 21.2 1.0 C A:ASN21 3.5 14.6 1.0 CG A:ASP104 3.6 12.8 1.0 OXT D:GLY114 3.7 20.3 1.0 CA A:CA202 3.7 13.5 1.0 C4 A:ZDC201 3.8 15.8 1.0 ND2 A:ASN103 3.8 14.6 1.0 CA A:ASP104 4.2 10.3 1.0 CB A:ASN21 4.2 14.3 1.0 N A:ASP104 4.3 10.0 1.0 CA A:SER22 4.4 16.4 1.0 N A:SER22 4.4 12.2 1.0 OD2 A:ASP104 4.4 13.7 1.0 CB A:ASP104 4.4 13.8 1.0 O4 A:ZDC201 4.5 17.3 1.0 C A:ASN103 4.5 10.1 1.0 CB A:ASP101 4.5 18.2 1.0 CA A:ASN21 4.5 12.6 1.0 OD2 A:ASP99 4.5 20.6 1.0 CB A:SER22 4.6 21.8 1.0 C1 A:ZDC201 4.7 28.9 1.0 O D:HOH333 4.7 28.1 1.0 CB A:ASN103 4.7 10.2 1.0 O A:ASN103 4.8 13.2 1.0 CA D:GLY114 4.8 16.1 1.0 N A:ASN103 4.9 13.8 1.0 CA A:ASN103 4.9 10.6 1.0

Calcium binding site 3 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:13.2 occ:1.00 OD2 B:ASP104 2.3 11.8 1.0 OD1 B:ASP99 2.4 19.6 1.0 OD1 B:ASP101 2.4 11.3 1.0 OE2 B:GLU95 2.4 16.5 1.0 O3 E:ZDC201 2.5 16.6 1.0 O4 E:ZDC201 2.5 11.1 1.0 OE1 B:GLU95 2.6 12.7 1.0 OD1 B:ASP104 2.6 11.2 1.0 CD B:GLU95 2.8 13.9 1.0 CG B:ASP104 2.8 10.8 1.0 C4 E:ZDC201 3.3 10.3 1.0 C3 E:ZDC201 3.3 14.0 1.0 CG B:ASP99 3.3 17.3 1.0 CG B:ASP101 3.5 12.4 1.0 OD2 B:ASP99 3.6 16.4 1.0 CA B:CA302 3.7 13.4 1.0 OD2 B:ASP101 4.0 14.1 1.0 OD1 B:ASP96 4.1 15.3 1.0 N B:ASP101 4.2 15.4 1.0 O E:HOH305 4.3 22.4 1.0 CG B:GLU95 4.3 12.5 1.0 CB B:ASP104 4.3 12.1 1.0 N B:ASN100 4.4 14.5 1.0 N B:TYR102 4.5 12.4 1.0 N B:ASP96 4.5 12.8 1.0 N B:GLY97 4.6 13.9 1.0 CB B:ASP101 4.6 15.9 1.0 C5 E:ZDC201 4.7 19.2 1.0 C2 E:ZDC201 4.7 14.1 1.0 CA B:GLU95 4.7 10.7 1.0 CB B:ASP99 4.7 17.2 1.0 OD1 B:ASN103 4.7 10.5 1.0 N B:ASP99 4.8 16.3 1.0 CA B:ASP101 4.8 15.0 1.0 O2 E:ZDC201 4.9 13.7 1.0 CG B:ASP96 4.9 14.0 1.0 CB B:GLU95 5.0 11.6 1.0 C B:ASP99 5.0 17.5 1.0

Calcium binding site 4 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:13.4 occ:1.00 OD1 B:ASN103 2.4 10.5 1.0 OD1 B:ASP104 2.4 11.2 1.0 O B:ASN21 2.4 12.5 1.0 O C:GLY114 2.4 14.1 1.0 O3 E:ZDC201 2.4 16.6 1.0 OD2 B:ASP101 2.5 14.1 1.0 O2 E:ZDC201 2.5 13.7 1.0 OD1 B:ASP101 3.0 11.3 1.0 CG B:ASP101 3.1 12.4 1.0 C3 E:ZDC201 3.3 14.0 1.0 CG B:ASN103 3.4 11.6 1.0 C2 E:ZDC201 3.4 14.1 1.0 C C:GLY114 3.4 16.8 1.0 CG B:ASP104 3.6 10.8 1.0 C B:ASN21 3.6 12.1 1.0 OXT C:GLY114 3.6 18.0 1.0 C4 E:ZDC201 3.7 10.3 1.0 CA B:CA301 3.7 13.2 1.0 ND2 B:ASN103 3.8 12.1 1.0 CB B:ASN21 4.2 11.3 1.0 CA B:ASP104 4.2 12.9 1.0 N B:ASP104 4.3 11.9 1.0 O4 E:ZDC201 4.4 11.1 1.0 CA B:SER22 4.4 15.1 1.0 OD2 B:ASP104 4.4 11.8 1.0 CB B:ASP104 4.4 12.1 1.0 N B:SER22 4.5 14.7 1.0 OD2 B:ASP99 4.5 16.4 1.0 C B:ASN103 4.5 15.6 1.0 CA B:ASN21 4.5 14.1 1.0 O B:HOH442 4.6 24.8 1.0 CB B:ASP101 4.6 15.9 1.0 CB B:SER22 4.6 12.7 1.0 C1 E:ZDC201 4.7 19.6 1.0 CB B:ASN103 4.8 11.4 1.0 CA C:GLY114 4.8 16.1 1.0 O B:ASN103 4.8 12.8 1.0 N B:ASN103 4.9 11.6 1.0 CA B:ASN103 5.0 11.6 1.0 O5 E:ZDC201 5.0 21.7 1.0 C5 E:ZDC201 5.0 19.2 1.0

Calcium binding site 5 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:15.2 occ:1.00 OD1 C:ASP99 2.4 18.6 1.0 OD1 C:ASP101 2.4 13.7 1.0 O4 C:ZDC201 2.4 15.2 1.0 OE2 C:GLU95 2.4 15.2 1.0 O3 C:ZDC201 2.5 16.6 1.0 OD2 C:ASP104 2.5 11.9 1.0 OE1 C:GLU95 2.5 14.8 1.0 OD1 C:ASP104 2.7 13.0 1.0 CD C:GLU95 2.8 14.7 1.0 CG C:ASP104 2.9 10.2 1.0 C4 C:ZDC201 3.2 20.6 1.0 C3 C:ZDC201 3.4 19.4 1.0 CG C:ASP99 3.4 15.2 1.0 CG C:ASP101 3.4 13.1 1.0 OD2 C:ASP99 3.6 20.0 1.0 CA C:CA203 3.7 14.8 1.0 OD2 C:ASP101 3.9 17.8 1.0 O C:HOH354 4.0 20.6 1.0 N C:ASP101 4.0 15.4 1.0 CG C:GLU95 4.3 13.7 1.0 OD1 C:ASP96 4.3 16.3 1.0 CB C:ASP104 4.4 12.1 1.0 N C:ASN100 4.5 17.2 1.0 N C:TYR102 4.5 12.3 1.0 N C:ASP96 4.5 14.4 1.0 CB C:ASP101 4.5 13.9 1.0 N C:GLY97 4.6 15.8 1.0 C2 C:ZDC201 4.7 19.7 1.0 C5 C:ZDC201 4.7 38.6 1.0 O2 C:ZDC201 4.7 13.4 1.0 CA C:ASP101 4.7 13.0 1.0 OD1 C:ASN103 4.7 11.1 1.0 CB C:ASP99 4.7 21.0 1.0 CA C:GLU95 4.7 13.3 1.0 N C:ASP99 4.8 16.2 1.0 C C:ASP101 4.9 15.3 1.0 CB C:GLU95 5.0 15.5 1.0 C C:ASP99 5.0 17.4 1.0

Calcium binding site 6 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca203 b:14.8 occ:1.00 OD1 C:ASN103 2.3 11.1 1.0 O C:ASN21 2.4 13.9 1.0 O2 C:ZDC201 2.4 13.4 1.0 O B:GLY114 2.4 14.6 1.0 OD1 C:ASP104 2.4 13.0 1.0 OD2 C:ASP101 2.4 17.8 1.0 O3 C:ZDC201 2.5 16.6 1.0 OD1 C:ASP101 3.0 13.7 1.0 CG C:ASP101 3.1 13.1 1.0 CG C:ASN103 3.4 13.3 1.0 C B:GLY114 3.4 18.6 1.0 C2 C:ZDC201 3.4 19.7 1.0 C3 C:ZDC201 3.4 19.4 1.0 OXT B:GLY114 3.6 20.5 1.0 C C:ASN21 3.6 15.6 1.0 CG C:ASP104 3.6 10.2 1.0 CA C:CA202 3.7 15.2 1.0 ND2 C:ASN103 3.8 13.7 1.0 C4 C:ZDC201 3.9 20.6 1.0 CA C:ASP104 4.2 11.5 1.0 CB C:ASN21 4.2 12.6 1.0 N C:ASP104 4.2 11.1 1.0 CA C:SER22 4.4 11.6 1.0 N C:SER22 4.4 14.7 1.0 C C:ASN103 4.5 9.4 1.0 O4 C:ZDC201 4.5 15.2 1.0 OD2 C:ASP104 4.5 11.9 1.0 CB C:ASP104 4.5 12.1 1.0 OD2 C:ASP99 4.5 20.0 1.0 CB C:ASP101 4.5 13.9 1.0 CA C:ASN21 4.6 9.2 1.0 CB C:SER22 4.6 18.3 1.0 O C:HOH363 4.7 24.1 1.0 CB C:ASN103 4.7 13.3 1.0 C1 C:ZDC201 4.7 42.8 1.0 CA B:GLY114 4.8 15.8 1.0 O C:ASN103 4.8 12.1 1.0 N C:ASN103 4.9 12.7 1.0 CA C:ASN103 4.9 11.9 1.0

Calcium binding site 7 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:17.0 occ:1.00 OD1 D:ASP101 2.3 13.6 1.0 OD1 D:ASP99 2.4 20.4 1.0 OD2 D:ASP104 2.4 16.8 1.0 OE2 D:GLU95 2.4 19.5 1.0 O4 D:ZDC201 2.4 18.9 1.0 O3 D:ZDC201 2.4 15.8 1.0 OE1 D:GLU95 2.5 17.7 1.0 OD1 D:ASP104 2.6 14.6 1.0 CD D:GLU95 2.8 16.5 1.0 CG D:ASP104 2.8 14.2 1.0 C4 D:ZDC201 3.3 16.2 1.0 CG D:ASP101 3.4 13.5 1.0 C3 D:ZDC201 3.4 16.2 1.0 CG D:ASP99 3.4 18.6 1.0 CA D:CA203 3.7 15.6 1.0 OD2 D:ASP99 3.7 20.7 1.0 OD2 D:ASP101 4.0 15.0 1.0 O D:HOH355 4.0 22.0 1.0 N D:ASP101 4.0 15.2 1.0 CG D:GLU95 4.3 16.6 1.0 OD1 D:ASP96 4.3 20.9 1.0 CB D:ASP104 4.4 12.1 1.0 N D:TYR102 4.4 15.1 1.0 N D:ASN100 4.5 17.4 1.0 N D:GLY97 4.5 19.3 1.0 N D:ASP96 4.5 16.7 1.0 CB D:ASP101 4.5 14.1 1.0 OD1 D:ASN103 4.6 13.6 1.0 CA D:ASP101 4.7 16.5 1.0 C2 D:ZDC201 4.7 17.8 1.0 C5 D:ZDC201 4.7 36.6 1.0 CA D:GLU95 4.7 14.5 1.0 N D:ASP99 4.8 19.0 1.0 CB D:ASP99 4.8 21.4 1.0 O2 D:ZDC201 4.8 18.3 1.0 C D:ASP101 4.9 15.1 1.0 CG D:ASP96 4.9 14.6 1.0 CB D:GLU95 5.0 13.1 1.0 C D:ASP99 5.0 16.8 1.0

Calcium binding site 8 out of 8 in the Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Discovery, Crystal Structures and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca203 b:15.6 occ:1.00 OD1 D:ASN103 2.3 13.6 1.0 OD1 D:ASP104 2.4 14.6 1.0 O D:ASN21 2.4 15.0 1.0 O2 D:ZDC201 2.5 18.3 1.0 O A:GLY114 2.5 18.1 1.0 O3 D:ZDC201 2.5 15.8 1.0 OD2 D:ASP101 2.5 15.0 1.0 OD1 D:ASP101 3.0 13.6 1.0 CG D:ASP101 3.1 13.5 1.0 CG D:ASN103 3.4 13.8 1.0 C3 D:ZDC201 3.4 16.2 1.0 C A:GLY114 3.4 21.6 1.0 C2 D:ZDC201 3.4 17.8 1.0 CG D:ASP104 3.6 14.2 1.0 OXT A:GLY114 3.6 21.4 1.0 C D:ASN21 3.6 13.9 1.0 CA D:CA202 3.7 17.0 1.0 ND2 D:ASN103 3.8 14.7 1.0 C4 D:ZDC201 3.8 16.2 1.0 CB D:ASN21 4.2 11.8 1.0 CA D:ASP104 4.2 14.1 1.0 N D:ASP104 4.2 12.9 1.0 O4 D:ZDC201 4.4 18.9 1.0 OD2 D:ASP104 4.4 16.8 1.0 CB D:ASP104 4.4 12.1 1.0 C D:ASN103 4.5 14.1 1.0 N D:SER22 4.5 14.1 1.0 OD2 D:ASP99 4.5 20.7 1.0 CA D:ASN21 4.6 12.9 1.0 CA D:SER22 4.6 14.7 1.0 CB D:ASP101 4.6 14.1 1.0 O A:HOH332 4.7 24.9 1.0 CB D:ASN103 4.7 11.3 1.0 C1 D:ZDC201 4.8 43.0 1.0 CA A:GLY114 4.8 13.3 1.0 O D:ASN103 4.8 12.8 1.0 CB D:SER22 4.8 16.9 1.0 N D:ASN103 4.9 13.2 1.0 CA D:ASN103 5.0 14.6 1.0

R.He, I.Di Bonaventura, R.Visini, B.H.Gan, Y.Fu, D.Probst, A.Luscher, T.Kohler, C.Van Delden, A.Stocker, W.Hong, T.Darbre, J.L.Reymond. Design, Crystal Structure and Atomic Force Microscopy Study of Thioether Ligated D,L-Cyclic Antimicrobial Peptides Against Multidrug Resistant Pseudomonas Aeruginosa. Chem Sci V. 8 7464 2017.
ISSN: ISSN 2041-6520
PubMed: 29163899
DOI: 10.1039/C7SC01599B