Cadmium in PDB 9bic: N-Me-D-LEU2,D-THR5-Clovibactin

The structure of N-Me-D-LEU2,D-THR5-Clovibactin, PDB code: 9bic was solved by A.G.Kreutzer, J.G.Griffin, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.04 / 2.05
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	23.504, 47.773, 54.078, 90, 90, 90
R / Rfree (%)	15.5 / 20.4

The binding sites of Cadmium atom in the N-Me-D-LEU2,D-THR5-Clovibactin (pdb code 9bic). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the N-Me-D-LEU2,D-THR5-Clovibactin, PDB code: 9bic:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the N-Me-D-LEU2,D-THR5-Clovibactin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of N-Me-D-LEU2,D-THR5-Clovibactin within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:14.0 occ:1.00 O A:PHE1 2.5 10.5 1.0 O G:PHE1 2.5 10.6 1.0 H2 G:PHE1 2.6 16.9 1.0 N G:PHE1 2.7 14.1 1.0 O A:HOH211 2.8 15.3 1.0 N A:PHE1 2.8 17.6 1.0 H3 A:PHE1 3.0 21.1 1.0 O G:HOH106 3.2 28.3 1.0 HB2 A:PHE1 3.2 14.2 1.0 C A:PHE1 3.3 10.9 1.0 C G:PHE1 3.3 12.1 1.0 H3 G:PHE1 3.4 16.9 1.0 CA A:PHE1 3.4 11.9 1.0 CA G:PHE1 3.4 19.9 1.0 H2 A:PHE1 3.5 21.1 1.0 HB2 G:PHE1 3.6 16.1 1.0 O G:HOH103 3.6 9.3 1.0 CB A:PHE1 3.8 11.8 1.0 CB G:PHE1 4.0 13.4 1.0 O A:HOH207 4.0 11.7 1.0 HD2 A:PHE1 4.1 15.7 1.0 HA G:PHE1 4.3 23.8 1.0 HA A:PHE1 4.3 14.3 1.0 HA A:MLU2 4.5 12.8 1.0 CG A:PHE1 4.5 13.6 1.0 N A:MLU2 4.6 9.4 1.0 CD2 A:PHE1 4.6 13.1 1.0 N G:MLU2 4.6 10.7 1.0 HA G:MLU2 4.6 12.7 1.0 HB3 A:PHE1 4.6 14.2 1.0 HD2 G:PHE1 4.7 16.9 1.0 CG G:PHE1 4.8 11.8 1.0 HB3 G:PHE1 4.8 16.1 1.0 HG A:MLU2 4.9 13.8 1.0 HD11 A:MLU2 5.0 17.0 1.0 HD12 G:MLU2 5.0 28.6 1.0

Cadmium binding site 2 out of 4 in the N-Me-D-LEU2,D-THR5-Clovibactin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of N-Me-D-LEU2,D-THR5-Clovibactin within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd101 b:10.9 occ:1.00 O D:PHE1 2.4 7.2 1.0 O B:PHE1 2.6 13.4 1.0 N B:PHE1 2.7 12.4 1.0 N D:PHE1 2.7 9.2 1.0 O D:HOH101 2.8 10.3 1.0 H3 B:PHE1 2.8 14.9 1.0 H2 D:PHE1 2.8 11.0 1.0 O B:HOH212 2.8 10.6 1.0 HB2 B:PHE1 3.1 10.4 1.0 HB2 D:PHE1 3.2 9.4 1.0 C D:PHE1 3.2 7.5 1.0 CA B:PHE1 3.3 15.4 1.0 C B:PHE1 3.3 9.6 1.0 CA D:PHE1 3.3 8.0 1.0 H2 B:PHE1 3.4 14.9 1.0 H3 D:PHE1 3.4 11.0 1.0 CB B:PHE1 3.6 8.6 1.0 CB D:PHE1 3.7 7.8 1.0 HD2 B:PHE1 3.8 12.4 1.0 HD2 D:PHE1 4.1 11.9 1.0 HA B:PHE1 4.2 18.5 1.0 HA D:PHE1 4.2 9.6 1.0 CD2 B:PHE1 4.3 10.3 1.0 CG B:PHE1 4.3 11.2 1.0 O B:HOH208 4.4 13.8 1.0 HB3 B:PHE1 4.4 10.4 1.0 CG D:PHE1 4.4 9.8 1.0 N D:MLU2 4.5 7.6 1.0 HA D:MLU2 4.5 9.1 1.0 CD2 D:PHE1 4.5 9.9 1.0 HB3 D:PHE1 4.5 9.4 1.0 N B:MLU2 4.6 8.5 1.0 HD23 B:MLU2 4.6 17.9 1.0 HD22 B:MLU2 4.7 17.9 1.0 O B:HOH213 4.7 14.8 1.0 HA B:MLU2 4.7 9.8 1.0 O D:DLY3 4.8 8.8 1.0 O B:HOH202 4.8 13.0 1.0 O D:HOH109 4.9 15.1 1.0 H D:DLY3 4.9 9.4 1.0

Cadmium binding site 3 out of 4 in the N-Me-D-LEU2,D-THR5-Clovibactin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of N-Me-D-LEU2,D-THR5-Clovibactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd102 b:10.0 occ:1.00 O C:PHE1 2.4 9.4 1.0 O H:PHE1 2.5 6.2 1.0 N C:PHE1 2.6 11.0 1.0 O C:HOH209 2.7 9.6 1.0 N H:PHE1 2.7 13.4 1.0 O C:HOH208 2.8 11.8 1.0 H3 H:PHE1 2.8 16.1 1.0 H3 C:PHE1 2.9 13.1 1.0 O H:HOH209 3.1 11.3 1.0 C C:PHE1 3.2 13.6 1.0 HB2 H:PHE1 3.2 7.9 1.0 HB3 C:PHE1 3.3 13.5 1.0 CA C:PHE1 3.3 10.1 1.0 H2 C:PHE1 3.3 13.1 1.0 C H:PHE1 3.3 6.1 1.0 CA H:PHE1 3.4 7.6 1.0 H2 H:PHE1 3.4 16.1 1.0 O C:HOH205 3.5 26.4 1.0 CB C:PHE1 3.8 11.3 1.0 CB H:PHE1 3.8 6.6 1.0 HD2 H:PHE1 4.0 10.8 1.0 HA C:PHE1 4.2 12.1 1.0 HB2 C:PHE1 4.3 13.5 1.0 HA H:PHE1 4.3 9.2 1.0 HZ2 C:DLY3 4.3 42.3 1.0 N C:MLU2 4.4 13.5 1.0 O H:HOH205 4.4 6.8 1.0 HB3 H:PHE1 4.6 7.9 1.0 H C:DLY3 4.6 11.1 1.0 HA H:MLU2 4.6 6.9 1.0 HA C:MLU2 4.6 12.3 1.0 CD2 H:PHE1 4.6 9.0 1.0 N H:MLU2 4.6 6.0 1.0 O H:HOH201 4.6 14.8 1.0 CG H:PHE1 4.6 8.3 1.0 HD2 C:PHE1 4.7 11.8 1.0 O C:HOH207 4.7 6.8 1.0 HG3 C:DLY3 4.8 24.5 1.0 O C:HOH210 4.9 29.8 1.0 HG H:MLU2 4.9 10.8 1.0 CG C:PHE1 5.0 11.0 1.0

Cadmium binding site 4 out of 4 in the N-Me-D-LEU2,D-THR5-Clovibactin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of N-Me-D-LEU2,D-THR5-Clovibactin within 5.0Å range: probe atom residue distance (Å) B Occ E:Cd101 b:15.2 occ:1.00 O E:PHE1 2.5 17.0 1.0 O F:PHE1 2.5 14.8 1.0 N F:PHE1 2.7 12.5 1.0 N E:PHE1 2.7 22.5 1.0 O F:HOH205 2.8 18.0 1.0 O E:HOH202 2.9 14.6 1.0 H3 F:PHE1 3.1 15.0 1.0 H2 E:PHE1 3.1 27.0 1.0 HB2 E:PHE1 3.1 18.8 1.0 HB3 F:PHE1 3.2 16.3 1.0 C F:PHE1 3.2 12.2 1.0 C E:PHE1 3.3 16.5 1.0 H2 F:PHE1 3.3 15.0 1.0 CA F:PHE1 3.3 13.7 1.0 CA E:PHE1 3.4 16.8 1.0 H3 E:PHE1 3.4 27.0 1.0 CB E:PHE1 3.7 15.7 1.0 CB F:PHE1 3.8 13.6 1.0 HA F:PHE1 4.2 16.5 1.0 HA E:PHE1 4.3 20.1 1.0 HB2 F:PHE1 4.3 16.3 1.0 HD2 E:PHE1 4.3 20.2 1.0 N F:MLU2 4.4 16.3 1.0 HB3 E:PHE1 4.4 18.8 1.0 HA F:MLU2 4.4 18.8 1.0 H F:DLY3 4.5 14.5 1.0 HA E:MLU2 4.6 23.1 1.0 N E:MLU2 4.6 16.0 1.0 HD3 F:DLY3 4.6 27.2 1.0 HD2 F:PHE1 4.6 16.3 1.0 CG E:PHE1 4.7 19.6 1.0 O F:HOH204 4.8 19.4 1.0 CD2 E:PHE1 4.8 16.9 1.0 O F:HOH202 4.8 13.1 1.0 CG F:PHE1 4.9 13.7 1.0 CA F:MLU2 5.0 15.7 1.0

J.E.H.Brunicardi, J.H.Griffin, M.J.Ferracane, A.G.Kreutzer, J.Small, A.T.Mendoza, J.W.Ziller, J.S.Nowick. Structure-Activity Relationship Studies of the Peptide Antibiotic Clovibactin. J.Org.Chem. V. 89 12479 2024.
ISSN: ISSN 0022-3263
PubMed: 39178334
DOI: 10.1021/ACS.JOC.4C01414