Cadmium in PDB 6xci: Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D

The structure of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D, PDB code: 6xci was solved by L.J.Worrall, T.Sun, V.K.Mulligan, N.C.J.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.80 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.168, 73.789, 77.654, 90, 90, 90
R / Rfree (%)	13.7 / 16

The structure of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Cadmium atom in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D (pdb code 6xci). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D, PDB code: 6xci:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd303 b:12.3 occ:0.90 NE2 B:HIS250 2.2 11.3 1.0 OD2 B:ASP124 2.2 13.0 1.0 O B:HOH404 2.3 12.0 1.0 SG B:CYS208 2.5 12.7 1.0 O B:HOH556 2.7 4.7 1.0 OXT B:ACT301 3.0 39.1 1.0 CD2 B:HIS250 3.2 11.8 1.0 CE1 B:HIS250 3.3 13.0 1.0 CG B:ASP124 3.3 13.2 1.0 CB B:CYS208 3.5 11.6 1.0 OD1 B:ASP124 3.6 13.4 1.0 C B:ACT301 3.8 33.6 1.0 ZN B:ZN302 3.8 10.9 1.0 O B:ACT301 4.0 33.0 1.0 NE2 B:HIS189 4.3 8.6 1.0 CE1 B:HIS189 4.3 9.7 1.0 CG B:HIS250 4.4 12.6 1.0 ND1 B:HIS250 4.4 11.3 1.0 CB B:SER249 4.4 10.4 1.0 CB B:ASP124 4.6 11.6 1.0 CA B:CYS208 4.6 11.2 1.0 OG B:SER249 4.8 12.4 1.0 NE2 B:HIS120 4.8 12.5 1.0 CE1 B:HIS120 4.8 8.9 1.0 CH3 B:ACT301 4.9 41.8 1.0

Cadmium binding site 2 out of 4 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd304 b:13.0 occ:0.90 OD2 B:ASP223 2.2 13.6 1.0 OE1 A:GLU227 2.3 16.8 1.0 O B:HOH554 2.3 23.2 1.0 OE2 B:GLU152 2.3 13.7 1.0 OE2 A:GLU227 2.3 16.8 1.0 OE1 B:GLU152 2.5 13.6 1.0 CD A:GLU227 2.6 15.7 1.0 CD B:GLU152 2.7 13.0 1.0 CG B:ASP223 2.9 13.9 1.0 OD1 B:ASP223 2.9 14.8 1.0 CG A:GLU227 4.2 14.1 1.0 O B:HOH504 4.2 12.6 1.0 NE2 A:HIS228 4.2 12.2 1.0 NE2 B:HIS122 4.2 12.2 1.0 CG B:GLU152 4.3 11.2 1.0 CB B:ASP223 4.3 12.2 1.0 CE1 A:HIS228 4.4 13.9 1.0 O B:HOH461 4.5 31.4 1.0 O B:HOH433 4.7 16.2 1.0 O A:HOH520 4.7 24.8 1.0 CD2 B:HIS122 4.7 10.9 1.0

Cadmium binding site 3 out of 4 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd305 b:13.5 occ:0.90 OD2 A:ASP223 2.2 16.3 1.0 OE1 B:GLU227 2.3 22.0 1.0 OE2 B:GLU227 2.4 22.8 1.0 OE2 A:GLU152 2.4 16.8 1.0 O A:HOH547 2.4 18.1 1.0 OE1 A:GLU152 2.5 15.9 1.0 CD B:GLU227 2.7 18.6 1.0 CD A:GLU152 2.8 14.8 1.0 OD1 A:ASP223 2.8 18.5 1.0 CG A:ASP223 2.9 17.7 1.0 NE2 A:HIS122 4.2 12.7 1.0 O A:HOH477 4.2 14.7 1.0 CG B:GLU227 4.2 15.4 1.0 NE2 B:HIS228 4.2 14.3 1.0 CG A:GLU152 4.3 12.3 1.0 CB A:ASP223 4.3 14.7 1.0 CE1 B:HIS228 4.5 12.9 1.0 O A:HOH443 4.7 18.1 1.0 O B:HOH533 4.8 24.2 1.0 CD2 A:HIS122 4.8 11.7 1.0

Cadmium binding site 4 out of 4 in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:12.6 occ:0.90 NE2 A:HIS250 2.2 11.0 1.0 OD2 A:ASP124 2.3 12.9 1.0 O H:HOH101 2.4 11.5 1.0 OE2 H:GLU5 2.5 25.9 1.0 SG A:CYS208 2.5 12.4 1.0 O A:HOH545 2.7 4.3 1.0 CD2 A:HIS250 3.2 12.0 1.0 CE1 A:HIS250 3.2 12.1 1.0 CG A:ASP124 3.3 13.1 1.0 CD H:GLU5 3.4 29.4 1.0 CB A:CYS208 3.6 10.9 1.0 OD1 A:ASP124 3.6 12.6 1.0 OE1 H:GLU5 3.7 24.7 1.0 ZN A:ZN301 3.9 11.8 1.0 NE2 A:HIS189 4.3 8.8 1.0 CE1 A:HIS189 4.3 10.0 1.0 ND1 A:HIS250 4.4 12.1 1.0 CG A:HIS250 4.4 12.2 1.0 CB A:SER249 4.5 10.6 1.0 CB A:ASP124 4.6 11.6 1.0 CA A:CYS208 4.7 11.7 1.0 CG H:GLU5 4.8 30.1 1.0 CD H:DPR6 4.8 33.2 1.0 OG A:SER249 4.9 11.6 1.0 NE2 A:HIS120 5.0 10.8 1.0

V.K.Mulligan, S.Workman, T.Sun, S.Rettie, X.Li, L.J.Worrall, T.W.Craven, D.T.King, P.Hosseinzadeh, A.M.Watkins, P.D.Renfrew, S.Guffy, J.W.Labonte, R.Moretti, R.Bonneau, N.C.J.Strynadka, D.Baker. Computationally Designed Peptide Macrocycle Inhibitors of New Delhi Metallo-Beta-Lactamase 1. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33723038
DOI: 10.1073/PNAS.2012800118