Zinc 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:

Cadmium

(Cd)

4 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Ndm-1 in Complex with Macrocycle Inhibitor NDM1I-3D, PDB code: 6xci:
Jump to Zinc binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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:Zn302 b:10.9 occ:1.00 O B:HOH404 1.9 12.0 1.0 NE2 B:HIS189 2.0 8.6 1.0 CE1 B:HIS120 2.0 8.9 1.0 ND1 B:HIS122 2.0 11.5 1.0 ND1 B:HIS120 3.0 12.5 1.0 CD2 B:HIS189 3.0 8.5 1.0 NE2 B:HIS120 3.0 12.5 1.0 CG B:HIS122 3.0 10.4 1.0 CE1 B:HIS122 3.0 12.2 1.0 CE1 B:HIS189 3.0 9.7 1.0 CB B:HIS122 3.3 9.8 1.0 O B:ACT301 3.4 33.0 1.0 CD B:CD303 3.8 12.3 0.9 OD1 B:ASP124 4.0 13.4 1.0 SG B:CYS208 4.0 12.7 1.0 C B:ACT301 4.1 33.6 1.0 CD2 B:HIS120 4.1 9.0 1.0 CG B:HIS189 4.1 9.0 1.0 CD2 B:HIS122 4.1 10.9 1.0 NE2 B:HIS122 4.1 12.2 1.0 ND1 B:HIS189 4.1 8.5 1.0 CG B:HIS120 4.2 10.0 1.0 CB B:CYS208 4.3 11.6 1.0 CG2 B:THR190 4.4 9.5 1.0 OXT B:ACT301 4.5 39.1 1.0 O B:HOH556 4.6 4.7 1.0 OD2 B:ASP124 4.6 13.0 1.0 CG B:ASP124 4.7 13.2 1.0 CA B:HIS122 4.8 9.2 1.0 O B:HOH530 5.0 35.6 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn 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 A:Zn301 b:11.8 occ:1.00 O H:HOH101 2.0 11.5 1.0 NE2 A:HIS189 2.0 8.8 1.0 ND1 A:HIS122 2.0 11.3 1.0 NE2 A:HIS120 2.1 10.8 1.0 CD2 A:HIS189 3.0 10.3 1.0 CG A:HIS122 3.0 11.0 1.0 CE1 A:HIS189 3.0 10.0 1.0 CD2 A:HIS120 3.0 9.8 1.0 CE1 A:HIS120 3.1 10.7 1.0 CE1 A:HIS122 3.1 11.9 1.0 CB A:HIS122 3.3 11.2 1.0 OE1 H:GLU5 3.8 24.7 1.0 OD1 A:ASP124 3.9 12.6 1.0 CD A:CD302 3.9 12.6 0.9 SG A:CYS208 3.9 12.4 1.0 CG A:HIS189 4.1 9.1 1.0 ND1 A:HIS120 4.1 10.6 1.0 ND1 A:HIS189 4.1 9.5 1.0 CG A:HIS120 4.2 10.3 1.0 CD2 A:HIS122 4.2 11.7 1.0 NE2 A:HIS122 4.2 12.7 1.0 CB A:CYS208 4.2 10.9 1.0 CG2 A:THR190 4.4 10.5 1.0 CD H:GLU5 4.7 29.4 1.0 CA A:HIS122 4.7 10.4 1.0 ND2 A:ASN220 4.7 22.0 1.0 O A:HOH545 4.7 4.3 1.0 CG A:ASP124 4.8 13.1 1.0 OD2 A:ASP124 4.8 12.9 1.0 OE2 H:GLU5 4.8 25.9 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