Zinc in PDB 6d1f: Crystal Structure of Ndm-1 Complexed with Compound 8

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 8:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Complexed with Compound 8, PDB code: 6d1f was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.32 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.510, 60.100, 41.750, 90.00, 97.97, 90.00
R / Rfree (%)	14.5 / 17.9

The structure of Crystal Structure of Ndm-1 Complexed with Compound 8 also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 8 (pdb code 6d1f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 Complexed with Compound 8, PDB code: 6d1f:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Ndm-1 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:8.8 occ:0.94 O09 A:P9T303 1.9 9.7 0.9 NE2 A:HIS189 2.0 8.9 1.0 ND1 A:HIS122 2.0 10.2 1.0 NE2 A:HIS120 2.1 8.4 1.0 O07 A:P9T303 2.9 9.9 0.9 P06 A:P9T303 2.9 10.4 0.9 CD2 A:HIS189 3.0 9.4 1.0 CE1 A:HIS120 3.0 8.4 1.0 CG A:HIS122 3.0 9.6 1.0 CE1 A:HIS189 3.0 9.2 1.0 CE1 A:HIS122 3.0 11.3 1.0 CD2 A:HIS120 3.0 7.2 1.0 CB A:HIS122 3.3 8.2 1.0 O08 A:P9T303 3.9 12.6 0.9 SG A:CYS208 3.9 8.8 1.0 OD1 A:ASP124 4.1 9.6 1.0 ND1 A:HIS120 4.1 8.2 1.0 ND1 A:HIS189 4.1 9.5 1.0 NE2 A:HIS122 4.1 11.8 1.0 CG A:HIS189 4.1 9.5 1.0 CD2 A:HIS122 4.1 10.9 1.0 CG A:HIS120 4.2 6.6 1.0 ZN A:ZN302 4.2 11.5 0.8 CB A:CYS208 4.3 9.9 1.0 C05 A:P9T303 4.3 12.2 0.9 CG2 A:THR190 4.4 9.9 1.0 OD2 A:ASP124 4.7 11.2 1.0 CA A:HIS122 4.8 7.2 1.0 OXT A:ACT304 4.8 13.7 1.0 CG A:ASP124 4.8 9.2 1.0 F12 A:P9T303 4.9 20.1 0.9 ND2 A:ASN220 4.9 13.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ndm-1 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.5 occ:0.77 O08 A:P9T303 1.8 12.6 0.9 NE2 A:HIS250 2.0 11.1 1.0 OXT A:ACT304 2.0 13.7 1.0 SG A:CYS208 2.3 8.8 1.0 CD2 A:HIS250 2.9 10.8 1.0 OD2 A:ASP124 2.9 11.2 1.0 P06 A:P9T303 3.0 10.4 0.9 CE1 A:HIS250 3.0 9.7 1.0 C A:ACT304 3.0 14.5 1.0 O09 A:P9T303 3.2 9.7 0.9 CB A:CYS208 3.3 9.9 1.0 CH3 A:ACT304 3.5 15.0 1.0 O07 A:P9T303 3.8 9.9 0.9 CG A:ASP124 4.0 9.2 1.0 CG A:HIS250 4.0 10.6 1.0 ND1 A:HIS250 4.1 10.1 1.0 O A:ACT304 4.2 16.5 1.0 ZN A:ZN301 4.2 8.8 0.9 CB A:SER249 4.2 8.7 1.0 CE1 A:HIS189 4.2 9.2 1.0 NE2 A:HIS189 4.3 8.9 1.0 OD1 A:ASP124 4.3 9.6 1.0 CA A:CYS208 4.3 9.8 1.0 C05 A:P9T303 4.3 12.2 0.9 O A:HOH582 4.5 34.4 1.0 OG A:SER249 4.6 8.6 1.0 NZ A:LYS211 4.9 16.1 1.0 C03 A:P9T303 4.9 15.2 0.9

O.A.Pemberton, P.Jaishankar, A.Akhtar, J.L.Adams, L.N.Shaw, A.R.Renslo, Y.Chen. Heteroaryl Phosphonates As Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. V. 62 8480 2019.
ISSN: ISSN 0022-2623
PubMed: 31483651
DOI: 10.1021/ACS.JMEDCHEM.9B00728