Zinc in PDB 6ny7: Crystal Structure of Ndm-1 D199N with Compound 16

All present enzymatic activity of Crystal Structure of Ndm-1 D199N with Compound 16:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 D199N with Compound 16, PDB code: 6ny7 was solved by A.Akhtar, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.07 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.571, 59.774, 42.531, 90.00, 97.88, 90.00
R / Rfree (%)	14.4 / 17.5

The structure of Crystal Structure of Ndm-1 D199N with Compound 16 also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 D199N with Compound 16 (pdb code 6ny7). 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 D199N with Compound 16, PDB code: 6ny7:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 D199N with Compound 16


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 D199N with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.6 occ:1.00 O A:HOH443 1.9 13.3 1.0 ND1 A:HIS122 2.0 14.6 1.0 NE2 A:HIS189 2.0 13.8 1.0 NE2 A:HIS120 2.1 13.2 1.0 O A:HOH416 2.5 19.2 1.0 CG A:HIS122 3.0 13.2 1.0 CE1 A:HIS189 3.0 15.1 1.0 CE1 A:HIS120 3.0 13.7 1.0 CE1 A:HIS122 3.0 15.3 1.0 CD2 A:HIS189 3.1 14.8 1.0 CD2 A:HIS120 3.1 12.0 1.0 CB A:HIS122 3.3 11.9 1.0 O12 A:L8J303 3.8 15.4 0.8 NE2 A:HIS122 4.1 15.3 1.0 CD2 A:HIS122 4.1 13.7 1.0 ND1 A:HIS189 4.1 14.6 1.0 ND1 A:HIS120 4.1 12.5 1.0 CG2 A:THR190 4.1 13.7 1.0 CG A:HIS189 4.2 14.8 1.0 CG A:HIS120 4.2 11.6 1.0 OD1 A:ASP124 4.3 13.8 1.0 O A:HOH605 4.3 25.2 1.0 O A:HOH568 4.3 23.6 1.0 O14 A:L8J303 4.4 17.3 0.8 ZN A:ZN302 4.6 14.6 1.0 SG A:CYS208 4.6 13.1 1.0 P11 A:L8J303 4.8 16.4 0.8 CB A:CYS208 4.8 14.0 1.0 CA A:HIS122 4.8 11.0 1.0 O A:HOH608 4.8 6.9 0.5 O A:HOH608 4.8 11.1 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 D199N with Compound 16


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 D199N with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.6 occ:1.00 O12 A:L8J303 1.9 15.4 0.8 OD2 A:ASP124 2.0 12.6 1.0 NE2 A:HIS250 2.1 12.7 1.0 SG A:CYS208 2.3 13.1 1.0 CE1 A:HIS250 3.0 11.6 1.0 CD2 A:HIS250 3.1 13.0 1.0 CG A:ASP124 3.1 12.5 1.0 P11 A:L8J303 3.2 16.4 0.8 O A:HOH443 3.2 13.3 1.0 CB A:CYS208 3.4 14.0 1.0 OD1 A:ASP124 3.5 13.8 1.0 C10 A:L8J303 3.6 24.4 0.8 O13 A:L8J303 3.9 18.9 0.8 CB A:SER249 4.1 12.2 1.0 ND1 A:HIS250 4.1 12.0 1.0 CG A:HIS250 4.2 12.4 1.0 CB A:ASP124 4.3 10.0 1.0 O14 A:L8J303 4.4 17.3 0.8 OG A:SER249 4.4 11.7 1.0 O A:HOH608 4.4 6.9 0.5 CA A:CYS208 4.5 13.2 1.0 ZN A:ZN301 4.6 15.6 1.0 NE2 A:HIS189 4.7 13.8 1.0 CE1 A:HIS189 4.7 15.1 1.0 CE1 A:HIS120 4.8 13.7 1.0 O A:HOH453 4.9 21.6 1.0 CE A:LYS125 5.0 11.5 1.0

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