Zinc in PDB 6o3r: Crystal Structure of Ndm-1 D199N with Compound 7

The structure of Crystal Structure of Ndm-1 D199N with Compound 7, PDB code: 6o3r 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)	21.85 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.663, 60.219, 42.504, 90.00, 97.98, 90.00
R / Rfree (%)	15.3 / 18.1

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 D199N with Compound 7 (pdb code 6o3r). 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 7, PDB code: 6o3r:
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 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.2 occ:1.00 O A:HOH421 2.0 13.2 1.0 ND1 A:HIS122 2.0 13.9 1.0 NE2 A:HIS189 2.1 14.1 1.0 NE2 A:HIS120 2.1 12.9 1.0 O A:HOH441 2.5 16.7 1.0 CG A:HIS122 3.0 12.2 1.0 CE1 A:HIS120 3.0 12.8 1.0 CE1 A:HIS122 3.0 13.7 1.0 CE1 A:HIS189 3.0 15.0 1.0 CD2 A:HIS189 3.1 13.6 1.0 CD2 A:HIS120 3.2 12.3 1.0 CB A:HIS122 3.3 11.3 1.0 O18 A:XJE303 3.8 14.4 0.8 NE2 A:HIS122 4.1 14.5 1.0 CD2 A:HIS122 4.2 13.8 1.0 ND1 A:HIS189 4.2 15.0 1.0 ND1 A:HIS120 4.2 13.4 1.0 CG2 A:THR190 4.2 16.0 1.0 CG A:HIS189 4.2 14.3 1.0 O A:HOH607 4.2 23.6 1.0 O A:HOH589 4.3 18.5 1.0 CG A:HIS120 4.3 12.8 1.0 OD1 A:ASP124 4.3 12.5 1.0 O17 A:XJE303 4.5 15.0 0.8 ZN A:ZN302 4.7 13.9 1.0 SG A:CYS208 4.7 13.2 1.0 CB A:CYS208 4.8 14.0 1.0 CA A:HIS122 4.8 11.1 1.0 P15 A:XJE303 4.8 13.5 0.8

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 D199N with Compound 7


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 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.9 occ:1.00 O18 A:XJE303 1.9 14.4 0.8 OD2 A:ASP124 2.0 12.7 1.0 NE2 A:HIS250 2.0 14.2 1.0 SG A:CYS208 2.3 13.2 1.0 CE1 A:HIS250 3.0 14.3 1.0 CD2 A:HIS250 3.1 15.1 1.0 CG A:ASP124 3.1 11.8 1.0 P15 A:XJE303 3.2 13.5 0.8 O A:HOH421 3.2 13.2 1.0 CB A:CYS208 3.4 14.0 1.0 C14 A:XJE303 3.5 15.9 0.8 OD1 A:ASP124 3.6 12.5 1.0 O16 A:XJE303 3.9 16.5 0.8 CB A:SER249 4.1 13.1 1.0 ND1 A:HIS250 4.1 14.4 1.0 CG A:HIS250 4.2 14.5 1.0 O17 A:XJE303 4.3 15.0 0.8 CB A:ASP124 4.3 11.4 1.0 OG A:SER249 4.4 12.2 1.0 CA A:CYS208 4.5 13.7 1.0 ZN A:ZN301 4.7 14.2 1.0 O02 A:XJE303 4.7 17.8 0.8 CE1 A:HIS120 4.8 12.8 1.0 NE2 A:HIS189 4.8 14.1 1.0 O A:HOH450 4.9 21.0 1.0 CE1 A:HIS189 4.9 15.0 1.0 CE A:LYS125 4.9 12.8 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