Zinc in PDB 6d1e: Crystal Structure of Ndm-1 Complexed with Compound 7

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 7:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Complexed with Compound 7, PDB code: 6d1e 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)	27.92 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.600, 60.160, 41.900, 90.00, 98.07, 90.00
R / Rfree (%)	14.3 / 17.3

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 7 (pdb code 6d1e). 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 7, PDB code: 6d1e:
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 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 Complexed with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.3 occ:0.93 O18 A:XJE303 1.9 11.1 0.8 ND1 A:HIS122 2.0 11.5 1.0 NE2 A:HIS189 2.0 11.0 1.0 NE2 A:HIS120 2.0 9.8 1.0 P15 A:XJE303 2.9 13.2 0.8 O17 A:XJE303 2.9 12.1 0.8 CE1 A:HIS120 3.0 10.5 1.0 CE1 A:HIS122 3.0 12.3 1.0 CE1 A:HIS189 3.0 11.5 1.0 CD2 A:HIS189 3.0 10.8 1.0 CG A:HIS122 3.0 10.9 1.0 CD2 A:HIS120 3.0 9.4 1.0 CB A:HIS122 3.4 9.0 1.0 O16 A:XJE303 3.8 16.3 0.8 SG A:CYS208 3.9 12.0 1.0 OD1 A:ASP124 4.0 12.2 1.0 ND1 A:HIS120 4.1 10.2 1.0 NE2 A:HIS122 4.1 12.6 1.0 ND1 A:HIS189 4.1 11.4 1.0 CD2 A:HIS122 4.1 11.9 1.0 CG A:HIS120 4.1 9.0 1.0 CG A:HIS189 4.2 10.8 1.0 ZN A:ZN302 4.2 15.9 0.6 CB A:CYS208 4.3 11.9 1.0 OD2 A:ASP124 4.4 13.8 1.0 CG2 A:THR190 4.4 11.8 1.0 C14 A:XJE303 4.5 15.7 0.8 CG A:ASP124 4.7 11.2 1.0 CA A:HIS122 4.8 7.9 1.0 OXT A:ACT304 4.9 18.8 0.9 ND2 A:ASN220 5.0 17.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed 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 Complexed with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.9 occ:0.55 O16 A:XJE303 1.7 16.3 0.8 NE2 A:HIS250 1.9 15.1 1.0 OXT A:ACT304 2.1 18.8 0.9 SG A:CYS208 2.2 12.0 1.0 OD2 A:ASP124 2.8 13.8 1.0 CD2 A:HIS250 2.8 14.9 1.0 P15 A:XJE303 2.9 13.2 0.8 CE1 A:HIS250 3.0 13.0 1.0 O18 A:XJE303 3.1 11.1 0.8 C A:ACT304 3.1 20.5 0.9 CB A:CYS208 3.2 11.9 1.0 CH3 A:ACT304 3.6 21.9 0.9 O17 A:XJE303 3.9 12.1 0.8 CG A:HIS250 4.0 14.2 1.0 CG A:ASP124 4.0 11.2 1.0 ND1 A:HIS250 4.0 13.0 1.0 C14 A:XJE303 4.1 15.7 0.8 CB A:SER249 4.1 10.4 1.0 ZN A:ZN301 4.2 10.3 0.9 CE1 A:HIS189 4.2 11.5 1.0 O A:ACT304 4.2 22.1 0.9 NE2 A:HIS189 4.3 11.0 1.0 CA A:CYS208 4.3 11.3 1.0 O A:HOH526 4.5 37.3 1.0 OD1 A:ASP124 4.5 12.2 1.0 C12 A:XJE303 4.6 19.9 0.8 OG A:SER249 4.6 10.2 1.0 C13 A:XJE303 4.8 18.2 0.8 NZ A:LYS211 4.9 19.6 1.0 ND1 A:HIS189 5.0 11.4 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