Zinc in PDB 6d1a: Crystal Structure of Ndm-1 Complexed with Compound 1

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

The structure of Crystal Structure of Ndm-1 Complexed with Compound 1, PDB code: 6d1a 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 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.780, 59.860, 42.020, 90.00, 97.78, 90.00
R / Rfree (%)	14.7 / 18.1

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 1 (pdb code 6d1a). 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 1, PDB code: 6d1a:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.1 occ:0.90 O13 A:TWB303 1.9 17.6 0.8 NE2 A:HIS189 2.0 16.0 1.0 ND1 A:HIS122 2.0 16.1 1.0 NE2 A:HIS120 2.1 13.0 1.0 O14 A:TWB303 2.9 16.6 0.8 P11 A:TWB303 2.9 19.8 0.8 CD2 A:HIS189 3.0 15.9 1.0 CE1 A:HIS120 3.0 13.9 1.0 CG A:HIS122 3.0 15.3 1.0 CE1 A:HIS189 3.0 15.7 1.0 CD2 A:HIS120 3.0 12.2 1.0 CE1 A:HIS122 3.0 16.8 1.0 CB A:HIS122 3.3 12.9 1.0 O12 A:TWB303 3.8 21.3 0.8 SG A:CYS208 3.9 16.6 1.0 ZN A:ZN302 4.0 19.3 0.6 OD1 A:ASP124 4.1 15.5 1.0 ND1 A:HIS120 4.1 13.9 1.0 ND1 A:HIS189 4.1 16.1 1.0 CG A:HIS189 4.1 16.5 1.0 NE2 A:HIS122 4.1 19.2 1.0 CG A:HIS120 4.2 12.6 1.0 CD2 A:HIS122 4.2 17.4 1.0 CB A:CYS208 4.2 17.9 1.0 C10 A:TWB303 4.2 24.7 0.8 CG2 A:THR190 4.4 15.8 1.0 OD2 A:ASP124 4.5 17.8 1.0 OXT A:ACT304 4.7 21.4 0.8 CG A:ASP124 4.8 15.8 1.0 CA A:HIS122 4.8 12.3 1.0 ND2 A:ASN220 5.0 23.4 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.3 occ:0.64 O12 A:TWB303 1.9 21.3 0.8 NE2 A:HIS250 2.0 18.8 1.0 OXT A:ACT304 2.0 21.4 0.8 SG A:CYS208 2.2 16.6 1.0 OD2 A:ASP124 2.6 17.8 1.0 P11 A:TWB303 2.9 19.8 0.8 CD2 A:HIS250 2.9 18.6 1.0 O13 A:TWB303 3.0 17.6 0.8 CE1 A:HIS250 3.0 18.7 1.0 C A:ACT304 3.1 22.3 0.8 CB A:CYS208 3.3 17.9 1.0 CH3 A:ACT304 3.5 24.2 0.8 O14 A:TWB303 3.7 16.6 0.8 CG A:ASP124 3.8 15.8 1.0 ZN A:ZN301 4.0 15.1 0.9 CG A:HIS250 4.1 19.2 1.0 ND1 A:HIS250 4.1 17.6 1.0 O A:ACT304 4.2 24.4 0.8 CE1 A:HIS189 4.2 15.7 1.0 NE2 A:HIS189 4.2 16.0 1.0 OD1 A:ASP124 4.2 15.5 1.0 CB A:SER249 4.3 15.9 1.0 CA A:CYS208 4.4 17.0 1.0 C10 A:TWB303 4.5 24.7 0.8 OG A:SER249 4.7 14.7 1.0 NZ A:LYS211 4.9 27.5 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