Zinc in PDB 6d1b: Crystal Structure of Ndm-1 Complexed with Compound 2

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 2:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Complexed with Compound 2, PDB code: 6d1b 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)	29.90 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.760, 59.800, 42.030, 90.00, 97.98, 90.00
R / Rfree (%)	14.9 / 18.4

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 2 (pdb code 6d1b). 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 2, PDB code: 6d1b:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.0 occ:0.89 O11 A:FUJ303 1.9 15.3 0.8 NE2 A:HIS189 2.0 15.6 1.0 ND1 A:HIS122 2.0 14.5 1.0 NE2 A:HIS120 2.0 13.3 1.0 O12 A:FUJ303 2.9 16.0 0.8 P09 A:FUJ303 2.9 18.1 0.8 CE1 A:HIS120 3.0 13.6 1.0 CD2 A:HIS189 3.0 15.1 1.0 CE1 A:HIS189 3.0 15.3 1.0 CE1 A:HIS122 3.0 16.2 1.0 CG A:HIS122 3.0 14.6 1.0 CD2 A:HIS120 3.0 12.8 1.0 CB A:HIS122 3.3 12.9 1.0 SG A:CYS208 3.9 15.4 1.0 O10 A:FUJ303 3.9 19.5 0.8 OD1 A:ASP124 4.0 14.6 1.0 ZN A:ZN302 4.1 16.7 0.6 ND1 A:HIS120 4.1 13.7 1.0 ND1 A:HIS189 4.1 16.2 1.0 NE2 A:HIS122 4.1 17.9 1.0 CG A:HIS189 4.1 16.2 1.0 CG A:HIS120 4.1 12.6 1.0 CD2 A:HIS122 4.2 16.0 1.0 CB A:CYS208 4.2 17.7 1.0 C08 A:FUJ303 4.3 21.7 0.8 CG2 A:THR190 4.4 16.6 1.0 OD2 A:ASP124 4.5 16.9 1.0 CG A:ASP124 4.7 14.8 1.0 OXT A:ACT304 4.8 18.1 0.7 CA A:HIS122 4.8 11.8 1.0 ND2 A:ASN220 5.0 24.7 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.7 occ:0.56 O10 A:FUJ303 1.9 19.5 0.8 NE2 A:HIS250 2.0 16.4 1.0 OXT A:ACT304 2.1 18.1 0.7 SG A:CYS208 2.2 15.4 1.0 OD2 A:ASP124 2.6 16.9 1.0 CD2 A:HIS250 2.9 17.2 1.0 P09 A:FUJ303 2.9 18.1 0.8 CE1 A:HIS250 3.0 16.1 1.0 O11 A:FUJ303 3.0 15.3 0.8 C A:ACT304 3.1 19.1 0.7 CB A:CYS208 3.3 17.7 1.0 CH3 A:ACT304 3.5 19.9 0.7 CG A:ASP124 3.8 14.8 1.0 O12 A:FUJ303 3.8 16.0 0.8 CG A:HIS250 4.1 17.4 1.0 ND1 A:HIS250 4.1 15.7 1.0 ZN A:ZN301 4.1 14.0 0.9 O A:ACT304 4.2 21.3 0.7 CE1 A:HIS189 4.2 15.3 1.0 NE2 A:HIS189 4.2 15.6 1.0 CB A:SER249 4.2 13.7 1.0 OD1 A:ASP124 4.3 14.6 1.0 C08 A:FUJ303 4.4 21.7 0.8 CA A:CYS208 4.4 16.3 1.0 C05 A:FUJ303 4.6 26.0 0.8 OG A:SER249 4.7 13.5 1.0 NZ A:LYS211 4.9 26.2 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