Zinc in PDB 6d1d: Crystal Structure of Ndm-1 Complexed with Compound 6

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 6:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Complexed with Compound 6, PDB code: 6d1d 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)	24.32 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.560, 60.290, 41.980, 90.00, 98.02, 90.00
R / Rfree (%)	13.5 / 16.1

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 6 (pdb code 6d1d). 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 6, PDB code: 6d1d:
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 6


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 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.0 occ:0.91 O11 A:GTV303 2.0 8.7 0.9 ND1 A:HIS122 2.0 9.5 1.0 NE2 A:HIS189 2.0 8.9 1.0 NE2 A:HIS120 2.1 8.9 1.0 O12 A:GTV303 2.9 10.3 0.9 P09 A:GTV303 2.9 10.8 0.9 CE1 A:HIS120 3.0 10.2 1.0 CE1 A:HIS122 3.0 10.4 1.0 CE1 A:HIS189 3.0 9.4 1.0 CD2 A:HIS189 3.0 9.5 1.0 CG A:HIS122 3.0 9.4 1.0 CD2 A:HIS120 3.0 7.5 1.0 CB A:HIS122 3.3 8.3 1.0 O10 A:GTV303 3.7 14.1 0.9 SG A:CYS208 4.0 11.5 1.0 OD1 A:ASP124 4.0 10.2 1.0 ND1 A:HIS120 4.1 8.9 1.0 NE2 A:HIS122 4.1 11.1 1.0 ND1 A:HIS189 4.1 10.1 1.0 CD2 A:HIS122 4.1 10.1 1.0 CG A:HIS120 4.2 7.6 1.0 CG A:HIS189 4.2 10.1 1.0 ZN A:ZN302 4.2 13.0 0.6 CB A:CYS208 4.3 12.6 1.0 C08 A:GTV303 4.4 12.7 0.9 CG2 A:THR190 4.4 10.0 1.0 OD2 A:ASP124 4.7 15.6 1.0 CG A:ASP124 4.8 11.4 1.0 C05 A:GTV303 4.8 14.3 0.9 CA A:HIS122 4.8 7.4 1.0 ND2 A:ASN220 4.9 14.1 1.0 OXT A:ACT304 4.9 14.7 0.7

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 6


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 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.0 occ:0.61 O10 A:GTV303 1.9 14.1 0.9 NE2 A:HIS250 2.0 12.6 1.0 OXT A:ACT304 2.1 14.7 0.7 SG A:CYS208 2.2 11.5 1.0 CD2 A:HIS250 2.8 12.8 1.0 P09 A:GTV303 3.0 10.8 0.9 OD2 A:ASP124 3.0 15.6 1.0 CE1 A:HIS250 3.0 10.9 1.0 O11 A:GTV303 3.1 8.7 0.9 C A:ACT304 3.1 16.4 0.7 CB A:CYS208 3.2 12.6 1.0 CH3 A:ACT304 3.6 17.9 0.7 O12 A:GTV303 3.9 10.3 0.9 CG A:HIS250 4.0 12.0 1.0 CG A:ASP124 4.0 11.4 1.0 ND1 A:HIS250 4.1 10.6 1.0 CB A:SER249 4.2 9.9 1.0 ZN A:ZN301 4.2 9.0 0.9 CE1 A:HIS189 4.2 9.4 1.0 O A:ACT304 4.2 18.6 0.7 CA A:CYS208 4.3 12.0 1.0 NE2 A:HIS189 4.3 8.9 1.0 C08 A:GTV303 4.3 12.7 0.9 OD1 A:ASP124 4.4 10.2 1.0 O A:HOH558 4.6 25.8 1.0 OG A:SER249 4.6 10.4 1.0 NZ A:LYS211 4.8 15.6 1.0 C13 A:GTV303 4.9 16.0 0.9 ND1 A:HIS189 5.0 10.1 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