Zinc in PDB 6d1h: Crystal Structure of Ndm-1 Complexed with Compound 11

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 11:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Complexed with Compound 11, PDB code: 6d1h 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)	27.93 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.030, 59.990, 41.670, 90.00, 97.88, 90.00
R / Rfree (%)	14.6 / 18

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Complexed with Compound 11 (pdb code 6d1h). 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 11, PDB code: 6d1h:
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 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.8 occ:1.00 O08 A:KED303 1.9 10.3 0.9 NE2 A:HIS189 2.0 10.0 1.0 ND1 A:HIS122 2.0 11.6 1.0 NE2 A:HIS120 2.1 9.3 1.0 P06 A:KED303 3.0 12.1 0.9 O07 A:KED303 3.0 13.1 0.9 CE1 A:HIS189 3.0 10.8 1.0 CE1 A:HIS122 3.0 12.6 1.0 CD2 A:HIS189 3.0 11.3 1.0 CG A:HIS122 3.0 10.9 1.0 CE1 A:HIS120 3.0 9.5 1.0 CD2 A:HIS120 3.1 9.1 1.0 CB A:HIS122 3.3 9.5 1.0 SG A:CYS208 3.9 10.9 1.0 O09 A:KED303 3.9 13.9 0.9 NE2 A:HIS122 4.1 14.0 1.0 ND1 A:HIS189 4.1 11.4 1.0 ND1 A:HIS120 4.1 8.7 1.0 OD1 A:ASP124 4.1 10.2 1.0 CD2 A:HIS122 4.1 13.1 1.0 CG A:HIS189 4.1 10.8 1.0 ZN A:ZN302 4.2 13.1 0.8 CG A:HIS120 4.2 7.8 1.0 CB A:CYS208 4.2 12.1 1.0 C05 A:KED303 4.3 14.8 0.9 CG2 A:THR190 4.4 11.4 1.0 OD2 A:ASP124 4.8 13.8 1.0 CA A:HIS122 4.8 8.3 1.0 OXT A:ACT304 4.8 14.4 0.9 CG A:ASP124 4.9 11.1 1.0 ND2 A:ASN220 5.0 16.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 11


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 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.1 occ:0.75 O09 A:KED303 1.9 13.9 0.9 NE2 A:HIS250 2.0 11.7 1.0 OXT A:ACT304 2.0 14.4 0.9 SG A:CYS208 2.3 10.9 1.0 CD2 A:HIS250 2.9 12.5 1.0 OD2 A:ASP124 2.9 13.8 1.0 P06 A:KED303 3.0 12.1 0.9 CE1 A:HIS250 3.0 10.9 1.0 C A:ACT304 3.0 15.5 0.9 O08 A:KED303 3.1 10.3 0.9 CB A:CYS208 3.3 12.1 1.0 CH3 A:ACT304 3.4 16.4 0.9 O07 A:KED303 3.8 13.1 0.9 CG A:ASP124 4.0 11.1 1.0 CG A:HIS250 4.1 12.2 1.0 ND1 A:HIS250 4.1 10.7 1.0 ZN A:ZN301 4.2 10.8 1.0 O A:ACT304 4.2 17.8 0.9 CE1 A:HIS189 4.2 10.8 1.0 CB A:SER249 4.3 10.1 1.0 NE2 A:HIS189 4.3 10.0 1.0 OD1 A:ASP124 4.3 10.2 1.0 CA A:CYS208 4.4 11.2 1.0 C05 A:KED303 4.4 14.8 0.9 OG A:SER249 4.7 10.2 1.0 C11 A:KED303 4.8 17.2 0.9 O A:HOH540 4.8 39.0 1.0 NZ A:LYS211 4.9 20.7 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