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

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

The structure of Crystal Structure of Ndm-1 with Compound 7, PDB code: 6mdu was solved by A.Akhtar, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.79 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.680, 58.870, 42.030, 90.00, 98.17, 90.00
R / Rfree (%)	16.7 / 19.6

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 with Compound 7 (pdb code 6mdu). 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 with Compound 7, PDB code: 6mdu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 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 with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.2 occ:1.00 O A:HOH413 1.9 12.1 1.0 ND1 A:HIS122 2.0 12.2 1.0 NE2 A:HIS189 2.0 12.2 1.0 NE2 A:HIS120 2.1 10.7 1.0 O A:HOH543 2.8 25.0 1.0 CE1 A:HIS122 3.0 13.5 1.0 CG A:HIS122 3.0 10.4 1.0 CD2 A:HIS189 3.0 11.8 1.0 CE1 A:HIS189 3.0 11.8 1.0 CE1 A:HIS120 3.1 10.7 1.0 CD2 A:HIS120 3.1 9.5 1.0 CB A:HIS122 3.3 8.8 1.0 NE2 A:HIS122 4.1 13.3 1.0 O01 A:N1G303 4.1 12.7 0.7 CD2 A:HIS122 4.1 11.8 1.0 OD1 A:ASP124 4.1 10.3 1.0 ND1 A:HIS189 4.1 12.4 1.0 CG A:HIS189 4.1 11.9 1.0 ND1 A:HIS120 4.2 9.6 1.0 N08 A:N1G303 4.2 10.2 0.7 CG2 A:THR190 4.2 11.9 1.0 CG A:HIS120 4.2 9.1 1.0 ZN A:ZN302 4.3 8.6 0.7 SG A:CYS208 4.3 10.0 1.0 N07 A:N1G303 4.4 12.0 0.7 O A:HOH598 4.5 40.5 1.0 CB A:CYS208 4.5 8.9 1.0 O A:HOH585 4.5 31.1 1.0 CA A:HIS122 4.8 8.5 1.0 O A:HOH524 4.9 13.9 1.0 OD2 A:ASP124 4.9 10.0 1.0 C04 A:N1G303 4.9 11.3 0.7 CG A:ASP124 5.0 9.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 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 with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:8.6 occ:0.70 OD2 A:ASP124 2.0 10.0 1.0 NE2 A:HIS250 2.0 10.0 1.0 N08 A:N1G303 2.1 10.2 0.7 SG A:CYS208 2.3 10.0 1.0 N07 A:N1G303 2.7 12.0 0.7 O A:HOH413 2.8 12.1 1.0 CE1 A:HIS250 3.0 9.9 1.0 CG A:ASP124 3.1 9.0 1.0 CD2 A:HIS250 3.1 10.0 1.0 C04 A:N1G303 3.2 11.3 0.7 O01 A:N1G303 3.4 12.7 0.7 OD1 A:ASP124 3.5 10.3 1.0 CB A:CYS208 3.5 8.9 1.0 N03 A:N1G303 3.8 11.9 0.7 C02 A:N1G303 3.9 12.2 0.7 N06 A:N1G303 4.0 12.6 0.7 ND1 A:HIS250 4.1 10.0 1.0 CG A:HIS250 4.2 10.2 1.0 N05 A:N1G303 4.2 12.3 0.7 CB A:SER249 4.3 9.8 1.0 ZN A:ZN301 4.3 14.2 1.0 CB A:ASP124 4.3 8.3 1.0 OG A:SER249 4.5 9.9 1.0 CA A:CYS208 4.6 10.2 1.0 NE2 A:HIS189 4.6 12.2 1.0 CE1 A:HIS189 4.8 11.8 1.0 CE1 A:HIS120 4.8 10.7 1.0 O A:HOH543 4.8 25.0 1.0

N.J.Torelli, A.Akhtar, K.Defrees, P.Jaishankar, O.A.Pemberton, X.Zhang, C.Johnson, A.R.Renslo, Y.Chen. Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery. Acs Infect Dis. V. 5 1013 2019.
ISSN: ESSN 2373-8227
PubMed: 30942078
DOI: 10.1021/ACSINFECDIS.9B00052