Zinc in PDB 6efj: Crystal Structure of Ndm-1 with Compound 9

All present enzymatic activity of Crystal Structure of Ndm-1 with Compound 9:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 with Compound 9, PDB code: 6efj 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)	33.97 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.980, 58.770, 41.980, 90.00, 97.48, 90.00
R / Rfree (%)	17.6 / 22.2

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 with Compound 9 (pdb code 6efj). 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 9, PDB code: 6efj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 with Compound 9


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 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.9 occ:1.00 O A:HOH451 1.9 15.6 1.0 NE2 A:HIS189 2.0 17.7 1.0 NE2 A:HIS120 2.0 9.2 1.0 ND1 A:HIS122 2.0 17.5 1.0 CE1 A:HIS120 3.0 9.1 1.0 CE1 A:HIS189 3.0 15.8 1.0 CG A:HIS122 3.0 11.6 1.0 CD2 A:HIS189 3.0 12.7 1.0 CE1 A:HIS122 3.0 14.9 1.0 CD2 A:HIS120 3.0 11.1 1.0 O A:HOH561 3.1 20.9 1.0 CB A:HIS122 3.3 12.3 1.0 O A:HOH495 3.8 30.8 1.0 ZN A:ZN302 3.9 15.1 0.8 SG A:CYS208 3.9 14.1 1.0 ND1 A:HIS120 4.1 11.6 1.0 OD1 A:ASP124 4.1 16.6 1.0 ND1 A:HIS189 4.1 15.9 1.0 NE2 A:HIS122 4.1 18.0 1.0 CG A:HIS189 4.1 14.1 1.0 CG A:HIS120 4.1 12.7 1.0 CD2 A:HIS122 4.1 17.0 1.0 CB A:CYS208 4.2 18.1 1.0 CG2 A:THR190 4.3 14.3 1.0 N08 A:O5E303 4.3 17.3 0.8 N07 A:O5E303 4.4 18.4 0.8 OD2 A:ASP124 4.7 15.6 1.0 CA A:HIS122 4.8 10.9 1.0 CG A:ASP124 4.8 11.3 1.0 O A:HOH581 4.9 26.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 with Compound 9


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 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.1 occ:0.78 N08 A:O5E303 2.0 17.3 0.8 NE2 A:HIS250 2.1 11.8 1.0 OD2 A:ASP124 2.1 15.6 1.0 SG A:CYS208 2.3 14.1 1.0 O A:HOH451 2.4 15.6 1.0 N07 A:O5E303 2.7 18.4 0.8 O01 A:O5E303 2.9 22.2 0.8 CD2 A:HIS250 3.0 15.2 1.0 CE1 A:HIS250 3.1 13.2 1.0 C04 A:O5E303 3.2 20.1 0.8 CG A:ASP124 3.3 11.3 1.0 CB A:CYS208 3.6 18.1 1.0 OD1 A:ASP124 3.7 16.6 1.0 C02 A:O5E303 3.8 20.9 0.8 N03 A:O5E303 3.9 22.0 0.8 ZN A:ZN301 3.9 15.9 1.0 N06 A:O5E303 4.0 21.4 0.8 ND1 A:HIS250 4.2 10.4 1.0 N05 A:O5E303 4.2 20.2 0.8 CG A:HIS250 4.2 13.4 1.0 O A:HOH561 4.3 20.9 1.0 CB A:SER249 4.4 12.8 1.0 NE2 A:HIS189 4.4 17.7 1.0 O A:HOH495 4.5 30.8 1.0 CE1 A:HIS189 4.5 15.8 1.0 CB A:ASP124 4.5 10.1 1.0 CA A:CYS208 4.6 16.0 1.0 OG A:SER249 4.7 13.4 1.0 CE1 A:HIS120 4.8 9.1 1.0 NE2 A:HIS120 4.9 9.2 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