Zinc in PDB 6lj8: Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04134

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04134:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04134, PDB code: 6lj8 was solved by H.Zhang, G.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.50 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.451, 59.861, 41.956, 90.00, 98.05, 90.00
R / Rfree (%)	14.3 / 16.7

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04134 (pdb code 6lj8). 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 in Complex with D-Captopril Derivative WSS04134, PDB code: 6lj8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04134


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 in Complex with D-Captopril Derivative WSS04134 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:11.1 occ:1.00 NE2 A:HIS189 2.0 11.7 1.0 ND1 A:HIS122 2.1 10.8 1.0 NE2 A:HIS120 2.1 10.1 1.0 S1 A:EG0301 2.3 13.2 1.0 CE1 A:HIS122 3.0 12.2 1.0 CE1 A:HIS189 3.0 12.1 1.0 CE1 A:HIS120 3.0 11.4 1.0 CD2 A:HIS189 3.1 11.1 1.0 CG A:HIS122 3.1 10.7 1.0 CD2 A:HIS120 3.1 10.0 1.0 C8 A:EG0301 3.1 12.3 1.0 CB A:HIS122 3.5 10.4 1.0 ZN A:ZN306 3.6 11.8 1.0 SG A:CYS208 4.0 12.2 1.0 CB A:CYS208 4.1 12.4 1.0 NE2 A:HIS122 4.1 12.8 1.0 ND1 A:HIS189 4.1 12.4 1.0 ND1 A:HIS120 4.2 11.8 1.0 OD1 A:ASP124 4.2 11.5 1.0 CG A:HIS189 4.2 11.8 1.0 CD2 A:HIS122 4.2 12.2 1.0 CG A:HIS120 4.2 10.5 1.0 CG2 A:THR190 4.5 13.3 1.0 C7 A:EG0301 4.6 13.3 1.0 OD2 A:ASP124 4.8 11.9 1.0 CA A:HIS122 4.9 10.0 1.0 CG A:ASP124 4.9 10.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS04134


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 in Complex with D-Captopril Derivative WSS04134 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn306 b:11.8 occ:1.00 OD2 A:ASP124 2.0 11.9 1.0 NE2 A:HIS250 2.0 10.2 1.0 S1 A:EG0301 2.3 13.2 1.0 SG A:CYS208 2.3 12.2 1.0 CG A:ASP124 3.0 10.5 1.0 CE1 A:HIS250 3.0 11.1 1.0 CD2 A:HIS250 3.1 10.3 1.0 C8 A:EG0301 3.3 12.3 1.0 OD1 A:ASP124 3.4 11.5 1.0 CB A:CYS208 3.4 12.4 1.0 ZN A:ZN305 3.6 11.1 1.0 C7 A:EG0301 3.8 13.3 1.0 ND1 A:HIS250 4.1 10.8 1.0 CG A:HIS250 4.2 10.6 1.0 CB A:ASP124 4.3 11.1 1.0 O A:HOH585 4.3 9.8 1.0 CB A:SER249 4.4 11.3 1.0 CE1 A:HIS120 4.5 11.4 1.0 NE2 A:HIS189 4.5 11.7 1.0 C3 A:EG0301 4.6 14.6 1.0 NE2 A:HIS120 4.6 10.1 1.0 C4 A:EG0301 4.6 16.1 1.0 C6 A:EG0301 4.6 14.3 1.0 CA A:CYS208 4.7 11.9 1.0 OG A:SER249 4.7 12.1 1.0 CE1 A:HIS189 4.8 12.1 1.0 N1 A:EG0301 4.9 14.3 1.0

G.Ma, S.Wang, K.Wu, W.Zhang, A.Ahmad, Q.Hao, X.Lei, H.Zhang. Structure-Guided Optimization of D-Captopril For Discovery of Potent Ndm-1 Inhibitors Bioorg.Med.Chem. V. 29 2020.
ISSN: ESSN 1464-3391
DOI: 10.1016/J.BMC.2020.115902