Zinc in PDB 6lip: Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS0218

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS0218:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS0218, PDB code: 6lip 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)	27.93 / 0.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.732, 59.908, 42.295, 90.00, 97.37, 90.00
R / Rfree (%)	12.5 / 14.4

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS0218 (pdb code 6lip). 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 WSS0218, PDB code: 6lip:
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 WSS0218


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 WSS0218 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:15.4 occ:1.00 NE2 A:HIS189 2.0 16.1 1.0 ND1 A:HIS122 2.0 15.6 1.0 NE2 A:HIS120 2.1 15.0 1.0 S2 A:EEL303 2.3 15.9 1.0 CE1 A:HIS122 3.0 16.3 1.0 CE1 A:HIS189 3.0 16.4 1.0 CD2 A:HIS120 3.0 15.1 1.0 CE1 A:HIS120 3.1 15.4 1.0 CG A:HIS122 3.1 15.4 1.0 CD2 A:HIS189 3.1 16.1 1.0 C8 A:EEL303 3.3 17.1 1.0 CB A:HIS122 3.4 14.9 1.0 ZN A:ZN302 3.7 15.1 1.0 SG A:CYS208 3.9 15.3 1.0 NE2 A:HIS122 4.1 17.0 1.0 OD1 A:ASP124 4.1 15.3 1.0 CB A:CYS208 4.1 16.1 1.0 ND1 A:HIS189 4.1 16.9 1.0 CG A:HIS120 4.1 14.9 1.0 ND1 A:HIS120 4.1 15.7 1.0 CD2 A:HIS122 4.2 16.4 1.0 CG A:HIS189 4.2 16.3 1.0 CG2 A:THR190 4.4 16.9 1.0 C6 A:EEL303 4.6 17.8 1.0 C5 A:EEL303 4.6 18.9 1.0 N1 A:EEL303 4.8 19.8 1.0 OD2 A:ASP124 4.9 15.3 1.0 CA A:HIS122 4.9 14.8 1.0 O A:HOH518 4.9 19.5 1.0 CG A:ASP124 4.9 14.2 1.0 C1 A:EEL303 4.9 20.1 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS0218


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 WSS0218 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.1 occ:1.00 NE2 A:HIS250 2.0 15.4 1.0 OD2 A:ASP124 2.0 15.3 1.0 S2 A:EEL303 2.3 15.9 1.0 SG A:CYS208 2.3 15.3 1.0 CG A:ASP124 2.9 14.2 1.0 CE1 A:HIS250 3.0 15.7 1.0 CD2 A:HIS250 3.1 15.7 1.0 OD1 A:ASP124 3.3 15.3 1.0 C8 A:EEL303 3.4 17.1 1.0 CB A:CYS208 3.4 16.1 1.0 ZN A:ZN301 3.7 15.4 1.0 C7 A:EEL303 3.9 18.7 1.0 ND1 A:HIS250 4.1 16.4 1.0 CG A:HIS250 4.2 16.1 1.0 CB A:SER249 4.3 15.2 1.0 CB A:ASP124 4.3 14.5 1.0 C6 A:EEL303 4.3 17.8 1.0 NE2 A:HIS189 4.5 16.1 1.0 NE2 A:HIS120 4.6 15.0 1.0 OG A:SER249 4.6 15.3 1.0 CE1 A:HIS120 4.7 15.4 1.0 CA A:CYS208 4.7 16.4 1.0 CE1 A:HIS189 4.7 16.4 1.0 CE A:LYS125 4.8 15.3 1.0 C5 A:EEL303 4.9 18.9 1.0 ND2 A:ASN220 5.0 21.9 1.0 CD A:LYS125 5.0 15.8 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