Zinc in PDB 6lj6: Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS05008

All present enzymatic activity of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS05008:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS05008, PDB code: 6lj6 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)	27.98 / 1.27
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.637, 59.765, 42.050, 90.00, 98.38, 90.00
R / Rfree (%)	14.2 / 16.6

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS05008 (pdb code 6lj6). 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 WSS05008, PDB code: 6lj6:
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 WSS05008


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 WSS05008 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:16.1 occ:1.00 OD2 A:ASP124 1.9 15.3 1.0 NE2 A:HIS250 2.1 14.9 1.0 S1 A:EFF301 2.3 16.4 1.0 SG A:CYS208 2.3 15.1 0.9 CG A:ASP124 3.0 12.9 1.0 CE1 A:HIS250 3.0 16.1 1.0 CD2 A:HIS250 3.1 15.5 1.0 C9 A:EFF301 3.3 17.6 1.0 OD1 A:ASP124 3.3 13.6 1.0 CB A:CYS208 3.4 17.4 1.0 ZN A:ZN303 3.6 15.1 1.0 C8 A:EFF301 3.8 16.4 1.0 ND1 A:HIS250 4.1 16.2 1.0 CG A:HIS250 4.2 16.2 1.0 CB A:ASP124 4.3 12.0 1.0 CB A:SER249 4.3 15.0 1.0 O A:HOH545 4.4 14.8 1.0 CE1 A:HIS120 4.5 14.6 1.0 NE2 A:HIS120 4.5 13.7 1.0 NE2 A:HIS189 4.5 16.7 1.0 C1 A:EFF301 4.6 19.6 1.0 C2 A:EFF301 4.6 19.8 1.0 C7 A:EFF301 4.6 18.6 1.0 OG A:SER249 4.6 14.1 1.0 CA A:CYS208 4.7 17.6 1.0 CE1 A:HIS189 4.8 17.8 1.0 N1 A:EFF301 4.9 20.1 1.0 CE A:LYS125 4.9 14.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ndm-1 in Complex with D-Captopril Derivative WSS05008


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 WSS05008 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:15.1 occ:1.00 NE2 A:HIS189 2.0 16.7 1.0 NE2 A:HIS120 2.1 13.7 1.0 ND1 A:HIS122 2.1 14.2 1.0 S1 A:EFF301 2.3 16.4 1.0 CE1 A:HIS189 3.0 17.8 1.0 CE1 A:HIS120 3.0 14.6 1.0 CE1 A:HIS122 3.0 15.6 1.0 CD2 A:HIS189 3.0 15.8 1.0 CD2 A:HIS120 3.1 13.8 1.0 CG A:HIS122 3.1 13.8 1.0 C9 A:EFF301 3.2 17.6 1.0 CB A:HIS122 3.4 13.4 1.0 ZN A:ZN302 3.6 16.1 1.0 SG A:CYS208 4.0 15.1 0.9 ND1 A:HIS189 4.1 17.7 1.0 CB A:CYS208 4.1 17.4 1.0 ND1 A:HIS120 4.1 14.2 1.0 NE2 A:HIS122 4.2 16.8 1.0 CG A:HIS189 4.2 17.2 1.0 OD1 A:ASP124 4.2 13.6 1.0 CG A:HIS120 4.2 12.9 1.0 CD2 A:HIS122 4.2 15.6 1.0 CG2 A:THR190 4.5 17.3 1.0 C8 A:EFF301 4.6 16.4 1.0 OD2 A:ASP124 4.7 15.3 1.0 CA A:HIS122 4.9 12.9 1.0 CG A:ASP124 4.9 12.9 1.0 ND2 A:ASN220 4.9 36.2 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