Zinc in PDB 4exs: Crystal Structure of Ndm-1 Bound to L-Captopril

All present enzymatic activity of Crystal Structure of Ndm-1 Bound to L-Captopril:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Bound to L-Captopril, PDB code: 4exs was solved by N.C.J.Strynadka, D.T.King, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.71 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.120, 107.120, 92.900, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 24.1

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to L-Captopril (pdb code 4exs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 Bound to L-Captopril, PDB code: 4exs:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 Bound to L-Captopril


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 Bound to L-Captopril within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:18.0 occ:1.00 NE2 B:HIS189 2.0 17.8 1.0 NE2 B:HIS120 2.1 12.8 1.0 ND1 B:HIS122 2.1 12.6 1.0 S B:X8Z301 2.4 11.3 0.6 CE1 B:HIS120 2.9 13.8 1.0 CE1 B:HIS189 3.0 14.9 1.0 CD2 B:HIS189 3.0 13.4 1.0 CE1 B:HIS122 3.0 12.9 1.0 CD2 B:HIS120 3.1 14.9 1.0 CG B:HIS122 3.1 13.1 1.0 C1 B:X8Z301 3.3 18.9 0.6 CB B:HIS122 3.5 13.3 1.0 ZN B:ZN303 3.5 17.7 0.8 SG B:CYS208 4.0 20.1 1.0 OD1 B:ASP124 4.0 15.9 1.0 ND1 B:HIS120 4.1 11.8 1.0 ND1 B:HIS189 4.1 15.2 1.0 CG B:HIS189 4.1 13.8 1.0 NE2 B:HIS122 4.2 12.5 1.0 CB B:CYS208 4.2 17.5 1.0 CG B:HIS120 4.2 13.8 1.0 CD2 B:HIS122 4.2 10.8 1.0 CG2 B:THR190 4.6 13.2 1.0 OD2 B:ASP124 4.6 18.2 1.0 C2 B:X8Z301 4.7 20.2 0.6 O1 B:X8Z301 4.8 23.6 0.6 CG B:ASP124 4.8 16.4 1.0 CA B:HIS122 4.9 13.8 1.0 C4 B:X8Z301 5.0 22.3 0.6

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 Bound to L-Captopril


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 Bound to L-Captopril within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:17.7 occ:0.75 OD2 B:ASP124 2.0 18.2 1.0 S B:X8Z301 2.1 11.3 0.6 NE2 B:HIS250 2.2 21.5 1.0 SG B:CYS208 2.3 20.1 1.0 CE1 B:HIS250 3.0 19.9 1.0 CG B:ASP124 3.0 16.4 1.0 C1 B:X8Z301 3.3 18.9 0.6 CD2 B:HIS250 3.3 23.3 1.0 OD1 B:ASP124 3.3 15.9 1.0 CB B:CYS208 3.4 17.5 1.0 ZN B:ZN302 3.5 18.0 1.0 C2 B:X8Z301 4.0 20.2 0.6 ND1 B:HIS250 4.2 20.1 1.0 CB B:SER249 4.3 20.8 1.0 CB B:ASP124 4.3 13.7 1.0 CE1 B:HIS120 4.4 13.8 1.0 C4 B:X8Z301 4.4 22.3 0.6 CG B:HIS250 4.4 22.9 1.0 NE2 B:HIS120 4.4 12.8 1.0 NE2 B:HIS189 4.5 17.8 1.0 C5 B:X8Z301 4.5 21.9 0.6 N B:X8Z301 4.5 22.2 0.6 OG B:SER249 4.6 21.1 1.0 CA B:CYS208 4.7 17.2 1.0 CE1 B:HIS189 4.7 14.9 1.0 CE B:LYS125 4.7 10.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 Bound to L-Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Ndm-1 Bound to L-Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:17.0 occ:1.00 NE2 A:HIS189 2.0 10.4 1.0 ND1 A:HIS122 2.1 9.6 1.0 NE2 A:HIS120 2.1 11.3 1.0 S A:X8Z301 2.3 32.6 1.0 CD2 A:HIS189 3.0 10.9 1.0 CD2 A:HIS120 3.0 10.6 1.0 CG A:HIS122 3.0 11.1 1.0 CE1 A:HIS189 3.0 7.0 1.0 CE1 A:HIS120 3.1 14.4 1.0 CE1 A:HIS122 3.1 9.7 1.0 CB A:HIS122 3.3 6.9 1.0 C1 A:X8Z301 3.5 42.7 1.0 ZN A:ZN303 3.6 14.2 0.8 SG A:CYS208 4.0 18.6 1.0 ND1 A:HIS189 4.1 9.8 1.0 CG A:HIS189 4.1 11.2 1.0 ND1 A:HIS120 4.1 13.9 1.0 CG A:HIS120 4.2 13.5 1.0 NE2 A:HIS122 4.2 8.4 1.0 CD2 A:HIS122 4.2 10.8 1.0 CB A:CYS208 4.2 11.6 1.0 OD1 A:ASP124 4.2 15.0 1.0 CG2 A:THR190 4.5 10.8 1.0 CA A:HIS122 4.7 9.2 1.0 OD2 A:ASP124 4.8 14.7 1.0 C2 A:X8Z301 4.9 45.7 1.0 CG A:ASP124 5.0 13.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 Bound to L-Captopril


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Ndm-1 Bound to L-Captopril within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:14.2 occ:0.75 OD2 A:ASP124 1.9 14.7 1.0 SG A:CYS208 2.1 18.6 1.0 NE2 A:HIS250 2.2 20.8 1.0 S A:X8Z301 2.3 32.6 1.0 CG A:ASP124 2.9 13.2 1.0 CE1 A:HIS250 3.1 20.8 1.0 CD2 A:HIS250 3.2 21.6 1.0 OD1 A:ASP124 3.2 15.0 1.0 C1 A:X8Z301 3.3 42.7 1.0 CB A:CYS208 3.5 11.6 1.0 ZN A:ZN302 3.6 17.0 1.0 C2 A:X8Z301 4.0 45.7 1.0 CB A:SER249 4.1 17.6 1.0 ND1 A:HIS250 4.2 21.4 1.0 CB A:ASP124 4.2 11.2 1.0 CG A:HIS250 4.3 22.0 1.0 NE2 A:HIS120 4.3 11.3 1.0 CE1 A:HIS120 4.4 14.4 1.0 OG A:SER249 4.4 16.3 1.0 NE2 A:HIS189 4.5 10.4 1.0 C5 A:X8Z301 4.5 49.1 1.0 CE A:LYS125 4.6 12.2 1.0 C4 A:X8Z301 4.6 48.1 1.0 CA A:CYS208 4.7 11.5 1.0 CE1 A:HIS189 4.8 7.0 1.0 N A:X8Z301 4.8 49.2 1.0 CG A:LYS125 5.0 7.8 1.0

D.T.King, L.J.Worrall, R.Gruninger, N.C.Strynadka. New Delhi Metallo-Beta-Lactamase: Structural Insights Into Beta-Lactam Recognition and Inhibition J.Am.Chem.Soc. V. 134 11362 2012.
ISSN: ISSN 0002-7863
PubMed: 22713171
DOI: 10.1021/JA303579D