Zinc in PDB 4exy: Crystal Structure of Ndm-1 Bound to Ethylene Glycol

All present enzymatic activity of Crystal Structure of Ndm-1 Bound to Ethylene Glycol:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Bound to Ethylene Glycol, PDB code: 4exy 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)	35.74 / 1.47
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	107.220, 107.220, 92.850, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 18.2

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to Ethylene Glycol (pdb code 4exy). 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 Ethylene Glycol, PDB code: 4exy:
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 Ethylene Glycol


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 Ethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:14.9 occ:0.85 OD2 A:ASP124 2.0 15.2 1.0 NE2 A:HIS250 2.1 13.8 1.0 O2 A:EDO301 2.3 6.4 1.0 SG A:CYS208 2.3 15.5 1.0 CG A:ASP124 3.0 13.2 1.0 CD2 A:HIS250 3.0 15.4 1.0 CE1 A:HIS250 3.1 16.3 1.0 C2 A:EDO301 3.1 19.8 1.0 OD1 A:ASP124 3.3 15.3 1.0 CB A:CYS208 3.4 13.5 1.0 ZN A:ZN303 3.7 12.6 0.9 C1 A:EDO301 3.7 22.1 1.0 ND1 A:HIS250 4.1 15.1 1.0 CG A:HIS250 4.2 14.2 1.0 CB A:SER249 4.3 14.0 1.0 CB A:ASP124 4.3 11.2 1.0 CE1 A:HIS120 4.3 16.6 1.0 O A:HOH475 4.4 25.1 1.0 NE2 A:HIS120 4.4 12.6 1.0 O1 A:EDO301 4.4 26.2 1.0 NE2 A:HIS189 4.5 11.6 1.0 CA A:CYS208 4.6 12.6 1.0 OG A:SER249 4.6 16.4 1.0 CE1 A:HIS189 4.7 14.5 1.0 CE A:LYS125 4.8 15.9 1.0

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


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 Ethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:12.6 occ:0.90 NE2 A:HIS120 2.0 12.6 1.0 NE2 A:HIS189 2.0 11.6 1.0 ND1 A:HIS122 2.0 11.4 1.0 O2 A:EDO301 2.3 6.4 1.0 CE1 A:HIS120 3.0 16.6 1.0 CD2 A:HIS120 3.0 11.3 1.0 CE1 A:HIS122 3.0 14.0 1.0 CE1 A:HIS189 3.0 14.5 1.0 CG A:HIS122 3.0 13.5 1.0 CD2 A:HIS189 3.0 11.9 1.0 C2 A:EDO301 3.0 19.8 1.0 CB A:HIS122 3.4 10.7 1.0 ZN A:ZN302 3.7 14.9 0.8 SG A:CYS208 4.1 15.5 1.0 ND1 A:HIS120 4.1 14.3 1.0 OD1 A:ASP124 4.1 15.3 1.0 CG A:HIS120 4.1 11.1 1.0 NE2 A:HIS122 4.1 15.2 1.0 CB A:CYS208 4.1 13.5 1.0 ND1 A:HIS189 4.1 14.1 1.0 CD2 A:HIS122 4.1 16.4 1.0 CG A:HIS189 4.2 11.8 1.0 CG2 A:THR190 4.5 12.3 1.0 C1 A:EDO301 4.6 22.1 1.0 OD2 A:ASP124 4.8 15.2 1.0 OD1 A:ASN220 4.9 45.2 1.0 CA A:HIS122 4.9 10.3 1.0 CG A:ASP124 4.9 13.2 1.0

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


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 Ethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:12.3 occ:0.80 OD2 B:ASP124 2.0 14.5 1.0 NE2 B:HIS250 2.1 12.1 1.0 SG B:CYS208 2.3 14.1 1.0 O1 B:EDO301 2.3 4.7 1.0 CE1 B:HIS250 3.0 12.3 1.0 CG B:ASP124 3.0 11.3 1.0 CD2 B:HIS250 3.1 13.7 1.0 C1 B:EDO301 3.2 16.8 1.0 OD1 B:ASP124 3.3 13.8 1.0 CB B:CYS208 3.4 13.2 1.0 ZN B:ZN303 3.6 11.2 0.9 C2 B:EDO301 3.7 19.5 1.0 ND1 B:HIS250 4.1 13.0 1.0 CG B:HIS250 4.2 11.1 1.0 CB B:SER249 4.2 12.2 1.0 CE1 B:HIS120 4.3 13.0 1.0 CB B:ASP124 4.3 12.9 1.0 O B:HOH542 4.4 26.5 1.0 NE2 B:HIS120 4.4 11.7 1.0 O2 B:EDO301 4.4 26.2 1.0 NE2 B:HIS189 4.5 11.7 1.0 OG B:SER249 4.6 15.2 1.0 CA B:CYS208 4.6 12.1 1.0 CE1 B:HIS189 4.7 13.8 1.0 CE B:LYS125 4.8 15.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 Bound to Ethylene Glycol


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 Ethylene Glycol within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:11.2 occ:0.90 NE2 B:HIS120 2.0 11.7 1.0 NE2 B:HIS189 2.0 11.7 1.0 ND1 B:HIS122 2.1 10.1 1.0 O1 B:EDO301 2.3 4.7 1.0 CE1 B:HIS120 2.9 13.0 1.0 CD2 B:HIS120 3.0 11.1 1.0 CD2 B:HIS189 3.0 8.7 1.0 CE1 B:HIS189 3.0 13.8 1.0 CE1 B:HIS122 3.0 12.0 1.0 C1 B:EDO301 3.1 16.8 1.0 CG B:HIS122 3.1 9.2 1.0 CB B:HIS122 3.4 9.9 1.0 ZN B:ZN302 3.6 12.3 0.8 SG B:CYS208 4.0 14.1 1.0 ND1 B:HIS120 4.0 13.8 1.0 OD1 B:ASP124 4.1 13.8 1.0 CG B:HIS120 4.1 10.1 1.0 CB B:CYS208 4.1 13.2 1.0 ND1 B:HIS189 4.1 13.1 1.0 NE2 B:HIS122 4.2 14.6 1.0 CG B:HIS189 4.2 9.3 1.0 CD2 B:HIS122 4.2 13.4 1.0 CG2 B:THR190 4.5 14.4 1.0 C2 B:EDO301 4.6 19.5 1.0 OD1 B:ASN220 4.7 44.3 1.0 OD2 B:ASP124 4.8 14.5 1.0 CA B:HIS122 4.8 9.3 1.0 CG B:ASP124 4.9 11.3 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