Zinc in PDB 4eyl: Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem

All present enzymatic activity of Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem, PDB code: 4eyl 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)	42.19 / 1.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.000, 106.000, 92.580, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.4

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


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 Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:19.8 occ:0.70 NE2 A:HIS250 2.1 22.9 1.0 NAN A:0RV301 2.2 20.0 1.0 OD2 A:ASP124 2.3 23.0 1.0 SG A:CYS208 2.3 22.7 1.0 OAI A:0RV301 2.5 20.0 1.0 CE1 A:HIS250 2.9 24.5 1.0 OAE A:0RV301 3.0 20.0 1.0 CAS A:0RV301 3.1 20.0 1.0 CD2 A:HIS250 3.2 27.0 1.0 CAZ A:0RV301 3.3 20.0 1.0 CG A:ASP124 3.3 19.7 1.0 H19 A:0RV301 3.3 20.0 1.0 CB A:CYS208 3.4 15.6 1.0 H26 A:0RV301 3.4 20.0 1.0 CAP A:0RV301 3.5 20.0 1.0 CAQ A:0RV301 3.5 20.0 1.0 OD1 A:ASP124 3.5 27.3 1.0 ZN A:ZN303 4.0 18.2 1.0 CBA A:0RV301 4.1 20.0 1.0 ND1 A:HIS250 4.1 25.7 1.0 CB A:SER249 4.2 21.1 1.0 H25 A:0RV301 4.2 20.0 1.0 CG A:HIS250 4.2 24.3 1.0 CAT A:0RV301 4.3 20.0 1.0 CAA A:0RV301 4.3 20.0 1.0 CAV A:0RV301 4.3 20.0 1.0 OAF A:0RV301 4.5 20.0 1.0 OG A:SER249 4.6 19.1 1.0 CA A:CYS208 4.6 15.6 1.0 NE2 A:HIS189 4.6 22.0 1.0 CB A:ASP124 4.6 16.1 1.0 OAH A:0RV301 4.7 20.0 1.0 CE1 A:HIS189 4.8 16.5 1.0 CAU A:0RV301 4.8 20.0 1.0 CE1 A:HIS120 4.9 15.6 1.0 H13 A:0RV301 4.9 20.0 1.0 NE2 A:HIS120 4.9 15.0 1.0 H20 A:0RV301 4.9 20.0 1.0

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


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 Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:18.2 occ:1.00 NE2 A:HIS189 2.1 22.0 1.0 ND1 A:HIS122 2.1 11.7 1.0 NE2 A:HIS120 2.2 15.0 1.0 OAI A:0RV301 2.3 20.0 1.0 OAF A:0RV301 2.7 20.0 1.0 CAQ A:0RV301 2.8 20.0 1.0 CD2 A:HIS189 3.0 16.9 1.0 H25 A:0RV301 3.0 20.0 1.0 CG A:HIS122 3.1 13.5 1.0 CD2 A:HIS120 3.1 12.2 1.0 CE1 A:HIS122 3.1 20.1 1.0 CE1 A:HIS189 3.1 16.5 1.0 CE1 A:HIS120 3.1 15.6 1.0 CB A:HIS122 3.3 9.2 1.0 CAA A:0RV301 4.0 20.0 1.0 ZN A:ZN302 4.0 19.8 0.7 SG A:CYS208 4.1 22.7 1.0 H26 A:0RV301 4.1 20.0 1.0 CG A:HIS189 4.2 16.9 1.0 NE2 A:HIS122 4.2 17.8 1.0 ND1 A:HIS189 4.2 13.3 1.0 CD2 A:HIS122 4.2 14.2 1.0 ND1 A:HIS120 4.2 15.7 1.0 CG A:HIS120 4.2 14.3 1.0 CB A:CYS208 4.2 15.6 1.0 CBA A:0RV301 4.2 20.0 1.0 OD1 A:ASP124 4.3 27.3 1.0 CG2 A:THR190 4.4 15.0 1.0 NAN A:0RV301 4.4 20.0 1.0 CAU A:0RV301 4.6 20.0 1.0 OAE A:0RV301 4.7 20.0 1.0 H24 A:0RV301 4.8 20.0 1.0 CA A:HIS122 4.8 11.5 1.0 H20 A:0RV301 4.8 20.0 1.0 CAZ A:0RV301 4.9 20.0 1.0 OAJ A:0RV301 5.0 20.0 1.0

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


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 Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:21.6 occ:0.60 NE2 B:HIS250 2.0 28.1 1.0 OD2 B:ASP124 2.1 22.6 1.0 NAN B:0RV301 2.3 20.0 1.0 SG B:CYS208 2.3 23.3 1.0 OAF B:0RV301 2.7 20.0 1.0 OAH B:0RV301 2.9 20.0 1.0 CE1 B:HIS250 3.0 21.6 1.0 CD2 B:HIS250 3.0 27.7 1.0 CG B:ASP124 3.2 18.9 1.0 CAS B:0RV301 3.2 20.0 1.0 CAP B:0RV301 3.4 20.0 1.0 CB B:CYS208 3.4 15.2 1.0 H19 B:0RV301 3.4 20.0 1.0 CAZ B:0RV301 3.4 20.0 1.0 OD1 B:ASP124 3.5 21.7 1.0 CAQ B:0RV301 3.7 20.0 1.0 ZN B:ZN303 3.9 17.1 0.9 CB B:SER249 4.1 19.5 1.0 ND1 B:HIS250 4.1 28.3 1.0 CG B:HIS250 4.1 25.4 1.0 CBA B:0RV301 4.3 20.0 1.0 CAT B:0RV301 4.3 20.0 1.0 CAV B:0RV301 4.4 20.0 1.0 H13 B:0RV301 4.4 20.0 1.0 H25 B:0RV301 4.4 20.0 1.0 OG B:SER249 4.4 15.3 1.0 H26 B:0RV301 4.5 20.0 1.0 CB B:ASP124 4.5 13.6 1.0 OAI B:0RV301 4.5 20.0 1.0 NE2 B:HIS189 4.6 13.6 1.0 OAE B:0RV301 4.6 20.0 1.0 CA B:CYS208 4.7 13.2 1.0 CE1 B:HIS120 4.7 14.6 1.0 NE2 B:HIS120 4.7 13.6 1.0 CE1 B:HIS189 4.8 13.8 1.0 CAA B:0RV301 4.8 20.0 1.0 CE B:LYS125 5.0 27.9 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem


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 Hydrolyzed Meropenem within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:17.1 occ:0.90 ND1 B:HIS122 2.1 17.6 1.0 NE2 B:HIS120 2.1 13.6 1.0 NE2 B:HIS189 2.1 13.6 1.0 OAF B:0RV301 2.2 20.0 1.0 CAQ B:0RV301 2.8 20.0 1.0 OAI B:0RV301 2.8 20.0 1.0 CD2 B:HIS189 3.0 10.4 1.0 CG B:HIS122 3.0 15.4 1.0 CE1 B:HIS122 3.0 14.9 1.0 CD2 B:HIS120 3.1 11.6 1.0 CE1 B:HIS120 3.1 14.6 1.0 CE1 B:HIS189 3.2 13.8 1.0 CB B:HIS122 3.3 11.9 1.0 H25 B:0RV301 3.4 20.0 1.0 ZN B:ZN302 3.9 21.6 0.6 SG B:CYS208 4.0 23.3 1.0 NE2 B:HIS122 4.1 16.5 1.0 CD2 B:HIS122 4.1 19.4 1.0 ND1 B:HIS120 4.2 12.0 1.0 CG B:HIS189 4.2 14.3 1.0 CG B:HIS120 4.2 11.0 1.0 OD1 B:ASP124 4.2 21.7 1.0 CBA B:0RV301 4.2 20.0 1.0 NAN B:0RV301 4.3 20.0 1.0 ND1 B:HIS189 4.3 10.9 1.0 CB B:CYS208 4.3 15.2 1.0 CAA B:0RV301 4.4 20.0 1.0 OAH B:0RV301 4.5 20.0 1.0 CG2 B:THR190 4.5 16.7 1.0 CA B:HIS122 4.8 10.5 1.0 CAU B:0RV301 4.8 20.0 1.0 H23 B:0RV301 4.8 20.0 1.0 CAZ B:0RV301 4.8 20.0 1.0 H20 B:0RV301 4.8 20.0 1.0 H26 B:0RV301 4.9 20.0 1.0 OD2 B:ASP124 4.9 22.6 1.0 CAS B:0RV301 5.0 20.0 1.0 CG B:ASP124 5.0 18.9 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