Zinc in PDB 5ypn: Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem Representing An EI2 Complex

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem Representing An EI2 Complex, PDB code: 5ypn was solved by H.Feng, W.Liu, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.98 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.730, 73.510, 76.530, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.4

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem Representing An EI2 Complex (pdb code 5ypn). 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 Representing An EI2 Complex, PDB code: 5ypn:
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 Representing An EI2 Complex


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 Representing An EI2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:27.4 occ:1.00 O72 A:LMP303 2.0 35.8 0.8 ND1 A:HIS122 2.0 41.4 1.0 NE2 A:HIS120 2.0 18.6 1.0 NE2 A:HIS189 2.1 37.9 1.0 CB A:HIS122 2.3 36.3 1.0 CG A:HIS122 2.4 37.9 1.0 C7 A:LMP303 2.6 37.6 0.8 O71 A:LMP303 2.6 41.2 0.8 CD2 A:HIS120 2.9 17.9 1.0 CE1 A:HIS120 3.0 19.6 1.0 CD2 A:HIS189 3.0 34.3 1.0 CE1 A:HIS189 3.1 39.8 1.0 CE1 A:HIS122 3.3 40.6 1.0 CD2 A:HIS122 3.7 37.5 1.0 CA A:HIS122 3.9 32.8 1.0 NE2 A:HIS122 4.1 38.4 1.0 CG A:HIS120 4.1 17.6 1.0 C6 A:LMP303 4.1 38.9 0.8 ND1 A:HIS120 4.1 18.6 1.0 ZN A:ZN302 4.1 29.7 1.0 OD2 A:ASP124 4.1 26.9 1.0 SG A:CYS208 4.2 23.6 1.0 ND1 A:HIS189 4.2 39.0 1.0 CG A:HIS189 4.2 33.7 1.0 O62 A:LMP303 4.3 42.2 0.8 N4 A:LMP303 4.4 40.2 0.8 CG2 A:THR190 4.4 22.4 1.0 C61 A:LMP303 4.4 40.9 0.8 CB A:CYS208 4.4 22.0 1.0 N A:HIS122 4.5 29.4 1.0 C A:HIS122 4.8 34.6 1.0 C5 A:LMP303 4.8 39.9 0.8

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem Representing An EI2 Complex


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 Representing An EI2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:29.7 occ:1.00 N4 A:LMP303 2.0 40.2 0.8 NE2 A:HIS250 2.1 32.0 1.0 SG A:CYS208 2.3 23.6 1.0 CE1 A:HIS250 2.3 32.6 1.0 OD2 A:ASP124 2.4 26.9 1.0 OD1 A:ASP124 2.4 34.4 1.0 O72 A:LMP303 2.6 35.8 0.8 CG A:ASP124 2.7 28.9 1.0 C5 A:LMP303 2.9 39.9 0.8 O32 A:LMP303 3.0 39.4 0.8 C3 A:LMP303 3.1 40.3 0.8 C7 A:LMP303 3.4 37.6 0.8 CD2 A:HIS250 3.4 31.6 1.0 C31 A:LMP303 3.5 39.4 0.8 CB A:CYS208 3.5 22.0 1.0 ND1 A:HIS250 3.6 32.7 1.0 C6 A:LMP303 3.7 38.9 0.8 O62 A:LMP303 3.9 42.2 0.8 C1 A:LMP303 3.9 40.5 0.8 ZN A:ZN301 4.1 27.4 1.0 CG A:HIS250 4.2 31.3 1.0 CB A:ASP124 4.2 27.2 1.0 C2 A:LMP303 4.2 41.7 0.8 CB A:SER249 4.3 20.2 1.0 O71 A:LMP303 4.4 41.2 0.8 C61 A:LMP303 4.5 40.9 0.8 OG A:SER249 4.6 19.4 1.0 NE2 A:HIS189 4.6 37.9 1.0 CE1 A:HIS120 4.6 19.6 1.0 CA A:CYS208 4.7 19.7 1.0 NE2 A:HIS120 4.7 18.6 1.0 O31 A:LMP303 4.8 39.1 0.8 CE1 A:HIS189 4.8 39.8 1.0 CE A:LYS125 4.9 23.1 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem Representing An EI2 Complex


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 Representing An EI2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.6 occ:1.00 ND1 B:HIS122 2.0 45.1 1.0 NE2 B:HIS120 2.0 24.6 1.0 NE2 B:HIS189 2.1 34.2 1.0 O72 B:LMP303 2.2 61.3 1.0 CB B:HIS122 2.3 34.6 1.0 CG B:HIS122 2.4 39.8 1.0 O71 B:LMP303 2.8 63.6 1.0 C7 B:LMP303 2.8 62.9 1.0 CD2 B:HIS120 2.9 24.4 1.0 CE1 B:HIS120 3.1 25.3 1.0 CD2 B:HIS189 3.1 33.7 1.0 CE1 B:HIS189 3.1 35.5 1.0 CE1 B:HIS122 3.2 42.7 1.0 CD2 B:HIS122 3.7 39.6 1.0 CA B:HIS122 3.9 30.7 1.0 NE2 B:HIS122 4.0 40.4 1.0 OD1 B:ASP124 4.1 34.7 1.0 CG B:HIS120 4.1 24.7 1.0 ND1 B:HIS120 4.1 24.6 1.0 ND1 B:HIS189 4.2 35.0 1.0 CG B:HIS189 4.2 33.6 1.0 C6 B:LMP303 4.3 64.4 1.0 SG B:CYS208 4.3 30.9 1.0 ZN B:ZN302 4.3 40.5 1.0 CG2 B:THR190 4.3 27.7 1.0 N B:HIS122 4.4 28.4 1.0 CB B:CYS208 4.5 29.6 1.0 N4 B:LMP303 4.6 66.6 1.0 C61 B:LMP303 4.6 64.2 1.0 C B:HIS122 4.8 30.8 1.0 CG B:ASP124 4.9 34.8 1.0 O62 B:LMP303 4.9 65.0 1.0 OD2 B:ASP124 4.9 37.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Meropenem Representing An EI2 Complex


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 Representing An EI2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:40.5 occ:1.00 N4 B:LMP303 2.0 66.6 1.0 NE2 B:HIS250 2.1 44.9 1.0 OD2 B:ASP124 2.1 37.6 1.0 SG B:CYS208 2.2 30.9 1.0 CE1 B:HIS250 2.6 45.5 1.0 O32 B:LMP303 2.7 67.3 1.0 O72 B:LMP303 2.9 61.3 1.0 C3 B:LMP303 3.0 67.4 1.0 CG B:ASP124 3.1 34.8 1.0 C5 B:LMP303 3.1 65.9 1.0 C31 B:LMP303 3.2 67.1 1.0 CD2 B:HIS250 3.3 47.5 1.0 CB B:CYS208 3.3 29.6 1.0 C7 B:LMP303 3.5 62.9 1.0 OD1 B:ASP124 3.6 34.7 1.0 ND1 B:HIS250 3.9 46.7 1.0 C6 B:LMP303 4.0 64.4 1.0 C1 B:LMP303 4.1 67.0 1.0 CB B:SER249 4.2 47.2 1.0 C2 B:LMP303 4.2 68.3 1.0 CG B:HIS250 4.2 48.1 1.0 ZN B:ZN301 4.3 30.6 1.0 O71 B:LMP303 4.3 63.6 1.0 CB B:ASP124 4.3 32.1 1.0 CA B:CYS208 4.4 29.7 1.0 O31 B:LMP303 4.5 66.7 1.0 OG B:SER249 4.5 46.7 1.0 O62 B:LMP303 4.5 65.0 1.0 NE2 B:HIS189 4.6 34.2 1.0 CE1 B:HIS189 4.7 35.5 1.0 CE1 B:HIS120 4.8 25.3 1.0 C61 B:LMP303 4.9 64.2 1.0 NE2 B:HIS120 5.0 24.6 1.0

H.Feng, X.Liu, S.Wang, J.Fleming, D.C.Wang, W.Liu. The Mechanism of Ndm-1-Catalyzed Carbapenem Hydrolysis Is Distinct From That of Penicillin or Cephalosporin Hydrolysis. Nat Commun V. 8 2242 2017.
ISSN: ESSN 2041-1723
PubMed: 29269938
DOI: 10.1038/S41467-017-02339-W