Zinc in PDB 5ypl: Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An Ep Complex

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

Resolution Low / High (Å)	42.28 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.220, 73.760, 77.430, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.4

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An Ep Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An Ep Complex (pdb code 5ypl). 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 Imipenem Representing An Ep Complex, PDB code: 5ypl:
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 Imipenem Representing An Ep 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 Imipenem Representing An Ep Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:22.0 occ:1.00 ND1 A:HIS122 2.0 20.9 1.0 NE2 A:HIS189 2.1 14.5 1.0 O72 A:HIW303 2.1 20.3 0.8 NE2 A:HIS120 2.1 18.3 1.0 C7 A:HIW303 2.7 30.7 0.8 O71 A:HIW303 2.8 31.7 0.8 CD2 A:HIS189 3.0 14.4 1.0 CE1 A:HIS122 3.0 23.9 1.0 CG A:HIS122 3.0 20.1 1.0 CE1 A:HIS120 3.0 19.6 1.0 CE1 A:HIS189 3.1 19.9 1.0 CD2 A:HIS120 3.1 16.8 1.0 CB A:HIS122 3.3 17.7 1.0 ZN A:ZN302 3.9 30.1 1.0 SG A:CYS208 3.9 22.0 1.0 NE2 A:HIS122 4.1 23.8 1.0 OD1 A:ASP124 4.1 21.5 1.0 ND1 A:HIS120 4.1 19.1 1.0 CB A:CYS208 4.1 17.0 1.0 CD2 A:HIS122 4.1 20.9 1.0 C6 A:HIW303 4.2 37.4 0.8 CG A:HIS189 4.2 17.4 1.0 ND1 A:HIS189 4.2 17.5 1.0 CG A:HIS120 4.2 17.4 1.0 O62 A:HIW303 4.5 39.4 0.8 N4 A:HIW303 4.5 46.8 0.8 CG2 A:THR190 4.5 20.9 1.0 C61 A:HIW303 4.7 37.8 0.8 OD2 A:ASP124 4.8 25.2 1.0 CA A:HIS122 4.8 18.7 1.0 C5 A:HIW303 4.8 42.8 0.8 CG A:ASP124 4.9 21.4 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An Ep 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 Imipenem Representing An Ep Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:30.1 occ:1.00 OD2 A:ASP124 2.0 25.2 1.0 NE2 A:HIS250 2.1 22.1 1.0 SG A:CYS208 2.3 22.0 1.0 N4 A:HIW303 2.4 46.8 0.8 O72 A:HIW303 2.5 20.3 0.8 CE1 A:HIS250 2.9 24.2 1.0 C5 A:HIW303 3.0 42.8 0.8 CG A:ASP124 3.1 21.4 1.0 CD2 A:HIS250 3.2 21.5 1.0 C7 A:HIW303 3.4 30.7 0.8 CB A:CYS208 3.4 17.0 1.0 O31 A:HIW303 3.4 50.4 0.8 OD1 A:ASP124 3.5 21.5 1.0 C3 A:HIW303 3.5 49.2 0.8 C6 A:HIW303 3.8 37.4 0.8 ZN A:ZN301 3.9 22.0 1.0 C31 A:HIW303 4.0 51.3 0.8 ND1 A:HIS250 4.1 23.9 1.0 CB A:SER249 4.1 23.0 1.0 O62 A:HIW303 4.2 39.4 0.8 CG A:HIS250 4.2 23.3 1.0 C1 A:HIW303 4.2 45.0 0.8 CB A:ASP124 4.3 20.5 1.0 O71 A:HIW303 4.4 31.7 0.8 OG A:SER249 4.4 24.1 1.0 NE2 A:HIS189 4.6 14.5 1.0 C2 A:HIW303 4.6 47.4 0.8 CA A:CYS208 4.6 16.9 1.0 C61 A:HIW303 4.7 37.8 0.8 CE1 A:HIS120 4.7 19.6 1.0 CE1 A:HIS189 4.8 19.9 1.0 NE2 A:HIS120 4.8 18.3 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 Imipenem Representing An Ep 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 Imipenem Representing An Ep Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:25.3 occ:1.00 ND1 B:HIS122 1.9 24.2 1.0 NE2 B:HIS189 2.0 22.6 1.0 O71 B:HIW303 2.1 18.4 0.7 NE2 B:HIS120 2.1 22.9 1.0 C7 B:HIW303 2.7 26.0 0.7 O72 B:HIW303 2.8 27.9 0.7 CD2 B:HIS189 2.9 20.7 1.0 CE1 B:HIS122 2.9 26.9 1.0 CG B:HIS122 3.0 23.1 1.0 CD2 B:HIS120 3.0 18.6 1.0 CE1 B:HIS189 3.1 24.4 1.0 CE1 B:HIS120 3.2 23.3 1.0 CB B:HIS122 3.3 22.6 1.0 ZN B:ZN302 3.9 35.1 1.0 SG B:CYS208 3.9 29.2 1.0 NE2 B:HIS122 4.0 29.8 1.0 CD2 B:HIS122 4.1 25.4 1.0 CB B:CYS208 4.1 23.8 1.0 CG B:HIS189 4.1 23.3 1.0 CG B:HIS120 4.1 19.7 1.0 ND1 B:HIS189 4.2 25.6 1.0 ND1 B:HIS120 4.2 22.2 1.0 OD1 B:ASP124 4.2 25.2 1.0 C6 B:HIW303 4.2 41.4 0.7 N4 B:HIW303 4.4 40.6 0.7 CG2 B:THR190 4.5 22.5 1.0 OD2 B:ASP124 4.8 34.1 1.0 O62 B:HIW303 4.8 47.7 0.7 CA B:HIS122 4.8 22.0 1.0 C5 B:HIW303 4.8 39.6 0.7 C62 B:HIW303 4.8 43.4 0.7 C61 B:HIW303 4.9 44.2 0.7 CG B:ASP124 4.9 29.0 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An Ep 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 Imipenem Representing An Ep Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:35.1 occ:1.00 OD2 B:ASP124 2.1 34.1 1.0 NE2 B:HIS250 2.1 33.1 1.0 N4 B:HIW303 2.2 40.6 0.7 SG B:CYS208 2.3 29.2 1.0 O71 B:HIW303 2.5 18.4 0.7 CE1 B:HIS250 2.9 31.2 1.0 C5 B:HIW303 3.0 39.6 0.7 CG B:ASP124 3.1 29.0 1.0 O31 B:HIW303 3.2 44.9 0.7 CD2 B:HIS250 3.2 32.9 1.0 C3 B:HIW303 3.3 42.2 0.7 C7 B:HIW303 3.4 26.0 0.7 CB B:CYS208 3.4 23.8 1.0 OD1 B:ASP124 3.6 25.2 1.0 C31 B:HIW303 3.7 44.9 0.7 C6 B:HIW303 3.8 41.4 0.7 ZN B:ZN301 3.9 25.3 1.0 ND1 B:HIS250 4.1 31.0 1.0 C1 B:HIW303 4.1 40.7 0.7 CB B:SER249 4.2 26.3 1.0 CG B:HIS250 4.3 34.1 1.0 O72 B:HIW303 4.3 27.9 0.7 CB B:ASP124 4.4 25.8 1.0 C2 B:HIW303 4.4 41.3 0.7 OG B:SER249 4.5 29.4 1.0 C62 B:HIW303 4.5 43.4 0.7 NE2 B:HIS189 4.5 22.6 1.0 CA B:CYS208 4.5 22.5 1.0 NE2 B:HIS120 4.6 22.9 1.0 CE1 B:HIS120 4.7 23.3 1.0 C61 B:HIW303 4.8 44.2 0.7 CE1 B:HIS189 4.8 24.4 1.0 O32 B:HIW303 4.9 47.0 0.7

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