Zinc in PDB 5ypi: Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex, PDB code: 5ypi 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)	42.42 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.380, 74.100, 154.520, 90.00, 90.26, 90.00
R / Rfree (%)	17.8 / 23.7

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex (pdb code 5ypi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex, PDB code: 5ypi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 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 EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:24.5 occ:1.00 O72 A:8YF303 2.0 32.2 0.9 ND1 A:HIS122 2.0 24.0 1.0 NE2 A:HIS120 2.0 22.9 1.0 NE2 A:HIS189 2.1 21.6 1.0 C7 A:8YF303 2.7 33.2 0.9 O71 A:8YF303 2.8 33.5 0.9 CE1 A:HIS120 2.9 22.9 1.0 CG A:HIS122 3.0 27.3 1.0 CD2 A:HIS189 3.0 21.2 1.0 CE1 A:HIS122 3.1 25.7 1.0 CD2 A:HIS120 3.1 22.9 1.0 CE1 A:HIS189 3.1 21.1 1.0 CB A:HIS122 3.2 26.3 1.0 SG A:CYS208 3.9 29.1 1.0 ND1 A:HIS120 4.0 22.9 1.0 CD2 A:HIS122 4.1 28.0 1.0 NE2 A:HIS122 4.2 23.9 1.0 N4 A:8YF303 4.2 35.1 0.9 CG A:HIS120 4.2 22.9 1.0 CG A:HIS189 4.2 24.8 1.0 C6 A:8YF303 4.2 34.1 0.9 CB A:CYS208 4.2 19.0 1.0 ZN A:ZN302 4.2 34.9 1.0 ND1 A:HIS189 4.2 22.7 1.0 OD1 A:ASP124 4.2 41.9 1.0 O62 A:8YF303 4.5 35.4 0.9 CG2 A:THR190 4.6 29.0 1.0 CA A:HIS122 4.7 26.9 1.0 C61 A:8YF303 4.7 32.4 0.9 C5 A:8YF303 4.7 35.6 0.9 OD2 A:ASP124 4.8 38.1 1.0 O32 A:8YF303 4.8 30.4 0.9 CG A:ASP124 4.9 37.8 1.0

Zinc binding site 2 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 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 EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:34.9 occ:1.00 N4 A:8YF303 1.9 35.1 0.9 NE2 A:HIS250 2.0 30.6 1.0 SG A:CYS208 2.2 29.1 1.0 OD2 A:ASP124 2.3 38.1 1.0 O32 A:8YF303 2.4 30.4 0.9 C3 A:8YF303 2.6 32.2 0.9 C31 A:8YF303 2.9 28.9 0.9 CE1 A:HIS250 2.9 26.8 1.0 C5 A:8YF303 3.1 35.6 0.9 CD2 A:HIS250 3.1 29.8 1.0 O72 A:8YF303 3.3 32.2 0.9 CB A:CYS208 3.4 19.0 1.0 CG A:ASP124 3.4 37.8 1.0 C7 A:8YF303 3.7 33.2 0.9 C2 A:8YF303 3.7 34.0 0.9 OD1 A:ASP124 3.9 41.9 1.0 C1 A:8YF303 3.9 35.5 0.9 ND1 A:HIS250 4.1 24.0 1.0 C6 A:8YF303 4.1 34.1 0.9 CB A:SER249 4.1 22.8 1.0 O31 A:8YF303 4.1 25.2 0.9 ZN A:ZN301 4.2 24.5 1.0 CG A:HIS250 4.2 23.8 1.0 O71 A:8YF303 4.3 33.5 0.9 CA A:CYS208 4.4 23.9 1.0 OG A:SER249 4.4 24.0 1.0 CB A:ASP124 4.6 31.0 1.0 NE2 A:HIS189 4.6 21.6 1.0 O62 A:8YF303 4.7 35.4 0.9 CE1 A:HIS189 4.8 21.1 1.0 CE1 A:HIS120 5.0 22.9 1.0

Zinc binding site 3 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 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 EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:25.9 occ:1.00 O72 B:8YF303 1.9 34.1 1.0 ND1 B:HIS122 2.0 25.7 1.0 NE2 B:HIS120 2.0 24.5 1.0 NE2 B:HIS189 2.1 27.4 1.0 C7 B:8YF303 2.6 32.5 1.0 O71 B:8YF303 2.8 27.6 1.0 CE1 B:HIS120 2.9 24.2 1.0 CD2 B:HIS189 2.9 23.8 1.0 CG B:HIS122 3.0 27.0 1.0 CE1 B:HIS122 3.0 30.7 1.0 CD2 B:HIS120 3.1 23.7 1.0 CE1 B:HIS189 3.2 27.2 1.0 CB B:HIS122 3.3 26.3 1.0 SG B:CYS208 4.0 37.5 1.0 ND1 B:HIS120 4.0 30.0 1.0 ZN B:ZN302 4.0 42.5 1.0 C6 B:8YF303 4.1 38.2 1.0 NE2 B:HIS122 4.1 30.2 1.0 CD2 B:HIS122 4.1 29.1 1.0 CG B:HIS120 4.1 27.5 1.0 CB B:CYS208 4.1 24.2 1.0 CG B:HIS189 4.1 26.4 1.0 N4 B:8YF303 4.2 40.1 1.0 ND1 B:HIS189 4.3 27.2 1.0 OD1 B:ASP124 4.3 41.5 1.0 C62 B:8YF303 4.4 43.6 1.0 CG2 B:THR190 4.4 24.4 1.0 C61 B:8YF303 4.6 43.0 1.0 C5 B:8YF303 4.7 40.1 1.0 CA B:HIS122 4.8 28.9 1.0 OD2 B:ASP124 4.9 43.9 1.0

Zinc binding site 4 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 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 EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:42.5 occ:1.00 N4 B:8YF303 2.0 40.1 1.0 NE2 B:HIS250 2.2 33.7 1.0 SG B:CYS208 2.3 37.5 1.0 OD2 B:ASP124 2.5 43.9 1.0 C5 B:8YF303 2.9 40.1 1.0 C3 B:8YF303 3.0 42.3 1.0 CE1 B:HIS250 3.0 33.1 1.0 O32 B:8YF303 3.0 49.0 1.0 O72 B:8YF303 3.1 34.1 1.0 CD2 B:HIS250 3.3 33.4 1.0 CB B:CYS208 3.3 24.2 1.0 C31 B:8YF303 3.4 47.0 1.0 C7 B:8YF303 3.5 32.5 1.0 CG B:ASP124 3.6 42.1 1.0 C6 B:8YF303 3.9 38.2 1.0 C1 B:8YF303 3.9 41.8 1.0 C2 B:8YF303 3.9 42.7 1.0 OD1 B:ASP124 4.0 41.5 1.0 ZN B:ZN301 4.0 25.9 1.0 ND1 B:HIS250 4.2 35.6 1.0 O71 B:8YF303 4.3 27.6 1.0 CB B:SER249 4.3 27.2 1.0 CG B:HIS250 4.3 33.7 1.0 CA B:CYS208 4.4 25.0 1.0 NE2 B:HIS189 4.5 27.4 1.0 OG B:SER249 4.6 28.4 1.0 O31 B:8YF303 4.6 50.5 1.0 CE1 B:HIS189 4.7 27.2 1.0 C61 B:8YF303 4.7 43.0 1.0 CE1 B:HIS120 4.8 24.2 1.0 CB B:ASP124 4.8 38.1 1.0

Zinc binding site 5 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:27.9 occ:1.00 O72 C:8YF303 1.9 31.2 0.9 ND1 C:HIS122 2.0 27.4 1.0 NE2 C:HIS189 2.1 27.4 1.0 NE2 C:HIS120 2.2 26.3 1.0 C7 C:8YF303 2.6 38.0 0.9 O71 C:8YF303 2.8 42.9 0.9 CG C:HIS122 2.9 26.0 1.0 CD2 C:HIS189 3.0 29.9 1.0 CE1 C:HIS120 3.1 29.3 1.0 CE1 C:HIS122 3.1 28.5 1.0 CD2 C:HIS120 3.1 26.0 1.0 CB C:HIS122 3.2 25.3 1.0 CE1 C:HIS189 3.2 27.3 1.0 C6 C:8YF303 4.1 37.9 0.9 CD2 C:HIS122 4.1 24.8 1.0 OD1 C:ASP124 4.1 33.3 1.0 N4 C:8YF303 4.2 37.7 0.9 NE2 C:HIS122 4.2 25.5 1.0 CG C:HIS189 4.2 29.2 1.0 ZN C:ZN302 4.2 36.2 1.0 ND1 C:HIS120 4.2 30.0 1.0 SG C:CYS208 4.2 37.2 1.0 CG C:HIS120 4.3 25.0 1.0 ND1 C:HIS189 4.3 27.4 1.0 O62 C:8YF303 4.3 36.7 0.9 CB C:CYS208 4.4 25.1 1.0 CG2 C:THR190 4.6 30.1 1.0 C5 C:8YF303 4.6 38.4 0.9 CA C:HIS122 4.7 26.4 1.0 C61 C:8YF303 4.7 38.2 0.9 OD2 C:ASP124 4.8 30.6 1.0 CG C:ASP124 4.9 29.0 1.0

Zinc binding site 6 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:36.2 occ:1.00 N4 C:8YF303 1.9 37.7 0.9 NE2 C:HIS250 2.0 35.1 1.0 OD2 C:ASP124 2.2 30.6 1.0 SG C:CYS208 2.4 37.2 1.0 CE1 C:HIS250 2.8 34.0 1.0 C3 C:8YF303 2.8 39.6 0.9 O32 C:8YF303 2.9 42.3 0.9 C5 C:8YF303 2.9 38.4 0.9 O72 C:8YF303 3.1 31.2 0.9 CD2 C:HIS250 3.1 30.3 1.0 C31 C:8YF303 3.3 42.3 0.9 CG C:ASP124 3.3 29.0 1.0 CB C:CYS208 3.4 25.1 1.0 C7 C:8YF303 3.7 38.0 0.9 C2 C:8YF303 3.7 39.6 0.9 C1 C:8YF303 3.8 40.0 0.9 OD1 C:ASP124 3.8 33.3 1.0 C6 C:8YF303 3.9 37.9 0.9 ND1 C:HIS250 4.0 36.2 1.0 CB C:SER249 4.2 33.2 1.0 CG C:HIS250 4.2 38.2 1.0 ZN C:ZN301 4.2 27.9 1.0 CA C:CYS208 4.5 25.2 1.0 O31 C:8YF303 4.5 43.0 0.9 OG C:SER249 4.5 32.4 1.0 CB C:ASP124 4.5 22.4 1.0 NE2 C:HIS189 4.5 27.4 1.0 O62 C:8YF303 4.6 36.7 0.9 O71 C:8YF303 4.7 42.9 0.9 CE1 C:HIS189 4.8 27.3 1.0 CE1 C:HIS120 4.9 29.3 1.0 C61 C:8YF303 4.9 38.2 0.9

Zinc binding site 7 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn301 b:26.9 occ:1.00 ND1 D:HIS122 2.0 33.8 1.0 O71 D:8YF303 2.0 25.6 0.9 NE2 D:HIS189 2.2 27.9 1.0 NE2 D:HIS120 2.3 30.2 1.0 C7 D:8YF303 2.8 32.0 0.9 CG D:HIS122 2.9 34.1 1.0 CE1 D:HIS122 3.0 30.7 1.0 O72 D:8YF303 3.0 39.9 0.9 CD2 D:HIS189 3.1 28.9 1.0 CD2 D:HIS120 3.2 26.7 1.0 CE1 D:HIS189 3.2 29.3 1.0 CB D:HIS122 3.2 34.4 1.0 CE1 D:HIS120 3.3 31.7 1.0 CD2 D:HIS122 4.1 30.6 1.0 NE2 D:HIS122 4.1 28.1 1.0 SG D:CYS208 4.1 31.0 1.0 OD1 D:ASP124 4.2 42.8 1.0 C6 D:8YF303 4.2 32.5 0.9 ZN D:ZN302 4.3 37.9 1.0 N4 D:8YF303 4.3 32.2 0.9 CG D:HIS189 4.3 30.8 1.0 ND1 D:HIS189 4.3 30.0 1.0 CB D:CYS208 4.3 22.5 1.0 CG D:HIS120 4.3 26.6 1.0 ND1 D:HIS120 4.3 29.3 1.0 O62 D:8YF303 4.4 34.3 0.9 CG2 D:THR190 4.4 27.4 1.0 C61 D:8YF303 4.7 33.8 0.9 CA D:HIS122 4.7 31.8 1.0 OD2 D:ASP124 4.8 37.5 1.0 C5 D:8YF303 4.8 32.6 0.9 CG D:ASP124 4.9 39.3 1.0 O31 D:8YF303 5.0 39.6 0.9

Zinc binding site 8 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:37.9 occ:1.00 N4 D:8YF303 2.0 32.2 0.9 NE2 D:HIS250 2.0 31.2 1.0 OD2 D:ASP124 2.2 37.5 1.0 SG D:CYS208 2.3 31.0 1.0 O31 D:8YF303 2.4 39.6 0.9 C3 D:8YF303 2.7 35.2 0.9 CE1 D:HIS250 2.9 32.0 1.0 C31 D:8YF303 3.0 38.4 0.9 CD2 D:HIS250 3.1 27.1 1.0 C5 D:8YF303 3.2 32.6 0.9 O71 D:8YF303 3.3 25.6 0.9 CB D:CYS208 3.3 22.5 1.0 CG D:ASP124 3.4 39.3 1.0 C7 D:8YF303 3.8 32.0 0.9 C2 D:8YF303 3.8 35.4 0.9 OD1 D:ASP124 3.9 42.8 1.0 C1 D:8YF303 4.0 34.1 0.9 ND1 D:HIS250 4.0 29.4 1.0 CB D:SER249 4.1 31.5 1.0 C6 D:8YF303 4.1 32.5 0.9 CG D:HIS250 4.2 28.1 1.0 O32 D:8YF303 4.2 39.3 0.9 ZN D:ZN301 4.3 26.9 1.0 CA D:CYS208 4.4 26.6 1.0 OG D:SER249 4.5 33.3 1.0 O62 D:8YF303 4.5 34.3 0.9 NE2 D:HIS189 4.5 27.9 1.0 CB D:ASP124 4.6 35.2 1.0 O72 D:8YF303 4.6 39.9 0.9 CE1 D:HIS189 4.8 29.3 1.0 CE D:LYS125 5.0 42.2 1.0 C61 D:8YF303 5.0 33.8 0.9

Zinc binding site 9 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn301 b:37.9 occ:1.00 ND1 E:HIS122 2.0 30.8 1.0 NE2 E:HIS189 2.1 35.8 1.0 NE2 E:HIS120 2.1 27.8 1.0 O71 E:8YF303 2.1 49.9 1.0 C7 E:8YF303 2.9 48.0 1.0 CE1 E:HIS120 2.9 23.3 1.0 CG E:HIS122 2.9 32.2 1.0 CE1 E:HIS122 3.0 30.6 1.0 CD2 E:HIS189 3.0 32.8 1.0 CE1 E:HIS189 3.0 35.5 1.0 O72 E:8YF303 3.0 44.9 1.0 CD2 E:HIS120 3.1 23.3 1.0 CB E:HIS122 3.2 31.1 1.0 ND1 E:HIS120 4.0 29.6 1.0 ZN E:ZN302 4.1 52.3 1.0 CD2 E:HIS122 4.1 32.1 1.0 NE2 E:HIS122 4.1 30.0 1.0 SG E:CYS208 4.1 50.9 1.0 ND1 E:HIS189 4.1 34.9 1.0 CG E:HIS120 4.2 30.4 1.0 CG E:HIS189 4.2 33.6 1.0 CB E:CYS208 4.2 28.7 1.0 N4 E:8YF303 4.3 50.2 1.0 OD1 E:ASP124 4.3 49.1 1.0 C6 E:8YF303 4.3 49.7 1.0 CG2 E:THR190 4.4 33.2 1.0 O62 E:8YF303 4.5 50.2 1.0 CA E:HIS122 4.7 29.6 1.0 C5 E:8YF303 4.8 50.8 1.0 OD2 E:ASP124 4.9 41.2 1.0 C61 E:8YF303 4.9 49.2 1.0

Zinc binding site 10 out of 16 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Ndm-1 Bound to Hydrolyzed Imipenem Representing An EI1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn302 b:52.3 occ:1.00 N4 E:8YF303 2.0 50.2 1.0 NE2 E:HIS250 2.1 42.8 1.0 SG E:CYS208 2.3 50.9 1.0 O31 E:8YF303 2.5 50.1 1.0 OD2 E:ASP124 2.5 41.2 1.0 C3 E:8YF303 2.8 49.8 1.0 CE1 E:HIS250 2.9 41.8 1.0 C31 E:8YF303 3.0 49.9 1.0 CD2 E:HIS250 3.2 44.6 1.0 C5 E:8YF303 3.2 50.8 1.0 CB E:CYS208 3.3 28.7 1.0 O71 E:8YF303 3.3 49.9 1.0 CG E:ASP124 3.6 43.2 1.0 C7 E:8YF303 3.7 48.0 1.0 C2 E:8YF303 3.9 50.6 1.0 C1 E:8YF303 4.0 51.1 1.0 ND1 E:HIS250 4.1 43.1 1.0 ZN E:ZN301 4.1 37.9 1.0 OD1 E:ASP124 4.1 49.1 1.0 C6 E:8YF303 4.1 49.7 1.0 CB E:SER249 4.2 42.0 1.0 CG E:HIS250 4.2 45.4 1.0 O32 E:8YF303 4.3 50.7 1.0 CA E:CYS208 4.4 33.4 1.0 O72 E:8YF303 4.4 44.9 1.0 NE2 E:HIS189 4.4 35.8 1.0 OG E:SER249 4.6 44.5 1.0 CE1 E:HIS189 4.6 35.5 1.0 CB E:ASP124 4.8 37.4 1.0 CE1 E:HIS120 4.8 23.3 1.0 NZ E:LYS211 4.9 50.4 1.0 O62 E:8YF303 4.9 50.2 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