Zinc in PDB 8gpd: Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V

The structure of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V, PDB code: 8gpd was solved by X.Shi, Y.Dai, Q.Zhang, W.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.08 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.14, 79.05, 134.28, 90, 90, 90
R / Rfree (%)	12.4 / 16

The structure of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V (pdb code 8gpd). 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 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V, PDB code: 8gpd:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V


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 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.5 occ:1.00 O A:HOH417 1.9 16.2 1.0 NE2 A:HIS189 2.1 9.0 1.0 ND1 A:HIS122 2.1 10.7 1.0 NE2 A:HIS120 2.2 10.9 1.0 O5 A:JXF303 2.7 21.3 1.0 CD2 A:HIS189 3.0 9.3 1.0 CE1 A:HIS122 3.0 11.5 1.0 CG A:HIS122 3.1 9.8 1.0 CD2 A:HIS120 3.1 8.8 1.0 CE1 A:HIS189 3.1 10.0 1.0 CE1 A:HIS120 3.1 9.9 1.0 H11 A:JXF303 3.2 22.1 1.0 H A:JXF303 3.3 24.7 1.0 CB A:HIS122 3.4 8.5 1.0 C15 A:JXF303 3.4 21.6 1.0 C8 A:JXF303 3.9 20.6 1.0 N1 A:JXF303 4.1 18.4 1.0 NE2 A:HIS122 4.2 13.2 1.0 OD1 A:ASP124 4.2 11.3 1.0 CG A:HIS189 4.2 8.8 1.0 CD2 A:HIS122 4.2 11.3 1.0 ND1 A:HIS189 4.2 10.3 1.0 ND1 A:HIS120 4.2 10.4 1.0 CG A:HIS120 4.3 8.3 1.0 O4 A:JXF303 4.3 24.2 1.0 CG2 A:THR190 4.3 9.6 1.0 SG A:CYS208 4.3 10.5 1.0 CB A:CYS208 4.4 9.2 1.0 ZN A:ZN302 4.5 13.3 1.0 C9 A:JXF303 4.6 18.8 1.0 O A:HOH613 4.7 26.9 1.0 H2 A:JXF303 4.7 20.4 1.0 CA A:HIS122 4.8 8.3 1.0 C10 A:JXF303 4.9 17.0 1.0 OD2 A:ASP124 5.0 11.6 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V


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 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.3 occ:1.00 NE2 A:HIS250 2.1 11.0 1.0 OD2 A:ASP124 2.1 11.6 1.0 H11 A:JXF303 2.2 22.1 1.0 N1 A:JXF303 2.2 18.4 1.0 O2 A:JXF303 2.2 15.3 1.0 SG A:CYS208 2.3 10.5 1.0 O A:HOH417 2.9 16.2 1.0 CD2 A:HIS250 3.0 13.4 1.0 C11 A:JXF303 3.1 17.0 1.0 C10 A:JXF303 3.1 17.0 1.0 CE1 A:HIS250 3.1 11.7 1.0 H14 A:JXF303 3.2 23.3 1.0 H1 A:JXF303 3.2 22.6 1.0 C9 A:JXF303 3.2 18.8 1.0 CG A:ASP124 3.3 10.3 1.0 CB A:CYS208 3.4 9.2 1.0 H13 A:JXF303 3.7 23.3 1.0 C13 A:JXF303 3.7 19.4 1.0 OD1 A:ASP124 3.7 11.3 1.0 H2 A:JXF303 3.9 20.4 1.0 H A:JXF303 3.9 24.7 1.0 C12 A:JXF303 3.9 17.5 1.0 CB A:SER249 4.2 11.1 1.0 ND1 A:HIS250 4.2 12.7 1.0 CG A:HIS250 4.2 13.6 1.0 C8 A:JXF303 4.2 20.6 1.0 O3 A:JXF303 4.3 18.1 1.0 O5 A:JXF303 4.5 21.3 1.0 CA A:CYS208 4.5 9.7 1.0 ZN A:ZN301 4.5 12.5 1.0 CB A:ASP124 4.5 10.2 1.0 S A:JXF303 4.5 19.6 1.0 OG A:SER249 4.6 11.1 1.0 H12 A:JXF303 4.6 23.3 1.0 NE2 A:HIS189 4.8 9.0 1.0 CE1 A:HIS189 4.8 10.0 1.0 C15 A:JXF303 4.9 21.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V


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 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:11.5 occ:1.00 O B:HOH411 1.9 15.1 1.0 ND1 B:HIS122 2.1 8.1 1.0 NE2 B:HIS189 2.1 8.9 1.0 NE2 B:HIS120 2.2 9.8 1.0 O5 B:JXF303 2.6 15.4 1.0 CD2 B:HIS189 3.0 8.4 1.0 CG B:HIS122 3.0 7.9 1.0 CE1 B:HIS122 3.1 9.4 1.0 CE1 B:HIS189 3.1 9.1 1.0 CD2 B:HIS120 3.1 8.1 1.0 CE1 B:HIS120 3.1 10.5 1.0 H11 B:JXF303 3.2 17.6 1.0 H B:JXF303 3.2 20.1 1.0 CB B:HIS122 3.3 7.8 1.0 C15 B:JXF303 3.4 16.8 1.0 C8 B:JXF303 3.8 16.7 1.0 N1 B:JXF303 4.0 14.7 1.0 OD1 B:ASP124 4.1 10.7 1.0 NE2 B:HIS122 4.2 12.0 1.0 CD2 B:HIS122 4.2 10.2 1.0 CG B:HIS189 4.2 7.5 1.0 ND1 B:HIS189 4.2 9.0 1.0 O4 B:JXF303 4.2 21.3 1.0 ND1 B:HIS120 4.2 11.2 1.0 CG2 B:THR190 4.3 9.1 1.0 CG B:HIS120 4.3 8.0 1.0 SG B:CYS208 4.3 9.8 1.0 CB B:CYS208 4.5 9.4 1.0 ZN B:ZN302 4.5 11.7 1.0 C9 B:JXF303 4.5 15.5 1.0 H2 B:JXF303 4.6 17.1 1.0 O B:HOH594 4.8 20.6 1.0 CA B:HIS122 4.8 7.5 1.0 C10 B:JXF303 4.9 14.3 1.0 OD2 B:ASP124 5.0 10.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V


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 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:11.7 occ:1.00 NE2 B:HIS250 2.1 9.5 1.0 OD2 B:ASP124 2.1 10.4 1.0 H11 B:JXF303 2.1 17.6 1.0 N1 B:JXF303 2.2 14.7 1.0 O2 B:JXF303 2.2 14.9 1.0 SG B:CYS208 2.3 9.8 1.0 O B:HOH411 3.0 15.1 1.0 C11 B:JXF303 3.0 14.2 1.0 CD2 B:HIS250 3.1 9.9 1.0 CE1 B:HIS250 3.1 9.6 1.0 C10 B:JXF303 3.1 14.3 1.0 H14 B:JXF303 3.1 21.0 1.0 C9 B:JXF303 3.2 15.5 1.0 CG B:ASP124 3.3 9.4 1.0 H1 B:JXF303 3.3 18.6 1.0 CB B:CYS208 3.4 9.4 1.0 H13 B:JXF303 3.7 21.0 1.0 C13 B:JXF303 3.7 17.5 1.0 OD1 B:ASP124 3.7 10.7 1.0 H2 B:JXF303 3.8 17.1 1.0 C12 B:JXF303 3.9 14.8 1.0 H B:JXF303 4.0 20.1 1.0 ND1 B:HIS250 4.2 10.0 1.0 CB B:SER249 4.2 9.1 1.0 CG B:HIS250 4.2 10.7 1.0 C8 B:JXF303 4.3 16.7 1.0 O3 B:JXF303 4.3 15.8 1.0 O5 B:JXF303 4.4 15.4 1.0 CA B:CYS208 4.5 10.2 1.0 ZN B:ZN301 4.5 11.5 1.0 CB B:ASP124 4.5 8.6 1.0 S B:JXF303 4.6 18.0 1.0 OG B:SER249 4.6 10.0 1.0 H12 B:JXF303 4.6 21.0 1.0 NE2 B:HIS189 4.7 8.9 1.0 CE1 B:HIS189 4.8 9.1 1.0 C15 B:JXF303 4.9 16.8 1.0

X.Shi, Y.Dai, Q.Zhang, W.Liu. Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin V To Be Published.