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

The structure of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin G, PDB code: 8gpe 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)	38.93 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.17, 79.16, 134.12, 90, 90, 90
R / Rfree (%)	13 / 16

The structure of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Penicillin G 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 G (pdb code 8gpe). 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 G, PDB code: 8gpe:
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 G


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 G within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:10.4 occ:1.00 O A:HOH420 1.8 13.1 1.0 ND1 A:HIS122 2.1 8.3 1.0 NE2 A:HIS189 2.1 7.8 1.0 NE2 A:HIS120 2.2 9.6 1.0 O3 A:PNK303 2.5 13.7 1.0 CD2 A:HIS189 3.0 7.5 1.0 CE1 A:HIS122 3.1 9.7 1.0 CG A:HIS122 3.1 7.5 1.0 HN1 A:PNK303 3.1 15.7 1.0 CE1 A:HIS189 3.1 9.0 1.0 H1 A:PNK303 3.1 17.5 1.0 CE1 A:HIS120 3.1 9.4 1.0 CD2 A:HIS120 3.1 7.8 1.0 C2 A:PNK303 3.3 14.2 1.0 CB A:HIS122 3.4 7.0 1.0 C1 A:PNK303 3.7 14.6 1.0 N1 A:PNK303 4.0 13.1 1.0 O4 A:PNK303 4.2 15.9 1.0 NE2 A:HIS122 4.2 10.1 1.0 OD1 A:ASP124 4.2 9.0 1.0 CD2 A:HIS122 4.2 9.0 1.0 CG A:HIS189 4.2 7.0 1.0 ND1 A:HIS189 4.2 8.7 1.0 ND1 A:HIS120 4.2 10.2 1.0 CG A:HIS120 4.3 7.5 1.0 CG2 A:THR190 4.3 9.2 1.0 SG A:CYS208 4.3 9.1 1.0 CB A:CYS208 4.4 8.2 1.0 C4 A:PNK303 4.5 12.8 1.0 ZN A:ZN302 4.5 10.9 1.0 H5 A:PNK303 4.7 15.6 1.0 CA A:HIS122 4.8 7.2 1.0 O A:HOH551 4.9 16.6 1.0 C5 A:PNK303 4.9 13.0 1.0 N2 A:PNK303 5.0 14.7 1.0 OD2 A:ASP124 5.0 8.9 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 G


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 G within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:10.9 occ:1.00 HN1 A:PNK303 2.0 15.7 1.0 NE2 A:HIS250 2.1 8.8 1.0 OD2 A:ASP124 2.1 8.9 1.0 N1 A:PNK303 2.2 13.1 1.0 O1 A:PNK303 2.2 13.3 1.0 SG A:CYS208 2.3 9.1 1.0 C9 A:PNK303 3.0 13.8 1.0 O A:HOH420 3.0 13.1 1.0 CD2 A:HIS250 3.1 10.3 1.0 C5 A:PNK303 3.1 13.0 1.0 H13A A:PNK303 3.1 19.5 1.0 CE1 A:HIS250 3.1 9.3 1.0 CG A:ASP124 3.3 8.0 1.0 C4 A:PNK303 3.3 12.8 1.0 H4 A:PNK303 3.3 15.4 1.0 CB A:CYS208 3.4 8.2 1.0 H13B A:PNK303 3.6 19.5 1.0 C13 A:PNK303 3.7 16.2 1.0 OD1 A:ASP124 3.7 9.0 1.0 C6 A:PNK303 3.9 13.1 1.0 H5 A:PNK303 3.9 15.6 1.0 H1 A:PNK303 4.0 17.5 1.0 CB A:SER249 4.2 8.9 1.0 ND1 A:HIS250 4.2 10.9 1.0 CG A:HIS250 4.2 10.8 1.0 O2 A:PNK303 4.2 14.2 1.0 C1 A:PNK303 4.3 14.6 1.0 O3 A:PNK303 4.4 13.7 1.0 CA A:CYS208 4.5 9.2 1.0 CB A:ASP124 4.5 9.2 1.0 ZN A:ZN301 4.5 10.4 1.0 S1 A:PNK303 4.6 15.3 1.0 OG A:SER249 4.6 9.3 1.0 H13 A:PNK303 4.7 19.5 1.0 NE2 A:HIS189 4.8 7.8 1.0 CE1 A:HIS189 4.9 9.0 1.0 C2 A:PNK303 4.9 14.2 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 G


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 G within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:11.6 occ:1.00 O B:HOH424 1.9 15.0 1.0 NE2 B:HIS189 2.1 9.2 1.0 ND1 B:HIS122 2.1 10.8 1.0 NE2 B:HIS120 2.2 10.1 1.0 O4 B:PNK303 2.5 17.4 1.0 CD2 B:HIS189 3.0 8.6 1.0 CG B:HIS122 3.1 8.9 1.0 CE1 B:HIS122 3.1 11.2 1.0 HN1 B:PNK303 3.1 19.6 1.0 CD2 B:HIS120 3.1 7.9 1.0 CE1 B:HIS189 3.1 9.9 1.0 CE1 B:HIS120 3.1 9.7 1.0 H1 B:PNK303 3.2 20.8 1.0 C2 B:PNK303 3.3 17.4 1.0 CB B:HIS122 3.4 8.4 1.0 C1 B:PNK303 3.8 17.3 1.0 N1 B:PNK303 4.0 16.3 1.0 OD1 B:ASP124 4.2 11.1 1.0 NE2 B:HIS122 4.2 11.8 1.0 CG B:HIS189 4.2 7.8 1.0 ND1 B:HIS189 4.2 10.2 1.0 CD2 B:HIS122 4.2 11.4 1.0 O3 B:PNK303 4.2 21.5 1.0 ND1 B:HIS120 4.2 8.9 1.0 CG B:HIS120 4.3 7.5 1.0 CG2 B:THR190 4.3 8.8 1.0 SG B:CYS208 4.3 9.9 1.0 CB B:CYS208 4.4 8.4 1.0 ZN B:ZN302 4.5 12.4 1.0 C4 B:PNK303 4.5 17.0 1.0 H5 B:PNK303 4.6 19.7 1.0 O B:HOH593 4.7 19.7 1.0 CA B:HIS122 4.8 7.5 1.0 C5 B:PNK303 4.9 16.4 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 G


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 G within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:12.4 occ:1.00 HN1 B:PNK303 2.0 19.6 1.0 NE2 B:HIS250 2.1 10.4 1.0 OD2 B:ASP124 2.1 9.7 1.0 N1 B:PNK303 2.2 16.3 1.0 O2 B:PNK303 2.2 14.0 1.0 SG B:CYS208 2.3 9.9 1.0 O B:HOH424 3.0 15.0 1.0 C9 B:PNK303 3.0 16.6 1.0 CD2 B:HIS250 3.0 11.9 1.0 C5 B:PNK303 3.1 16.4 1.0 H13A B:PNK303 3.1 23.5 1.0 CE1 B:HIS250 3.1 10.2 1.0 C4 B:PNK303 3.2 17.0 1.0 H4 B:PNK303 3.3 20.4 1.0 CG B:ASP124 3.3 9.5 1.0 CB B:CYS208 3.4 8.4 1.0 H13B B:PNK303 3.7 23.5 1.0 C13 B:PNK303 3.7 19.6 1.0 OD1 B:ASP124 3.8 11.1 1.0 C6 B:PNK303 3.9 15.9 1.0 H5 B:PNK303 3.9 19.7 1.0 H1 B:PNK303 4.0 20.8 1.0 CG B:HIS250 4.2 12.4 1.0 CB B:SER249 4.2 10.2 1.0 ND1 B:HIS250 4.2 11.4 1.0 O1 B:PNK303 4.2 16.2 1.0 C1 B:PNK303 4.3 17.3 1.0 O4 B:PNK303 4.4 17.4 1.0 ZN B:ZN301 4.5 11.6 1.0 CA B:CYS208 4.5 9.3 1.0 CB B:ASP124 4.5 9.8 1.0 S1 B:PNK303 4.5 18.7 1.0 OG B:SER249 4.6 9.9 1.0 H13 B:PNK303 4.7 23.5 1.0 NE2 B:HIS189 4.8 9.2 1.0 CE1 B:HIS189 4.9 9.9 1.0 C2 B:PNK303 4.9 17.4 1.0

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