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

The structure of Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin, PDB code: 8gpc 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)	33.59 / 1.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.26, 79.11, 134.35, 90, 90, 90
R / Rfree (%)	13 / 16

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

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 at PH5.5 (Succinate) in Complex with Hydrolyzed Ampicillin (pdb code 8gpc). 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 Ampicillin, PDB code: 8gpc:
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 Ampicillin


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 Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.2 occ:1.00 O A:HOH417 1.9 14.7 1.0 ND1 A:HIS122 2.1 10.3 1.0 NE2 A:HIS189 2.1 10.3 1.0 NE2 A:HIS120 2.2 11.1 1.0 O4 A:ZZ7303 2.4 16.8 1.0 CD2 A:HIS189 3.0 9.1 1.0 CE1 A:HIS122 3.0 11.6 1.0 CG A:HIS122 3.0 9.8 1.0 CE1 A:HIS120 3.1 11.4 1.0 CE1 A:HIS189 3.1 10.1 1.0 CD2 A:HIS120 3.2 9.0 1.0 H3 A:ZZ7303 3.2 17.6 1.0 H14 A:ZZ7303 3.3 19.8 1.0 C15 A:ZZ7303 3.3 16.5 1.0 CB A:HIS122 3.4 10.3 1.0 C14 A:ZZ7303 3.8 16.5 1.0 N3 A:ZZ7303 4.0 14.7 1.0 NE2 A:HIS122 4.1 11.8 1.0 CD2 A:HIS122 4.2 10.4 1.0 OD1 A:ASP124 4.2 11.6 1.0 OXT A:ZZ7303 4.2 18.2 1.0 ND1 A:HIS189 4.2 10.7 1.0 CG A:HIS189 4.2 8.3 1.0 ND1 A:HIS120 4.2 10.3 1.0 CG2 A:THR190 4.3 11.3 1.0 CG A:HIS120 4.3 8.6 1.0 SG A:CYS208 4.3 10.9 1.0 CB A:CYS208 4.4 10.5 1.0 C13 A:ZZ7303 4.5 15.6 1.0 ZN A:ZN302 4.5 13.2 1.0 H12 A:ZZ7303 4.7 17.9 1.0 O A:HOH554 4.8 18.5 1.0 CA A:HIS122 4.8 8.9 1.0 C12 A:ZZ7303 4.9 14.9 1.0 H13 A:ZZ7303 5.0 18.7 1.0

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


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 Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:13.2 occ:1.00 NE2 A:HIS250 2.1 11.9 1.0 OD2 A:ASP124 2.1 11.6 1.0 H3 A:ZZ7303 2.2 17.6 1.0 N3 A:ZZ7303 2.2 14.7 1.0 O2 A:ZZ7303 2.2 16.1 1.0 SG A:CYS208 2.4 10.9 1.0 O A:HOH417 3.0 14.7 1.0 C2 A:ZZ7303 3.0 17.3 1.0 CD2 A:HIS250 3.0 12.4 1.0 CE1 A:HIS250 3.1 11.3 1.0 C12 A:ZZ7303 3.1 14.9 1.0 H11C A:ZZ7303 3.1 22.5 1.0 C13 A:ZZ7303 3.2 15.6 1.0 H13 A:ZZ7303 3.2 18.7 1.0 CG A:ASP124 3.3 11.1 1.0 CB A:CYS208 3.4 10.5 1.0 C1 A:ZZ7303 3.7 18.8 1.0 OD1 A:ASP124 3.7 11.6 1.0 H12C A:ZZ7303 3.7 22.5 1.0 H12 A:ZZ7303 3.9 17.9 1.0 C6 A:ZZ7303 3.9 15.6 1.0 H14 A:ZZ7303 4.1 19.8 1.0 ND1 A:HIS250 4.2 12.8 1.0 CG A:HIS250 4.2 12.0 1.0 CB A:SER249 4.2 10.2 1.0 O1 A:ZZ7303 4.2 17.4 1.0 C14 A:ZZ7303 4.3 16.5 1.0 O4 A:ZZ7303 4.3 16.8 1.0 CA A:CYS208 4.5 11.5 1.0 S1 A:ZZ7303 4.5 17.8 1.0 ZN A:ZN301 4.5 12.2 1.0 CB A:ASP124 4.5 11.0 1.0 OG A:SER249 4.6 11.6 1.0 H13C A:ZZ7303 4.6 22.5 1.0 NE2 A:HIS189 4.8 10.3 1.0 C15 A:ZZ7303 4.8 16.5 1.0 CE1 A:HIS189 4.8 10.1 1.0

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


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 Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:12.6 occ:1.00 O B:HOH415 1.9 14.9 1.0 ND1 B:HIS122 2.1 11.9 1.0 NE2 B:HIS189 2.1 10.2 1.0 NE2 B:HIS120 2.2 10.9 1.0 O4 B:ZZ7303 2.4 17.2 1.0 CE1 B:HIS122 3.0 13.1 1.0 CD2 B:HIS189 3.0 9.8 1.0 CG B:HIS122 3.1 10.1 1.0 CE1 B:HIS189 3.1 11.0 1.0 CE1 B:HIS120 3.1 10.9 1.0 CD2 B:HIS120 3.1 9.7 1.0 H3 B:ZZ7303 3.2 21.2 1.0 C15 B:ZZ7303 3.3 17.2 1.0 H14 B:ZZ7303 3.3 20.3 1.0 CB B:HIS122 3.4 10.2 1.0 C14 B:ZZ7303 3.8 16.9 1.0 N3 B:ZZ7303 4.0 17.7 1.0 OXT B:ZZ7303 4.1 19.1 1.0 NE2 B:HIS122 4.1 13.8 1.0 CD2 B:HIS122 4.2 13.0 1.0 OD1 B:ASP124 4.2 12.2 1.0 CG B:HIS189 4.2 9.7 1.0 ND1 B:HIS189 4.2 11.1 1.0 ND1 B:HIS120 4.2 10.3 1.0 CG B:HIS120 4.3 8.5 1.0 CG2 B:THR190 4.3 11.2 1.0 SG B:CYS208 4.3 11.5 1.0 CB B:CYS208 4.4 9.6 1.0 ZN B:ZN302 4.5 13.6 1.0 C13 B:ZZ7303 4.6 16.3 1.0 H12 B:ZZ7303 4.7 20.0 1.0 O B:HOH574 4.8 22.3 1.0 CA B:HIS122 4.9 9.5 1.0 C12 B:ZZ7303 4.9 16.6 1.0

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


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 Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:13.6 occ:1.00 NE2 B:HIS250 2.1 12.9 1.0 OD2 B:ASP124 2.2 12.4 1.0 H3 B:ZZ7303 2.2 21.2 1.0 N3 B:ZZ7303 2.2 17.7 1.0 O2 B:ZZ7303 2.2 15.3 1.0 SG B:CYS208 2.4 11.5 1.0 O B:HOH415 2.9 14.9 1.0 C2 B:ZZ7303 3.0 16.8 1.0 CD2 B:HIS250 3.0 12.8 1.0 C12 B:ZZ7303 3.1 16.6 1.0 CE1 B:HIS250 3.1 13.0 1.0 H11C B:ZZ7303 3.2 21.3 1.0 C13 B:ZZ7303 3.2 16.3 1.0 H13 B:ZZ7303 3.2 19.6 1.0 CG B:ASP124 3.3 11.5 1.0 CB B:CYS208 3.5 9.6 1.0 H12C B:ZZ7303 3.7 21.3 1.0 C1 B:ZZ7303 3.7 17.7 1.0 OD1 B:ASP124 3.8 12.2 1.0 H12 B:ZZ7303 3.9 20.0 1.0 C6 B:ZZ7303 3.9 15.1 1.0 H14 B:ZZ7303 4.0 20.3 1.0 ND1 B:HIS250 4.2 12.9 1.0 CG B:HIS250 4.2 13.0 1.0 O1 B:ZZ7303 4.2 17.6 1.0 CB B:SER249 4.2 12.1 1.0 C14 B:ZZ7303 4.2 16.9 1.0 O4 B:ZZ7303 4.3 17.2 1.0 CA B:CYS208 4.5 11.1 1.0 CB B:ASP124 4.5 11.0 1.0 ZN B:ZN301 4.5 12.6 1.0 S1 B:ZZ7303 4.5 18.0 1.0 H13C B:ZZ7303 4.7 21.3 1.0 OG B:SER249 4.7 12.0 1.0 C15 B:ZZ7303 4.8 17.2 1.0 NE2 B:HIS189 4.8 10.2 1.0 CE1 B:HIS189 4.9 11.0 1.0

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