Zinc in PDB 6jkb: Crystal Structure of Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin

All present enzymatic activity of Crystal Structure of Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin:
3.5.2.6;

The structure of Crystal Structure of Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin, PDB code: 6jkb was solved by T.Kamo, K.Kuroda, S.Kondo, U.Hayashi, S.Fudo, M.Nukaga, T.Hoshino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.62 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.111, 79.248, 132.617, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 24.8

The binding sites of Zinc atom in the Crystal Structure of Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin (pdb code 6jkb). 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 Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin, PDB code: 6jkb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Metallo-Beta-Lactamse, Ndm-1, 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 Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:61.1 occ:1.00 O1 A:ZZ7303 2.0 56.7 1.0 NE2 A:HIS224 2.1 59.2 1.0 OD2 A:ASP98 2.3 54.8 1.0 SG A:CYS182 2.5 45.6 1.0 N3 A:ZZ7303 2.7 67.2 1.0 CE1 A:HIS224 2.8 52.4 1.0 C2 A:ZZ7303 3.0 65.4 1.0 CD2 A:HIS224 3.3 54.4 1.0 C12 A:ZZ7303 3.4 71.1 1.0 CG A:ASP98 3.4 47.9 1.0 O4 A:ZZ7303 3.5 65.0 1.0 CB A:CYS182 3.6 50.0 1.0 C16 A:ZZ7303 3.8 64.0 1.0 C13 A:ZZ7303 3.8 71.0 1.0 C14 A:ZZ7303 3.9 64.3 1.0 ND1 A:HIS224 4.0 57.3 1.0 OD1 A:ASP98 4.0 49.9 1.0 C15 A:ZZ7303 4.1 71.7 1.0 O2 A:ZZ7303 4.1 63.4 1.0 CB A:SER223 4.1 45.7 1.0 C6 A:ZZ7303 4.2 70.1 1.0 CG A:HIS224 4.3 56.1 1.0 OG A:SER223 4.5 47.1 1.0 CB A:ASP98 4.5 41.7 1.0 ZN A:ZN302 4.6 53.7 1.0 CA A:CYS182 4.6 44.2 1.0 NE2 A:HIS163 4.8 52.2 1.0 CE1 A:HIS163 4.9 47.3 1.0 S1 A:ZZ7303 5.0 95.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Metallo-Beta-Lactamse, Ndm-1, 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 Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:53.7 occ:1.00 O4 A:ZZ7303 1.9 65.0 1.0 ND1 A:HIS96 2.1 48.6 1.0 NE2 A:HIS94 2.2 51.3 1.0 NE2 A:HIS163 2.2 52.2 1.0 C15 A:ZZ7303 2.9 71.7 1.0 CD2 A:HIS163 2.9 48.3 1.0 CD2 A:HIS94 3.0 46.9 1.0 CE1 A:HIS96 3.0 46.9 1.0 CG A:HIS96 3.1 55.5 1.0 CE1 A:HIS94 3.2 42.5 1.0 OXT A:ZZ7303 3.2 71.4 1.0 CB A:HIS96 3.4 51.3 1.0 CE1 A:HIS163 3.4 47.3 1.0 SG A:CYS182 4.1 45.6 1.0 NE2 A:HIS96 4.1 51.0 1.0 CG A:HIS163 4.1 48.9 1.0 CG A:HIS94 4.2 44.4 1.0 CD2 A:HIS96 4.2 48.5 1.0 ND1 A:HIS94 4.2 42.3 1.0 C14 A:ZZ7303 4.2 64.3 1.0 CG2 A:THR164 4.2 37.4 1.0 CB A:CYS182 4.3 50.0 1.0 OD1 A:ASP98 4.4 49.9 1.0 ND1 A:HIS163 4.4 50.3 1.0 N3 A:ZZ7303 4.5 67.2 1.0 ZN A:ZN301 4.6 61.1 1.0 OD2 A:ASP98 4.8 54.8 1.0 CA A:HIS96 4.9 45.1 1.0 O1 A:ZZ7303 5.0 56.7 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Metallo-Beta-Lactamse, Ndm-1, 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 Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:53.3 occ:1.00 OXT B:ZZ7303 1.5 71.3 1.0 ND1 B:HIS96 2.1 51.3 1.0 NE2 B:HIS163 2.1 50.0 1.0 NE2 B:HIS94 2.1 57.0 1.0 C15 B:ZZ7303 2.2 74.6 1.0 O4 B:ZZ7303 2.5 78.5 1.0 CD2 B:HIS163 2.8 48.9 1.0 CD2 B:HIS94 3.0 46.5 1.0 CE1 B:HIS94 3.0 53.9 1.0 CE1 B:HIS96 3.0 54.2 1.0 CG B:HIS96 3.1 53.6 1.0 CE1 B:HIS163 3.3 52.6 1.0 CB B:HIS96 3.5 46.6 1.0 C14 B:ZZ7303 3.5 67.7 1.0 O B:HOH405 3.8 64.6 1.0 N1 B:ZZ7303 3.9 71.4 1.0 CG B:HIS163 4.0 54.9 1.0 ND1 B:HIS94 4.1 56.0 1.0 CG B:HIS94 4.1 53.2 1.0 NE2 B:HIS96 4.2 49.3 1.0 SG B:CYS182 4.2 58.4 1.0 CD2 B:HIS96 4.2 53.6 1.0 CG2 B:THR164 4.2 37.5 1.0 ND1 B:HIS163 4.3 51.7 1.0 CB B:CYS182 4.3 53.2 1.0 ZN B:ZN302 4.6 62.6 1.0 OD1 B:ASP98 4.7 54.7 1.0 C13 B:ZZ7303 4.8 69.2 1.0 C3 B:ZZ7303 4.8 77.5 1.0 N3 B:ZZ7303 4.8 61.7 1.0 CA B:HIS96 4.9 51.0 1.0 N2 B:ZZ7303 5.0 80.8 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Metallo-Beta-Lactamse, Ndm-1, 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 Metallo-Beta-Lactamse, Ndm-1, in Complex with Hydrolyzed Ampicillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:62.6 occ:1.00 NE2 B:HIS224 2.1 56.9 1.0 N3 B:ZZ7303 2.1 61.7 1.0 O4 B:ZZ7303 2.2 78.5 1.0 C13 B:ZZ7303 2.3 69.2 1.0 SG B:CYS182 2.3 58.4 1.0 OD2 B:ASP98 2.7 54.5 1.0 C14 B:ZZ7303 2.7 67.7 1.0 C15 B:ZZ7303 2.8 74.6 1.0 CD2 B:HIS224 3.0 52.0 1.0 CE1 B:HIS224 3.2 53.6 1.0 CB B:CYS182 3.2 53.2 1.0 C12 B:ZZ7303 3.6 72.2 1.0 CG B:ASP98 3.8 51.5 1.0 CB B:SER223 3.9 50.4 1.0 OXT B:ZZ7303 4.0 71.3 1.0 S1 B:ZZ7303 4.0 85.0 1.0 O1 B:ZZ7303 4.0 68.7 1.0 N1 B:ZZ7303 4.1 71.4 1.0 CG B:HIS224 4.2 53.0 1.0 OG B:SER223 4.2 46.6 1.0 CA B:CYS182 4.2 51.0 1.0 ND1 B:HIS224 4.2 52.9 1.0 C6 B:ZZ7303 4.3 73.1 1.0 C2 B:ZZ7303 4.3 68.2 1.0 OD1 B:ASP98 4.4 54.7 1.0 C16 B:ZZ7303 4.5 65.7 1.0 ZN B:ZN301 4.6 53.3 1.0 NE2 B:HIS163 4.7 50.0 1.0 CE1 B:HIS163 4.8 52.6 1.0 N B:CYS182 4.9 47.4 1.0 CB B:ASP98 5.0 48.4 1.0 NZ B:LYS185 5.0 46.4 1.0

T.Kamo, K.Kuroda, S.Kondo, U.Hayashi, S.Fudo, M.Nukaga, T.Hoshino. Identification of the Inhibitory Compounds For Metallo-Beta-Lactamases To Be Published.