Zinc in PDB 6kzl: Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2, PDB code: 6kzl was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.51 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.720, 74.040, 77.430, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 19.2

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2 (pdb code 6kzl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2, PDB code: 6kzl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 Metallo-Beta-Lactamase in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:14.8 occ:1.00 NE2 A:HIS189 2.0 13.5 1.0 NE2 A:HIS120 2.1 12.7 1.0 ND1 A:HIS122 2.1 13.9 1.0 N2 A:E1C309 2.1 16.9 1.0 O2 A:E1C309 2.8 15.8 1.0 S1 A:E1C309 2.9 15.6 1.0 CD2 A:HIS189 3.0 13.8 1.0 CE1 A:HIS120 3.0 14.0 1.0 CE1 A:HIS189 3.0 15.2 1.0 CG A:HIS122 3.0 13.4 1.0 CD2 A:HIS120 3.1 14.6 1.0 CE1 A:HIS122 3.1 16.0 1.0 CB A:HIS122 3.3 14.1 1.0 ZN A:ZN302 3.5 15.1 1.0 O1 A:E1C309 3.6 16.2 1.0 O4 A:E1C309 3.8 14.7 1.0 OD1 A:ASP124 4.0 16.0 1.0 SG A:CYS208 4.0 14.2 1.0 CB A:CYS208 4.1 13.5 1.0 CG A:HIS189 4.1 13.2 1.0 ND1 A:HIS189 4.1 13.4 1.0 ND1 A:HIS120 4.1 14.8 1.0 CG A:HIS120 4.2 13.3 1.0 CD2 A:HIS122 4.2 15.7 1.0 NE2 A:HIS122 4.2 15.6 1.0 C2 A:E1C309 4.4 15.4 1.0 CG2 A:THR190 4.5 15.5 1.0 OD2 A:ASP124 4.6 16.8 1.0 C10 A:E1C309 4.6 16.7 1.0 CG A:ASP124 4.7 17.0 1.0 CA A:HIS122 4.8 13.2 1.0 C3 A:E1C309 4.9 15.7 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 Metallo-Beta-Lactamase in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:15.1 occ:1.00 N2 A:E1C309 2.1 16.9 1.0 NE2 A:HIS250 2.1 14.1 1.0 O4 A:E1C309 2.1 14.7 1.0 OD2 A:ASP124 2.1 16.8 1.0 SG A:CYS208 2.3 14.2 1.0 C10 A:E1C309 3.0 16.7 1.0 CD2 A:HIS250 3.1 16.0 1.0 CE1 A:HIS250 3.1 16.5 1.0 CG A:ASP124 3.1 17.0 1.0 S1 A:E1C309 3.1 15.6 1.0 C3 A:E1C309 3.3 15.7 1.0 C2 A:E1C309 3.3 15.4 1.0 CB A:CYS208 3.3 13.5 1.0 OD1 A:ASP124 3.5 16.0 1.0 ZN A:ZN301 3.5 14.8 1.0 O2 A:E1C309 3.9 15.8 1.0 CG A:HIS250 4.2 15.2 1.0 ND1 A:HIS250 4.2 16.5 1.0 O3 A:E1C309 4.2 14.4 1.0 NE2 A:HIS189 4.2 13.5 1.0 O1 A:E1C309 4.2 16.2 1.0 CB A:SER249 4.3 14.6 1.0 CB A:ASP124 4.4 16.2 1.0 C4 A:E1C309 4.4 15.6 1.0 CE1 A:HIS189 4.5 15.2 1.0 C1 A:E1C309 4.5 16.5 1.0 CA A:CYS208 4.5 13.2 1.0 CE1 A:HIS120 4.5 14.0 1.0 NE2 A:HIS120 4.5 12.7 1.0 OG A:SER249 4.6 14.8 1.0 N1 A:E1C309 4.9 17.6 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 Metallo-Beta-Lactamase in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn303 b:19.3 occ:1.00 NE2 A:HIS27 1.9 22.9 1.0 OE2 A:GLU152 2.0 16.9 1.0 OE1 B:GLU227 2.1 20.9 1.0 OD2 A:ASP223 2.1 17.0 1.0 CD B:GLU227 2.7 23.7 1.0 CD A:GLU152 2.7 16.0 1.0 OE2 B:GLU227 2.7 26.4 1.0 OE1 A:GLU152 2.8 19.2 1.0 CG A:ASP223 2.8 16.6 1.0 OD1 A:ASP223 2.9 20.8 1.0 CE1 A:HIS27 2.9 23.4 1.0 CD2 A:HIS27 2.9 24.8 1.0 O A:HOH551 3.9 20.7 1.0 O A:HOH473 3.9 31.6 1.0 ND1 A:HIS27 4.0 22.2 1.0 NE2 B:HIS228 4.1 21.1 1.0 CG A:HIS27 4.1 23.6 1.0 CE1 B:HIS228 4.1 22.0 1.0 CG A:GLU152 4.2 17.3 1.0 CG B:GLU227 4.2 22.5 1.0 NE2 A:HIS122 4.2 15.6 1.0 CB A:ASP223 4.2 16.8 1.0 O B:HOH557 4.3 27.7 1.0 O A:HOH528 4.5 29.9 1.0 O A:HOH496 4.5 31.9 1.0 CD2 A:HIS122 4.7 15.7 1.0 CB B:GLU227 4.8 21.1 1.0 O A:HOH447 5.0 20.2 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 Metallo-Beta-Lactamase in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:17.8 occ:1.00 ND1 B:HIS122 2.0 13.8 1.0 NE2 B:HIS189 2.0 17.4 1.0 NE2 B:HIS120 2.1 17.3 1.0 N2 B:E1C304 2.2 14.4 1.0 O1 B:E1C304 2.7 15.8 1.0 CE1 B:HIS122 2.9 18.4 1.0 S1 B:E1C304 2.9 17.6 1.0 CD2 B:HIS189 3.0 17.0 1.0 CE1 B:HIS189 3.0 17.8 1.0 CG B:HIS122 3.0 14.9 1.0 CD2 B:HIS120 3.1 16.7 1.0 CE1 B:HIS120 3.1 18.7 1.0 CB B:HIS122 3.4 15.1 1.0 ZN B:ZN302 3.5 17.7 1.0 O2 B:E1C304 3.6 16.4 1.0 SG B:CYS208 3.9 16.3 1.0 O4 B:E1C304 3.9 18.7 1.0 OD1 B:ASP124 4.0 18.8 1.0 NE2 B:HIS122 4.0 16.6 1.0 CB B:CYS208 4.1 16.0 1.0 CD2 B:HIS122 4.1 14.3 1.0 ND1 B:HIS189 4.1 18.6 1.0 CG B:HIS189 4.1 15.4 1.0 ND1 B:HIS120 4.2 17.1 1.0 CG B:HIS120 4.2 16.3 1.0 C2 B:E1C304 4.3 17.0 1.0 OD2 B:ASP124 4.5 19.2 1.0 CG2 B:THR190 4.6 17.3 1.0 C10 B:E1C304 4.6 17.7 1.0 CG B:ASP124 4.7 17.9 1.0 CA B:HIS122 4.9 15.3 1.0 C3 B:E1C304 4.9 17.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 Metallo-Beta-Lactamase in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:17.7 occ:1.00 N2 B:E1C304 2.0 14.4 1.0 NE2 B:HIS250 2.1 19.7 1.0 OD2 B:ASP124 2.2 19.2 1.0 O4 B:E1C304 2.2 18.7 1.0 SG B:CYS208 2.3 16.3 1.0 CD2 B:HIS250 3.0 20.4 1.0 C10 B:E1C304 3.1 17.7 1.0 S1 B:E1C304 3.1 17.6 1.0 CE1 B:HIS250 3.1 21.0 1.0 CG B:ASP124 3.2 17.9 1.0 C2 B:E1C304 3.3 17.0 1.0 C3 B:E1C304 3.3 17.8 1.0 CB B:CYS208 3.4 16.0 1.0 ZN B:ZN301 3.5 17.8 1.0 OD1 B:ASP124 3.6 18.8 1.0 O1 B:E1C304 3.9 15.8 1.0 CG B:HIS250 4.2 18.3 1.0 NE2 B:HIS189 4.2 17.4 1.0 ND1 B:HIS250 4.2 19.5 1.0 O2 B:E1C304 4.3 16.4 1.0 CB B:SER249 4.3 17.3 1.0 O3 B:E1C304 4.3 16.8 1.0 C4 B:E1C304 4.4 18.5 1.0 CB B:ASP124 4.5 15.4 1.0 C1 B:E1C304 4.5 19.9 1.0 NE2 B:HIS120 4.5 17.3 1.0 CA B:CYS208 4.5 15.6 1.0 CE1 B:HIS189 4.5 17.8 1.0 CE1 B:HIS120 4.5 18.7 1.0 OG B:SER249 4.6 17.9 1.0 N1 B:E1C304 5.0 19.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor X2


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 Metallo-Beta-Lactamase in Complex with Inhibitor X2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:28.0 occ:0.50 OE1 A:GLU227 2.1 45.7 1.0 OE2 B:GLU152 2.1 30.9 1.0 OD2 B:ASP223 2.2 29.3 1.0 OE2 A:GLU227 2.6 46.8 1.0 CD A:GLU227 2.7 39.5 1.0 OE1 B:GLU152 2.7 28.2 1.0 CD B:GLU152 2.7 29.9 1.0 CG B:ASP223 2.8 30.4 1.0 OD1 B:ASP223 2.8 34.7 1.0 O B:HOH571 3.9 27.2 1.0 NE2 A:HIS228 4.0 21.9 1.0 CE1 A:HIS228 4.0 23.2 1.0 CG A:GLU227 4.2 30.6 1.0 CG B:GLU152 4.2 28.4 1.0 CB B:ASP223 4.3 26.4 1.0 NE2 B:HIS122 4.3 16.6 1.0 O B:HOH548 4.4 29.0 1.0 CD2 B:HIS122 4.8 14.3 1.0 O B:HOH420 4.9 31.9 1.0 CB A:GLU227 4.9 23.8 1.0

J.Wachino, J.Wachino. N/A N/A.