Zinc in PDB 6kxi: Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor NO9

The structure of Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor NO9, PDB code: 6kxi was solved by J.Wachino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.62 / 1.38
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.550, 73.660, 77.750, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 15.7

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor NO9 (pdb code 6kxi). 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 NO9, PDB code: 6kxi:
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 NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:6.7 occ:1.00 NE2 A:HIS189 2.0 6.5 1.0 ND1 A:HIS122 2.1 6.6 1.0 NE2 A:HIS120 2.1 6.5 1.0 N1 A:NO9607 2.1 6.9 1.0 O3 A:NO9607 2.8 7.7 1.0 S A:NO9607 2.9 7.6 1.0 CD2 A:HIS189 3.0 6.4 1.0 CE1 A:HIS122 3.0 7.7 1.0 CE1 A:HIS120 3.0 6.9 1.0 CE1 A:HIS189 3.0 7.0 1.0 CD2 A:HIS120 3.1 6.1 1.0 CG A:HIS122 3.1 6.1 1.0 CB A:HIS122 3.4 5.8 1.0 ZN A:ZN602 3.5 7.3 1.0 O2 A:NO9607 3.6 9.8 1.0 O5 A:NO9607 3.8 8.2 1.0 SG A:CYS208 3.9 7.3 1.0 OD1 A:ASP124 4.0 6.9 1.0 CB A:CYS208 4.1 8.1 1.0 ND1 A:HIS120 4.1 7.1 1.0 ND1 A:HIS189 4.1 6.1 1.0 NE2 A:HIS122 4.1 8.0 1.0 CG A:HIS189 4.1 6.3 1.0 CD2 A:HIS122 4.2 6.5 1.0 CG A:HIS120 4.2 6.2 1.0 C1 A:NO9607 4.3 8.3 1.0 OD2 A:ASP124 4.5 8.6 1.0 CG2 A:THR190 4.5 7.4 1.0 CG A:ASP124 4.7 7.3 1.0 C5 A:NO9607 4.7 8.2 1.0 CA A:HIS122 4.9 5.5 1.0 C2 A:NO9607 4.9 8.7 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:7.3 occ:1.00 N1 A:NO9607 2.1 6.9 1.0 O5 A:NO9607 2.1 8.2 1.0 NE2 A:HIS250 2.1 7.7 1.0 OD2 A:ASP124 2.1 8.6 1.0 SG A:CYS208 2.3 7.3 1.0 C5 A:NO9607 3.1 8.2 1.0 CD2 A:HIS250 3.1 7.5 1.0 S A:NO9607 3.1 7.6 1.0 CE1 A:HIS250 3.1 7.9 1.0 CG A:ASP124 3.1 7.3 1.0 C1 A:NO9607 3.2 8.3 1.0 C2 A:NO9607 3.2 8.7 1.0 CB A:CYS208 3.3 8.1 1.0 OD1 A:ASP124 3.5 6.9 1.0 ZN A:ZN601 3.5 6.7 1.0 O3 A:NO9607 3.9 7.7 1.0 NE2 A:HIS189 4.2 6.5 1.0 O4 A:NO9607 4.2 9.6 1.0 ND1 A:HIS250 4.2 7.9 1.0 CG A:HIS250 4.2 7.8 1.0 O2 A:NO9607 4.2 9.8 1.0 C3 A:NO9607 4.3 10.1 1.0 C4 A:NO9607 4.3 10.2 1.0 CB A:SER249 4.3 7.2 1.0 CE1 A:HIS189 4.4 7.0 1.0 CB A:ASP124 4.4 6.4 1.0 CA A:CYS208 4.5 7.6 1.0 NE2 A:HIS120 4.5 6.5 1.0 CE1 A:HIS120 4.5 6.9 1.0 OG A:SER249 4.6 7.0 1.0 O1 A:NO9607 4.8 10.2 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:11.7 occ:1.00 NE2 A:HIS27 1.9 14.6 1.0 OD2 A:ASP223 2.0 10.3 1.0 OE2 A:GLU152 2.1 11.2 1.0 OE1 B:GLU227 2.1 16.5 1.0 OE2 B:GLU227 2.1 22.9 1.0 OE1 A:GLU152 2.3 12.4 1.0 CD B:GLU227 2.4 15.1 1.0 CD A:GLU152 2.6 10.2 1.0 CG A:ASP223 2.8 11.1 1.0 OD1 A:ASP223 2.9 13.3 1.0 CD2 A:HIS27 2.9 13.8 1.0 CE1 A:HIS27 2.9 17.4 1.0 O A:HOH831 3.9 12.5 1.0 O A:HOH708 4.0 28.5 1.0 NE2 B:HIS228 4.0 9.4 1.0 CG B:GLU227 4.0 13.7 1.0 ND1 A:HIS27 4.0 18.2 1.0 CG A:HIS27 4.0 16.0 1.0 CG A:GLU152 4.1 9.4 1.0 CB A:ASP223 4.2 9.5 1.0 CE1 B:HIS228 4.2 8.5 1.0 NE2 A:HIS122 4.2 8.0 1.0 O A:HOH780 4.4 27.6 1.0 O A:HOH854 4.6 28.2 1.0 CD2 A:HIS122 4.7 6.5 1.0 O B:HOH609 4.7 21.8 1.0 CB B:GLU227 4.8 10.7 1.0 O A:HOH769 4.9 11.3 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:6.7 occ:1.00 NE2 B:HIS189 2.0 5.5 1.0 N1 B:NO9305 2.0 7.2 1.0 ND1 B:HIS122 2.1 7.5 1.0 NE2 B:HIS120 2.1 6.2 1.0 O3 B:NO9305 2.8 7.3 1.0 S B:NO9305 2.9 7.6 1.0 CD2 B:HIS189 3.0 6.0 1.0 CE1 B:HIS189 3.0 6.5 1.0 CE1 B:HIS122 3.0 7.3 1.0 CE1 B:HIS120 3.0 6.9 1.0 CG B:HIS122 3.1 6.5 1.0 CD2 B:HIS120 3.1 6.0 1.0 CB B:HIS122 3.4 6.8 1.0 ZN B:ZN302 3.5 7.0 1.0 O2 B:NO9305 3.6 9.1 1.0 O4 B:NO9305 3.8 7.0 1.0 SG B:CYS208 3.9 6.9 1.0 OD1 B:ASP124 4.0 7.8 1.0 ND1 B:HIS189 4.1 6.2 1.0 CB B:CYS208 4.1 6.2 1.0 ND1 B:HIS120 4.1 6.8 1.0 CG B:HIS189 4.1 5.9 1.0 NE2 B:HIS122 4.2 7.7 1.0 CD2 B:HIS122 4.2 7.6 1.0 CG B:HIS120 4.2 6.0 1.0 C1 B:NO9305 4.3 8.6 1.0 CG2 B:THR190 4.5 7.2 1.0 OD2 B:ASP124 4.5 8.0 1.0 C5 B:NO9305 4.6 8.3 1.0 CG B:ASP124 4.7 6.9 1.0 CA B:HIS122 4.8 6.0 1.0 C2 B:NO9305 4.9 7.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:7.0 occ:1.00 NE2 B:HIS250 2.1 6.7 1.0 OD2 B:ASP124 2.1 8.0 1.0 O4 B:NO9305 2.1 7.0 1.0 N1 B:NO9305 2.1 7.2 1.0 SG B:CYS208 2.3 6.9 1.0 C5 B:NO9305 3.0 8.3 1.0 CD2 B:HIS250 3.1 7.2 1.0 CE1 B:HIS250 3.1 7.2 1.0 CG B:ASP124 3.1 6.9 1.0 S B:NO9305 3.2 7.6 1.0 C2 B:NO9305 3.2 7.8 1.0 C1 B:NO9305 3.2 8.6 1.0 CB B:CYS208 3.3 6.2 1.0 OD1 B:ASP124 3.5 7.8 1.0 ZN B:ZN301 3.5 6.7 1.0 O3 B:NO9305 4.0 7.3 1.0 ND1 B:HIS250 4.2 7.2 1.0 NE2 B:HIS189 4.2 5.5 1.0 O5 B:NO9305 4.2 8.7 1.0 CG B:HIS250 4.2 7.2 1.0 C4 B:NO9305 4.2 9.2 1.0 O2 B:NO9305 4.3 9.1 1.0 CB B:SER249 4.3 6.8 1.0 C3 B:NO9305 4.3 9.5 1.0 CE1 B:HIS189 4.4 6.5 1.0 CB B:ASP124 4.4 6.5 1.0 CA B:CYS208 4.5 6.4 1.0 NE2 B:HIS120 4.5 6.2 1.0 CE1 B:HIS120 4.5 6.9 1.0 OG B:SER249 4.6 7.0 1.0 O1 B:NO9305 4.8 8.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Ndm-1 Metallo-Beta-Lactamase in Complex with Inhibitor NO9


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 NO9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:19.0 occ:1.00 OD2 B:ASP223 2.0 13.8 1.0 OE1 A:GLU227 2.1 15.1 0.5 OE2 B:GLU152 2.1 15.7 1.0 OE1 B:GLU152 2.7 15.0 1.0 CD B:GLU152 2.7 15.1 1.0 CG B:ASP223 2.8 15.0 1.0 CD A:GLU227 2.8 16.5 0.5 OE2 A:GLU227 2.9 19.4 0.5 OD1 B:ASP223 2.9 19.2 1.0 O B:HOH575 3.9 13.4 1.0 NE2 A:HIS228 4.0 12.3 1.0 CG A:GLU227 4.1 15.0 0.5 CE1 A:HIS228 4.2 12.2 1.0 CB B:ASP223 4.2 11.4 1.0 CG B:GLU152 4.2 12.2 1.0 CG A:GLU227 4.2 15.1 0.5 NE2 B:HIS122 4.3 7.7 1.0 O B:HOH597 4.4 28.9 1.0 CD2 B:HIS122 4.8 7.6 1.0 O A:HOH882 4.8 24.3 1.0 CD A:GLU227 4.9 16.8 0.5 CB A:GLU227 4.9 13.2 0.5 O B:HOH430 4.9 17.4 1.0 CB A:GLU227 4.9 13.3 0.5 OE2 A:GLU227 5.0 21.4 0.5

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