Zinc in PDB 6ogo: Crystal Structure of Ndm-9 Metallo-Beta-Lactamase

The structure of Crystal Structure of Ndm-9 Metallo-Beta-Lactamase, PDB code: 6ogo was solved by J.E.Raczynska, B.Imiolczyk, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	61.46 / 1.43
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	122.929, 122.929, 38.501, 90.00, 90.00, 120.00
R / Rfree (%)	7.4 / 11.6

The structure of Crystal Structure of Ndm-9 Metallo-Beta-Lactamase also contains other interesting chemical elements:

Chlorine

(Cl)

9 atoms

The binding sites of Zinc atom in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase (pdb code 6ogo). 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-9 Metallo-Beta-Lactamase, PDB code: 6ogo:
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-9 Metallo-Beta-Lactamase


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-9 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:12.1 occ:1.00 O2 A:PO4306 2.0 11.3 1.0 NE2 A:HIS120 2.0 11.5 1.0 ND1 A:HIS122 2.0 11.6 1.0 NE2 A:HIS189 2.1 9.3 1.0 CD2 A:HIS189 3.0 10.9 1.0 CD2 A:HIS120 3.0 11.0 1.0 CE1 A:HIS120 3.0 10.5 1.0 O3 A:PO4306 3.0 11.5 1.0 P A:PO4306 3.0 11.8 1.0 CE1 A:HIS122 3.0 11.0 1.0 CG A:HIS122 3.0 13.5 1.0 CE1 A:HIS189 3.1 10.0 1.0 CB A:HIS122 3.3 11.1 1.0 SG A:CYS208 3.8 11.4 1.0 O1 A:PO4306 3.9 12.7 1.0 OD1 A:ASP124 4.0 13.3 1.0 ND1 A:HIS120 4.1 9.5 1.0 CG A:HIS120 4.1 11.1 1.0 CG A:HIS189 4.1 9.8 1.0 NE2 A:HIS122 4.2 12.3 1.0 CD2 A:HIS122 4.2 13.0 1.0 O4 A:PO4306 4.2 13.4 1.0 ND1 A:HIS189 4.2 10.2 1.0 ZN A:ZN302 4.3 12.7 1.0 CB A:CYS208 4.3 10.9 1.0 CG2 A:THR190 4.5 13.5 1.0 O A:HOH423 4.6 19.0 1.0 CA A:HIS122 4.8 9.9 1.0 OD2 A:ASP124 4.8 16.6 1.0 CG A:ASP124 4.9 12.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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-9 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:12.7 occ:1.00 O1 A:PO4306 2.0 12.7 1.0 NE2 A:HIS250 2.1 10.9 1.0 SG A:CYS208 2.3 11.4 1.0 CL A:CL303 2.4 13.8 1.0 CD2 A:HIS250 3.1 12.3 1.0 CE1 A:HIS250 3.1 11.7 1.0 P A:PO4306 3.2 11.8 1.0 CB A:CYS208 3.3 10.9 1.0 O2 A:PO4306 3.4 11.3 1.0 OD2 A:ASP124 3.7 16.6 1.0 CE1 A:HIS189 3.9 10.0 1.0 O3 A:PO4306 4.0 11.5 1.0 NE2 A:HIS189 4.1 9.3 1.0 CA A:CYS208 4.1 10.2 1.0 ND1 A:HIS250 4.2 11.1 1.0 CB A:SER249 4.2 11.3 1.0 CG A:HIS250 4.2 10.4 1.0 ZN A:ZN301 4.3 12.1 1.0 O4 A:PO4306 4.3 13.4 1.0 OG A:SER249 4.5 13.1 1.0 ND1 A:HIS189 4.6 10.2 1.0 CG A:ASP124 4.7 12.8 1.0 NZ A:LYS211 4.8 15.9 1.0 O A:HOH488 4.8 17.8 1.0 OD1 A:ASP124 4.9 13.3 1.0 CD2 A:HIS189 5.0 10.9 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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-9 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:14.3 occ:1.00 O2 B:PO4306 2.0 14.7 1.0 NE2 B:HIS189 2.0 12.9 1.0 NE2 B:HIS120 2.0 12.7 1.0 ND1 B:HIS122 2.1 14.7 1.0 CD2 B:HIS120 3.0 11.6 1.0 CD2 B:HIS189 3.0 12.8 1.0 CE1 B:HIS189 3.0 11.4 1.0 CE1 B:HIS122 3.0 14.7 1.0 P B:PO4306 3.0 15.2 1.0 O4 B:PO4306 3.0 16.8 1.0 CE1 B:HIS120 3.0 12.3 1.0 CG B:HIS122 3.1 14.6 1.0 CB B:HIS122 3.4 16.6 1.0 SG B:CYS208 3.8 14.6 1.0 O1 B:PO4306 3.8 13.4 1.0 OD1 B:ASP124 3.9 15.2 1.0 CG B:HIS120 4.1 11.5 1.0 ND1 B:HIS120 4.1 13.3 1.0 NE2 B:HIS122 4.1 15.2 1.0 ND1 B:HIS189 4.1 13.0 1.0 CG B:HIS189 4.1 12.6 1.0 CD2 B:HIS122 4.2 15.8 1.0 O3 B:PO4306 4.2 17.1 1.0 ZN B:ZN302 4.3 16.2 1.0 CB B:CYS208 4.3 10.7 1.0 CG2 B:THR190 4.5 14.6 1.0 O B:HOH421 4.6 32.9 1.0 CA B:HIS122 4.8 13.5 1.0 CG B:ASP124 4.8 15.9 1.0 OD2 B:ASP124 4.8 21.3 1.0 O B:HOH467 5.0 16.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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-9 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:16.2 occ:1.00 NE2 B:HIS250 2.0 13.5 1.0 O1 B:PO4306 2.0 13.4 1.0 SG B:CYS208 2.3 14.6 1.0 CL B:CL303 2.4 18.0 1.0 CD2 B:HIS250 3.0 13.3 1.0 CE1 B:HIS250 3.1 16.3 1.0 P B:PO4306 3.2 15.2 1.0 CB B:CYS208 3.3 10.7 1.0 O2 B:PO4306 3.4 14.7 1.0 OD2 B:ASP124 3.5 21.3 1.0 CE1 B:HIS189 3.9 11.4 1.0 O4 B:PO4306 4.0 16.8 1.0 CA B:CYS208 4.1 11.6 1.0 ND1 B:HIS250 4.1 16.0 1.0 CG B:HIS250 4.1 15.9 1.0 NE2 B:HIS189 4.2 12.9 1.0 CB B:SER249 4.2 13.5 1.0 ZN B:ZN301 4.3 14.3 1.0 O3 B:PO4306 4.3 17.1 1.0 CG B:ASP124 4.5 15.9 1.0 OG B:SER249 4.6 15.3 1.0 ND1 B:HIS189 4.6 13.0 1.0 NZ B:LYS211 4.8 20.9 1.0 OD1 B:ASP124 4.8 15.2 1.0 O B:HOH463 4.8 21.2 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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-9 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:15.7 occ:1.00 O2 C:PO4306 2.0 18.6 1.0 ND1 C:HIS122 2.0 19.5 1.0 NE2 C:HIS189 2.0 12.8 1.0 NE2 C:HIS120 2.0 15.0 1.0 CD2 C:HIS189 2.9 13.8 1.0 CD2 C:HIS120 3.0 15.2 1.0 CE1 C:HIS122 3.0 18.2 1.0 O1 C:PO4306 3.0 17.2 1.0 CG C:HIS122 3.0 15.4 1.0 CE1 C:HIS120 3.0 13.5 1.0 P C:PO4306 3.0 15.7 1.0 CE1 C:HIS189 3.1 15.4 1.0 CB C:HIS122 3.3 12.8 1.0 SG C:CYS208 3.8 15.1 1.0 O4 C:PO4306 3.9 15.3 1.0 OD1 C:ASP124 4.0 18.6 1.0 NE2 C:HIS122 4.1 17.2 1.0 CG C:HIS189 4.1 13.8 1.0 ND1 C:HIS120 4.1 15.0 1.0 CG C:HIS120 4.1 14.0 1.0 CD2 C:HIS122 4.1 17.8 1.0 ND1 C:HIS189 4.2 13.6 1.0 O3 C:PO4306 4.3 19.1 1.0 CB C:CYS208 4.3 13.0 1.0 ZN C:ZN302 4.3 16.9 1.0 CG2 C:THR190 4.5 14.6 1.0 O C:HOH421 4.6 23.7 1.0 CA C:HIS122 4.8 12.9 1.0 OD2 C:ASP124 4.8 19.3 1.0 CG C:ASP124 4.8 16.0 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Ndm-9 Metallo-Beta-Lactamase


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-9 Metallo-Beta-Lactamase within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:16.9 occ:1.00 O4 C:PO4306 2.0 15.3 1.0 NE2 C:HIS250 2.0 16.8 1.0 SG C:CYS208 2.3 15.1 1.0 CL C:CL303 2.4 19.1 1.0 CD2 C:HIS250 3.0 16.9 1.0 CE1 C:HIS250 3.1 15.0 1.0 P C:PO4306 3.1 15.7 1.0 CB C:CYS208 3.2 13.0 1.0 O2 C:PO4306 3.3 18.6 1.0 OD2 C:ASP124 3.6 19.3 1.0 CE1 C:HIS189 3.8 15.4 1.0 O1 C:PO4306 3.9 17.2 1.0 CA C:CYS208 4.1 12.5 1.0 NE2 C:HIS189 4.1 12.8 1.0 CG C:HIS250 4.2 15.9 1.0 ND1 C:HIS250 4.2 14.6 1.0 CB C:SER249 4.2 13.9 1.0 ZN C:ZN301 4.3 15.7 1.0 O3 C:PO4306 4.3 19.1 1.0 OG C:SER249 4.5 15.3 1.0 CG C:ASP124 4.6 16.0 1.0 ND1 C:HIS189 4.6 13.6 1.0 NZ C:LYS211 4.8 20.0 1.0 OD1 C:ASP124 4.9 18.6 1.0 O C:HOH451 4.9 21.6 1.0 CD2 C:HIS189 5.0 13.8 1.0

J.E.Raczynska, B.Imiolczyk, M.Komorowska, J.Czyrko, J.Sliwiak, K.Brzezinski, M.Jaskolski. Flexible Loop of New Delhi Metallo-Beta-Lactamase Modulates Its Activity Towards Different Substrates To Be Published.