Zinc in PDB 6c89: Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics

The structure of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics, PDB code: 6c89 was solved by T.Palzkill, Z.Sun, B.Sankaran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.24 / 1.75
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.167, 68.861, 68.441, 92.23, 77.03, 91.84
R / Rfree (%)	15.6 / 20

The structure of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics (pdb code 6c89). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics, PDB code: 6c89:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:20.7 occ:0.90 NE2 A:HIS263 2.0 17.3 1.0 O A:HOH585 2.1 18.1 1.0 OD2 A:ASP120 2.1 24.3 1.0 SG A:CYS221 2.2 18.3 1.0 CE1 A:HIS263 2.9 18.5 1.0 O A:HOH623 2.9 28.3 1.0 CD2 A:HIS263 3.1 20.5 1.0 CG A:ASP120 3.1 18.0 1.0 CB A:CYS221 3.4 15.7 1.0 OD1 A:ASP120 3.4 16.3 1.0 ZN A:ZN402 3.5 16.7 1.0 ND1 A:HIS263 4.1 16.7 1.0 CB A:SER262 4.1 15.5 1.0 CG A:HIS263 4.2 20.1 1.0 NE2 A:HIS196 4.3 15.4 1.0 CB A:ASP120 4.4 10.8 1.0 NE2 A:HIS116 4.4 10.4 1.0 CE1 A:HIS116 4.5 17.8 1.0 OG A:SER262 4.5 20.0 1.0 CA A:CYS221 4.6 13.6 1.0 CE1 A:HIS196 4.6 16.4 1.0 CE A:LYS121 4.9 21.0 1.0 NH1 A:ARG224 5.0 21.4 1.0

Zinc binding site 2 out of 8 in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:16.7 occ:1.00 O A:HOH585 1.9 18.1 1.0 ND1 A:HIS118 2.0 13.7 1.0 NE2 A:HIS116 2.1 10.4 1.0 NE2 A:HIS196 2.1 15.4 1.0 CD2 A:HIS196 2.9 13.3 1.0 CE1 A:HIS118 2.9 13.8 1.0 CD2 A:HIS116 3.0 12.7 1.0 CE1 A:HIS116 3.0 17.8 1.0 CG A:HIS118 3.0 14.1 1.0 CE1 A:HIS196 3.2 16.4 1.0 CB A:HIS118 3.4 14.2 1.0 ZN A:ZN401 3.5 20.7 0.9 SG A:CYS221 3.8 18.3 1.0 CB A:CYS221 3.9 15.7 1.0 OD1 A:ASP120 4.0 16.3 1.0 NE2 A:HIS118 4.0 18.6 1.0 ND1 A:HIS116 4.1 13.6 1.0 CD2 A:HIS118 4.1 14.8 1.0 CG A:HIS196 4.1 12.2 1.0 CG A:HIS116 4.1 12.6 1.0 ND1 A:HIS196 4.2 15.8 1.0 O A:HOH623 4.3 28.3 1.0 CG2 A:THR197 4.5 12.3 1.0 OD2 A:ASP120 4.6 24.3 1.0 CG A:ASP120 4.8 18.0 1.0 CA A:HIS118 4.9 13.3 1.0

Zinc binding site 3 out of 8 in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:21.9 occ:0.87 NE2 B:HIS263 2.1 24.1 1.0 O B:HOH608 2.1 19.1 1.0 OD2 B:ASP120 2.1 22.9 1.0 SG B:CYS221 2.3 19.9 1.0 O B:HOH588 2.3 31.9 1.0 CD2 B:HIS263 3.0 22.7 1.0 CE1 B:HIS263 3.1 19.6 1.0 CG B:ASP120 3.1 20.2 1.0 CB B:CYS221 3.4 19.9 1.0 OD1 B:ASP120 3.5 18.9 1.0 ZN B:ZN402 3.6 18.4 1.0 ND1 B:HIS263 4.2 24.2 1.0 CG B:HIS263 4.2 19.3 1.0 CB B:SER262 4.2 17.6 1.0 CB B:ASP120 4.4 15.1 1.0 CE1 B:HIS116 4.5 18.3 1.0 CA B:CYS221 4.5 17.6 1.0 NE2 B:HIS116 4.6 17.8 1.0 OG B:SER262 4.6 21.3 1.0 CE B:LYS121 4.8 23.2 1.0 O B:HOH516 4.9 32.3 1.0

Zinc binding site 4 out of 8 in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:18.4 occ:1.00 ND1 B:HIS118 1.9 16.0 1.0 O B:HOH608 2.1 19.1 1.0 NE2 B:HIS116 2.1 17.8 1.0 CE1 B:HIS118 2.9 19.3 1.0 CG B:HIS118 3.0 13.2 1.0 CE1 B:HIS116 3.0 18.3 1.0 CD2 B:HIS116 3.1 17.3 1.0 CB B:HIS118 3.4 13.6 1.0 ZN B:ZN401 3.6 21.9 0.9 O B:HOH588 3.8 31.9 1.0 SG B:CYS221 3.9 19.9 1.0 NE2 B:HIS118 4.0 21.0 1.0 CD2 B:HIS118 4.1 19.2 1.0 CB B:CYS221 4.1 19.9 1.0 ND1 B:HIS116 4.1 17.9 1.0 OD1 B:ASP120 4.1 18.9 1.0 CG B:HIS116 4.2 14.3 1.0 CG2 B:THR197 4.4 16.9 1.0 OD2 B:ASP120 4.7 22.9 1.0 CA B:HIS118 4.9 15.1 1.0 CG B:ASP120 4.9 20.2 1.0

Zinc binding site 5 out of 8 in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:19.3 occ:1.00 O C:HOH623 2.0 18.2 1.0 NE2 C:HIS263 2.0 14.9 1.0 OD2 C:ASP120 2.0 19.1 1.0 SG C:CYS221 2.2 15.3 1.0 CE1 C:HIS263 3.0 14.7 1.0 CG C:ASP120 3.0 16.1 1.0 CD2 C:HIS263 3.1 14.2 1.0 CB C:CYS221 3.4 15.5 1.0 OD1 C:ASP120 3.4 15.5 1.0 ZN C:ZN402 3.5 16.2 1.0 ND1 C:HIS263 4.1 15.6 1.0 CB C:SER262 4.1 11.1 1.0 CG C:HIS263 4.2 16.7 1.0 NE2 C:HIS196 4.3 10.6 1.0 CB C:ASP120 4.4 14.3 1.0 NE2 C:HIS116 4.4 13.4 1.0 CE1 C:HIS116 4.4 15.2 1.0 OG C:SER262 4.5 16.9 1.0 CA C:CYS221 4.6 13.0 1.0 CE1 C:HIS196 4.7 13.8 1.0 CE C:LYS121 4.9 19.1 1.0 O C:HOH524 4.9 23.6 1.0 CD C:LYS121 4.9 18.5 1.0 CG C:LYS121 5.0 16.3 1.0

Zinc binding site 6 out of 8 in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:16.2 occ:1.00 O C:HOH623 2.0 18.2 1.0 ND1 C:HIS118 2.0 15.3 1.0 NE2 C:HIS196 2.1 10.6 1.0 NE2 C:HIS116 2.1 13.4 1.0 CD2 C:HIS196 2.9 10.8 1.0 CE1 C:HIS118 3.0 18.4 1.0 CE1 C:HIS116 3.0 15.2 1.0 CG C:HIS118 3.0 15.8 1.0 CD2 C:HIS116 3.0 11.1 1.0 CE1 C:HIS196 3.2 13.8 1.0 CB C:HIS118 3.4 10.6 1.0 ZN C:ZN401 3.5 19.3 1.0 SG C:CYS221 3.9 15.3 1.0 CB C:CYS221 3.9 15.5 1.0 OD1 C:ASP120 4.1 15.5 1.0 NE2 C:HIS118 4.1 18.2 1.0 ND1 C:HIS116 4.1 13.4 1.0 CG C:HIS196 4.1 11.3 1.0 CD2 C:HIS118 4.1 16.5 1.0 CG C:HIS116 4.1 13.1 1.0 ND1 C:HIS196 4.2 12.8 1.0 CG2 C:THR197 4.6 12.0 1.0 OD2 C:ASP120 4.6 19.1 1.0 CG C:ASP120 4.8 16.1 1.0 CA C:HIS118 4.9 10.7 1.0

Zinc binding site 7 out of 8 in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:20.9 occ:0.92 O D:HOH620 2.0 16.8 1.0 OD2 D:ASP120 2.0 18.6 1.0 NE2 D:HIS263 2.1 17.3 1.0 SG D:CYS221 2.2 17.4 1.0 CG D:ASP120 3.0 16.6 1.0 CE1 D:HIS263 3.1 18.3 1.0 CD2 D:HIS263 3.1 20.1 1.0 OD1 D:ASP120 3.3 22.1 1.0 CB D:CYS221 3.4 17.2 1.0 ZN D:ZN402 3.5 16.7 1.0 CB D:SER262 4.2 15.7 1.0 ND1 D:HIS263 4.2 17.2 1.0 CG D:HIS263 4.2 17.3 1.0 CE1 D:HIS116 4.3 17.7 1.0 NE2 D:HIS116 4.3 12.9 1.0 NE2 D:HIS196 4.3 14.1 1.0 CB D:ASP120 4.4 12.7 1.0 CE D:LYS121 4.5 26.1 1.0 OG D:SER262 4.5 19.5 1.0 CA D:CYS221 4.6 14.6 1.0 CE1 D:HIS196 4.7 14.8 1.0 NH1 D:ARG224 4.8 23.1 1.0

Zinc binding site 8 out of 8 in the Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Ndm-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements For the Hydrolysis of Penicillin Versus Carbapenem Antibiotics within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:16.7 occ:1.00 NE2 D:HIS196 2.0 14.1 1.0 NE2 D:HIS116 2.0 12.9 1.0 O D:HOH620 2.1 16.8 1.0 ND1 D:HIS118 2.1 17.8 1.0 CD2 D:HIS196 2.9 15.0 1.0 CD2 D:HIS116 2.9 15.2 1.0 CE1 D:HIS116 3.0 17.7 1.0 CE1 D:HIS196 3.0 14.8 1.0 CE1 D:HIS118 3.1 11.6 1.0 CG D:HIS118 3.1 15.9 1.0 CB D:HIS118 3.4 13.8 1.0 ZN D:ZN401 3.5 20.9 0.9 SG D:CYS221 3.8 17.4 1.0 CB D:CYS221 3.9 17.2 1.0 ND1 D:HIS116 4.1 16.6 1.0 CG D:HIS116 4.1 15.8 1.0 CG D:HIS196 4.1 10.6 1.0 ND1 D:HIS196 4.1 14.3 1.0 OD1 D:ASP120 4.1 22.1 1.0 NE2 D:HIS118 4.2 18.2 1.0 CD2 D:HIS118 4.2 16.9 1.0 CG2 D:THR197 4.5 14.8 1.0 OD2 D:ASP120 4.7 18.6 1.0 CA D:HIS118 4.8 10.0 1.0 CG D:ASP120 4.9 16.6 1.0

Z.Sun, L.Hu, B.Sankaran, B.V.V.Prasad, T.Palzkill. Differential Active Site Requirements For Ndm-1 Beta-Lactamase Hydrolysis of Carbapenem Versus Penicillin and Cephalosporin Antibiotics. Nat Commun V. 9 4524 2018.
ISSN: ESSN 2041-1723
PubMed: 30375382
DOI: 10.1038/S41467-018-06839-1