Zinc in PDB 3s0z: Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1)

The structure of Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1), PDB code: 3s0z was solved by Y.Guo, J.Wang, G.J.Niu, W.Q.Shui, Y.N.Sun, Z.Y.Lou, Z.H.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	40.696, 40.696, 215.292, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 26.7

The binding sites of Zinc atom in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1) (pdb code 3s0z). 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 New Delhi Metallo-Beta-Lactamase (Ndm-1), PDB code: 3s0z:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1)


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 New Delhi Metallo-Beta-Lactamase (Ndm-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:11.8 occ:1.00 O A:HOH368 2.0 27.3 1.0 SG A:CYS208 2.0 16.8 1.0 OD2 A:ASP124 2.8 18.1 1.0 ZN A:ZN1002 3.1 38.5 1.0 NE2 A:HIS250 3.2 15.7 1.0 CB A:CYS208 3.7 14.6 1.0 NE2 A:HIS189 3.7 10.3 1.0 CD2 A:HIS250 3.8 16.9 1.0 CG A:ASP124 3.9 16.9 1.0 CE1 A:HIS189 4.1 12.8 1.0 CE1 A:HIS250 4.3 14.9 1.0 CA A:CYS208 4.6 14.5 1.0 NZ A:LYS211 4.6 6.1 1.0 OD1 A:ASP124 4.6 16.3 1.0 CD2 A:HIS189 4.7 11.0 1.0 CB A:ASP124 4.8 15.6 1.0 OG A:SER249 4.9 20.7 1.0 CE A:LYS125 4.9 12.7 1.0 CE A:LYS211 4.9 6.2 1.0 CB A:ASN220 5.0 20.2 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1)


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 New Delhi Metallo-Beta-Lactamase (Ndm-1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:38.5 occ:1.00 NE2 A:HIS189 2.2 10.3 1.0 CD2 A:HIS189 2.9 11.0 1.0 NE2 A:HIS120 3.0 16.4 1.0 CD2 A:HIS122 3.0 12.8 1.0 SG A:CYS208 3.1 16.8 1.0 ZN A:ZN1001 3.1 11.8 1.0 CG A:HIS122 3.1 13.5 1.0 OD2 A:ASP124 3.2 18.1 1.0 CE1 A:HIS189 3.4 12.8 1.0 OD1 A:ASP124 3.4 16.3 1.0 CB A:HIS122 3.6 14.4 1.0 NE2 A:HIS122 3.6 11.2 1.0 CG A:ASP124 3.7 16.9 1.0 ND1 A:HIS122 3.7 13.0 1.0 CB A:CYS208 3.8 14.6 1.0 CE1 A:HIS120 3.8 17.2 1.0 CE1 A:HIS122 3.9 12.9 1.0 CD2 A:HIS120 4.1 16.5 1.0 O A:HOH368 4.1 27.3 1.0 CG A:HIS189 4.2 12.4 1.0 ND1 A:HIS189 4.4 13.3 1.0 CG A:LYS125 4.8 16.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1)


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 New Delhi Metallo-Beta-Lactamase (Ndm-1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:20.2 occ:1.00 SG B:CYS208 1.9 24.4 1.0 OD2 B:ASP124 2.7 21.1 1.0 O B:HOH341 2.8 30.5 1.0 NE2 B:HIS250 3.1 21.0 1.0 CE1 B:HIS250 3.2 19.1 1.0 CB B:CYS208 3.3 19.7 1.0 CG B:ASP124 3.6 20.1 1.0 ZN B:ZN1002 3.8 25.9 1.0 O B:HOH44 3.8 19.3 1.0 CA B:CYS208 4.1 19.5 1.0 CD2 B:HIS250 4.2 20.2 1.0 NE2 B:HIS189 4.3 12.4 1.0 OD1 B:ASP124 4.3 21.3 1.0 CE1 B:HIS189 4.3 12.4 1.0 ND1 B:HIS250 4.4 19.1 1.0 CB B:ASP124 4.5 18.4 1.0 CG B:HIS250 4.9 19.9 1.0 O B:CYS208 4.9 19.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of New Delhi Metallo-Beta-Lactamase (Ndm-1)


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 New Delhi Metallo-Beta-Lactamase (Ndm-1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:25.9 occ:1.00 NE2 B:HIS120 2.1 10.9 1.0 ND1 B:HIS122 2.5 17.8 1.0 CB B:HIS122 2.9 17.2 1.0 CE1 B:HIS120 2.9 8.7 1.0 NE2 B:HIS189 2.9 12.4 1.0 CG B:HIS122 3.1 17.4 1.0 CD2 B:HIS189 3.1 12.6 1.0 CD2 B:HIS120 3.2 11.7 1.0 SG B:CYS208 3.2 24.4 1.0 CB B:CYS208 3.4 19.7 1.0 OD1 B:ASP124 3.5 21.3 1.0 OD2 B:ASP124 3.6 21.1 1.0 CE1 B:HIS122 3.7 16.4 1.0 ZN B:ZN1001 3.8 20.2 1.0 CG B:ASP124 4.0 20.1 1.0 CE1 B:HIS189 4.1 12.4 1.0 ND1 B:HIS120 4.1 11.4 1.0 CG B:HIS120 4.3 12.9 1.0 CG B:HIS189 4.3 12.6 1.0 CD2 B:HIS122 4.3 16.7 1.0 CA B:HIS122 4.4 16.9 1.0 CG B:LYS125 4.5 15.2 1.0 NE2 B:HIS122 4.6 15.8 1.0 ND1 B:HIS189 4.8 10.8 1.0 O B:HOH341 4.8 30.5 1.0 CG2 B:THR190 4.9 9.8 1.0 CA B:CYS208 4.9 19.5 1.0 C B:HIS122 5.0 17.0 1.0 N B:HIS122 5.0 16.2 1.0

Y.Guo, J.Wang, G.Niu, W.Shui, Y.Sun, H.Zhou, Y.Zhang, C.Yang, Z.Lou, Z.Rao. A Structural View of the Antibiotic Degradation Enzyme Ndm-1 From A Superbug. Protein Cell 2011.
ISSN: ESSN 1674-8018
PubMed: 21637961
DOI: 10.1007/S13238-011-1055-9