Zinc in PDB 4eyb: Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin

All present enzymatic activity of Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin, PDB code: 4eyb was solved by N.C.J.Strynadka, D.T.King, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.42 / 1.16
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.200, 79.370, 134.150, 90.00, 90.00, 90.00
R / Rfree (%)	13.5 / 16.4

The binding sites of Zinc atom in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin (pdb code 4eyb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin, PDB code: 4eyb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Bound to Hydrolyzed Oxacillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:7.6 occ:0.90 NE2 A:HIS250 2.0 7.1 1.0 NAP A:0WO303 2.1 8.6 1.0 OD2 A:ASP124 2.1 8.0 1.0 OAH A:0WO303 2.2 9.1 1.0 SG A:CYS208 2.4 7.1 1.0 O A:HOH598 2.9 10.8 1.0 CAT A:0WO303 3.0 8.9 1.0 CD2 A:HIS250 3.0 7.8 1.0 CE1 A:HIS250 3.0 7.5 1.0 CBB A:0WO303 3.0 8.8 1.0 CB A:0WO303 3.2 10.2 1.0 CG A:ASP124 3.3 7.5 1.0 CB A:CYS208 3.4 6.9 1.0 CAC A:0WO303 3.6 10.8 1.0 OD1 A:ASP124 3.8 8.2 1.0 CBC A:0WO303 3.9 8.9 1.0 ND1 A:HIS250 4.1 8.2 1.0 CG A:HIS250 4.1 8.0 1.0 OAE A:0WO303 4.2 10.7 1.0 CB A:SER249 4.2 7.9 1.0 CA A:0WO303 4.3 10.3 1.0 O A:0WO303 4.4 11.1 1.0 SAR A:0WO303 4.5 11.8 1.0 CA A:CYS208 4.5 6.6 1.0 CB A:ASP124 4.5 7.8 1.0 ZN A:ZN302 4.5 7.7 0.9 OG A:SER249 4.6 7.6 1.0 NE2 A:HIS189 4.8 7.1 1.0 CE1 A:HIS189 4.8 7.0 1.0 C A:0WO303 4.8 10.4 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Bound to Hydrolyzed Oxacillin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:7.7 occ:0.90 ND1 A:HIS122 1.9 7.9 1.0 O A:HOH598 2.0 10.8 1.0 NE2 A:HIS189 2.0 7.1 1.0 NE2 A:HIS120 2.1 8.1 1.0 O A:0WO303 2.5 11.1 1.0 CE1 A:HIS122 2.9 8.1 1.0 CG A:HIS122 3.0 7.3 1.0 CD2 A:HIS189 3.0 7.1 1.0 CE1 A:HIS189 3.0 7.0 1.0 CE1 A:HIS120 3.1 7.4 1.0 CD2 A:HIS120 3.1 8.3 1.0 CB A:HIS122 3.3 6.7 1.0 C A:0WO303 3.3 10.4 1.0 CA A:0WO303 3.9 10.3 1.0 NAP A:0WO303 4.0 8.6 1.0 NE2 A:HIS122 4.0 11.0 1.0 CD2 A:HIS122 4.1 9.1 1.0 ND1 A:HIS189 4.1 6.7 1.0 CG A:HIS189 4.2 6.0 1.0 OD1 A:ASP124 4.2 8.2 1.0 ND1 A:HIS120 4.2 7.4 1.0 OXT A:0WO303 4.2 13.2 1.0 CG A:HIS120 4.3 6.5 1.0 CG2 A:THR190 4.4 8.1 1.0 SG A:CYS208 4.4 7.1 1.0 CB A:CYS208 4.5 6.9 1.0 ZN A:ZN301 4.5 7.6 0.9 CB A:0WO303 4.6 10.2 1.0 O A:HOH449 4.7 18.7 1.0 CA A:HIS122 4.8 6.9 1.0 CBB A:0WO303 4.9 8.8 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Bound to Hydrolyzed Oxacillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:7.7 occ:0.90 ND1 B:HIS122 1.9 8.0 1.0 O B:HOH558 2.0 12.1 1.0 NE2 B:HIS189 2.0 7.6 1.0 NE2 B:HIS120 2.1 8.1 1.0 O B:0WO301 2.5 12.1 1.0 CE1 B:HIS122 2.9 9.2 1.0 CG B:HIS122 3.0 6.9 1.0 CD2 B:HIS189 3.0 7.2 1.0 CE1 B:HIS189 3.0 6.8 1.0 CE1 B:HIS120 3.1 8.2 1.0 CD2 B:HIS120 3.1 7.2 1.0 CB B:HIS122 3.3 6.1 1.0 C B:0WO301 3.4 10.7 1.0 CA B:0WO301 3.9 9.8 1.0 NAP B:0WO301 4.0 9.8 1.0 NE2 B:HIS122 4.1 9.9 1.0 CD2 B:HIS122 4.1 9.0 1.0 ND1 B:HIS189 4.1 7.0 1.0 CG B:HIS189 4.2 6.2 1.0 OD1 B:ASP124 4.2 8.7 1.0 ND1 B:HIS120 4.2 8.2 1.0 CG B:HIS120 4.3 6.9 1.0 CG2 B:THR190 4.3 7.9 1.0 OXT B:0WO301 4.3 16.3 1.0 SG B:CYS208 4.4 7.8 1.0 CB B:CYS208 4.5 7.2 1.0 CB B:0WO301 4.5 10.9 1.0 ZN B:ZN303 4.6 8.0 0.9 O B:HOH561 4.6 18.8 1.0 CA B:HIS122 4.8 6.2 1.0 CBB B:0WO301 4.9 10.1 1.0 OD2 B:ASP124 5.0 8.6 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Bound to Hydrolyzed Oxacillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:8.0 occ:0.90 NE2 B:HIS250 2.0 7.8 1.0 NAP B:0WO301 2.1 9.8 1.0 OAH B:0WO301 2.1 10.6 1.0 OD2 B:ASP124 2.2 8.6 1.0 SG B:CYS208 2.4 7.8 1.0 CAT B:0WO301 2.9 8.9 1.0 CD2 B:HIS250 3.0 9.3 1.0 O B:HOH558 3.0 12.1 1.0 CE1 B:HIS250 3.0 8.8 1.0 CBB B:0WO301 3.0 10.1 1.0 CB B:0WO301 3.2 10.9 1.0 CG B:ASP124 3.3 8.4 1.0 CB B:CYS208 3.4 7.2 1.0 CAC B:0WO301 3.7 11.8 1.0 OD1 B:ASP124 3.8 8.7 1.0 CBC B:0WO301 3.9 9.4 1.0 ND1 B:HIS250 4.1 9.2 1.0 CG B:HIS250 4.1 10.0 1.0 OAE B:0WO301 4.2 10.6 1.0 CB B:SER249 4.2 8.2 1.0 CA B:0WO301 4.3 9.8 1.0 O B:0WO301 4.4 12.1 1.0 CA B:CYS208 4.5 7.3 1.0 SAR B:0WO301 4.5 12.2 1.0 CB B:ASP124 4.5 7.6 1.0 ZN B:ZN302 4.6 7.7 0.9 OG B:SER249 4.6 8.7 1.0 NE2 B:HIS189 4.8 7.6 1.0 C B:0WO301 4.8 10.7 1.0 CE1 B:HIS189 4.8 6.8 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Ndm-1 Bound to Hydrolyzed Oxacillin


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 Bound to Hydrolyzed Oxacillin within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn304 b:12.5 occ:0.50 O B:HOH562 1.9 27.5 1.0 OD2 B:ASP223 2.0 14.3 1.0 OE2 B:GLU152 2.5 25.8 1.0 OE1 B:GLU152 2.6 17.4 1.0 CD B:GLU152 2.8 13.7 1.0 CG B:ASP223 2.9 13.0 1.0 OD1 B:ASP223 2.9 20.6 1.0 NE2 B:HIS122 4.0 9.9 1.0 O B:HOH413 4.0 13.4 1.0 CB B:ASP223 4.3 11.5 1.0 CG B:GLU152 4.3 10.7 1.0 O B:HOH525 4.5 33.7 1.0 CD2 B:HIS122 4.7 9.0 1.0

D.T.King, L.J.Worrall, R.Gruninger, N.C.Strynadka. New Delhi Metallo-Beta-Lactamase: Structural Insights Into Beta-Lactam Recognition and Inhibition J.Am.Chem.Soc. V. 134 11362 2012.
ISSN: ISSN 0002-7863
PubMed: 22713171
DOI: 10.1021/JA303579D