Zinc in PDB 5wig: Structure of New Delhi Metallo-Beta-Lactamase 4 (Ndm-4)

The structure of Structure of New Delhi Metallo-Beta-Lactamase 4 (Ndm-4), PDB code: 5wig was solved by J.Vanpelt, C.Williams, R.C.Page, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.18 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.414, 59.154, 84.500, 90.00, 98.70, 90.00
R / Rfree (%)	20 / 22.5

The binding sites of Zinc atom in the Structure of New Delhi Metallo-Beta-Lactamase 4 (Ndm-4) (pdb code 5wig). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of New Delhi Metallo-Beta-Lactamase 4 (Ndm-4), PDB code: 5wig:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of New Delhi Metallo-Beta-Lactamase 4 (Ndm-4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:16.9 occ:1.00 NE2 A:HIS189 2.3 27.5 1.0 O A:HOH420 2.3 27.7 1.0 ND1 A:HIS122 2.4 19.5 1.0 NE2 A:HIS120 2.4 19.8 1.0 CD2 A:HIS189 2.9 22.7 1.0 CG A:HIS122 3.2 14.7 1.0 CD2 A:HIS120 3.3 24.8 1.0 CE1 A:HIS122 3.4 15.9 1.0 CB A:HIS122 3.4 13.1 1.0 CE1 A:HIS120 3.4 23.2 1.0 CE1 A:HIS189 3.5 27.5 1.0 ZN A:ZN302 3.7 20.1 1.0 O A:HOH606 3.9 29.4 1.0 SG A:CYS208 3.9 20.3 1.0 O A:HOH629 4.0 43.3 1.0 CB A:CYS208 4.1 20.9 1.0 OD1 A:ASP124 4.2 25.0 1.0 CG A:HIS189 4.2 23.5 1.0 CG2 A:THR190 4.3 17.7 1.0 CD2 A:HIS122 4.4 17.1 1.0 CG A:HIS120 4.4 17.5 1.0 NE2 A:HIS122 4.4 20.9 1.0 ND1 A:HIS189 4.4 26.0 1.0 ND1 A:HIS120 4.4 20.9 1.0 OD2 A:ASP124 4.8 24.9 1.0 CA A:HIS122 4.8 12.7 1.0 CG A:ASP124 4.9 22.3 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of New Delhi Metallo-Beta-Lactamase 4 (Ndm-4) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:20.1 occ:1.00 NE2 A:HIS250 2.3 20.9 1.0 OD2 A:ASP124 2.4 24.9 1.0 O A:HOH420 2.4 27.7 1.0 O A:HOH606 2.4 29.4 1.0 SG A:CYS208 2.5 20.3 1.0 CD2 A:HIS250 3.0 19.2 1.0 CG A:ASP124 3.3 22.3 1.0 CE1 A:HIS250 3.4 25.0 1.0 CB A:CYS208 3.5 20.9 1.0 OD1 A:ASP124 3.6 25.0 1.0 ZN A:ZN301 3.7 16.9 1.0 O A:HOH629 4.1 43.3 1.0 CB A:SER249 4.2 16.3 1.0 NE2 A:HIS189 4.2 27.5 1.0 CG A:HIS250 4.2 19.8 1.0 O A:HOH535 4.3 34.4 1.0 ND1 A:HIS250 4.4 25.9 1.0 CB A:ASP124 4.6 12.2 1.0 OG A:SER249 4.6 15.7 1.0 CA A:CYS208 4.6 17.3 1.0 CE1 A:HIS189 4.7 27.5 1.0 NE2 A:HIS120 4.8 19.8 1.0 O A:HOH636 4.9 45.4 1.0 CE1 A:HIS120 5.0 23.2 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of New Delhi Metallo-Beta-Lactamase 4 (Ndm-4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:15.5 occ:1.00 O B:HOH439 2.3 25.0 1.0 NE2 B:HIS189 2.3 19.1 1.0 ND1 B:HIS122 2.4 14.7 1.0 NE2 B:HIS120 2.4 18.8 1.0 CD2 B:HIS189 3.0 13.9 1.0 CG B:HIS122 3.2 14.8 1.0 CD2 B:HIS120 3.2 16.8 1.0 CB B:HIS122 3.3 14.8 1.0 CE1 B:HIS122 3.4 13.1 1.0 CE1 B:HIS120 3.4 20.2 1.0 CE1 B:HIS189 3.4 19.4 1.0 ZN B:ZN302 3.5 20.5 1.0 O B:HOH619 3.6 39.7 1.0 O B:HOH616 3.9 29.9 1.0 SG B:CYS208 3.9 17.1 1.0 OD1 B:ASP124 4.0 20.7 1.0 CB B:CYS208 4.0 15.8 1.0 CG B:HIS189 4.3 14.7 1.0 CG2 B:THR190 4.3 12.6 1.0 CD2 B:HIS122 4.4 15.9 1.0 CG B:HIS120 4.4 15.4 1.0 ND1 B:HIS189 4.4 19.0 1.0 NE2 B:HIS122 4.5 16.9 1.0 ND1 B:HIS120 4.5 17.5 1.0 OD2 B:ASP124 4.8 23.1 1.0 CG B:ASP124 4.8 19.9 1.0 CA B:HIS122 4.8 12.4 1.0 O B:HOH620 4.9 33.8 1.0 O B:HOH493 5.0 22.1 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of New Delhi Metallo-Beta-Lactamase 4 (Ndm-4) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:20.5 occ:1.00 O B:HOH439 2.3 25.0 1.0 OD2 B:ASP124 2.3 23.1 1.0 NE2 B:HIS250 2.4 20.1 1.0 O B:HOH616 2.4 29.9 1.0 SG B:CYS208 2.5 17.1 1.0 CG B:ASP124 3.1 19.9 1.0 CD2 B:HIS250 3.2 16.6 1.0 OD1 B:ASP124 3.3 20.7 1.0 CE1 B:HIS250 3.4 16.9 1.0 CB B:CYS208 3.4 15.8 1.0 ZN B:ZN301 3.5 15.5 1.0 O B:HOH619 3.6 39.7 1.0 O B:HOH492 4.2 29.7 1.0 NE2 B:HIS189 4.3 19.1 1.0 CB B:SER249 4.3 16.0 1.0 CB B:ASP124 4.4 13.5 1.0 CG B:HIS250 4.4 20.0 1.0 ND1 B:HIS250 4.4 17.6 1.0 CE1 B:HIS189 4.6 19.4 1.0 CA B:CYS208 4.7 14.6 1.0 NE2 B:HIS120 4.7 18.8 1.0 OG B:SER249 4.7 15.4 1.0 CE1 B:HIS120 4.9 20.2 1.0

A.C.Stewart, C.R.Bethel, J.Vanpelt, A.Bergstrom, Z.Cheng, C.G.Miller, C.Williams, R.Poth, M.Morris, O.Lahey, J.C.Nix, D.L.Tierney, R.C.Page, M.W.Crowder, R.A.Bonomo, W.Fast. Clinical Variants of New Delhi Metallo-Beta-Lactamase Are Evolving to Overcome Zinc Scarcity. Acs Infect Dis. V. 3 927 2017.
ISSN: ESSN 2373-8227
PubMed: 28965402
DOI: 10.1021/ACSINFECDIS.7B00128