Zinc in PDB 5wih: Structure of New Delhi Metallo-Beta-Lactamase 12 (Ndm-12)

The structure of Structure of New Delhi Metallo-Beta-Lactamase 12 (Ndm-12), PDB code: 5wih 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)	33.72 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.619, 58.697, 41.674, 90.00, 98.64, 90.00
R / Rfree (%)	18.7 / 22.1

The binding sites of Zinc atom in the Structure of New Delhi Metallo-Beta-Lactamase 12 (Ndm-12) (pdb code 5wih). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of New Delhi Metallo-Beta-Lactamase 12 (Ndm-12), PDB code: 5wih:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of New Delhi Metallo-Beta-Lactamase 12 (Ndm-12)


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 12 (Ndm-12) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:23.3 occ:1.00 O A:HOH404 2.3 35.7 1.0 NE2 A:HIS120 2.4 18.1 1.0 NE2 A:HIS189 2.4 22.9 1.0 ND1 A:HIS122 2.4 26.7 1.0 CD2 A:HIS189 2.9 22.4 1.0 CG A:HIS122 2.9 21.7 1.0 CD2 A:HIS120 3.1 18.4 1.0 CB A:HIS122 3.2 19.3 1.0 CE1 A:HIS122 3.3 25.6 1.0 CE1 A:HIS120 3.5 20.9 1.0 CE1 A:HIS189 3.6 23.5 1.0 ZN A:ZN302 3.8 22.2 1.0 SG A:CYS208 3.9 20.1 1.0 CD2 A:HIS122 3.9 23.3 1.0 O A:HOH555 4.1 33.7 1.0 NE2 A:HIS122 4.1 23.1 1.0 CB A:CYS208 4.1 19.4 1.0 CG A:HIS189 4.2 20.0 1.0 OD1 A:ASP124 4.3 29.5 1.0 CG2 A:THR190 4.3 18.6 1.0 CG A:HIS120 4.3 17.0 1.0 ND1 A:HIS120 4.5 19.6 1.0 ND1 A:HIS189 4.5 22.1 1.0 OD2 A:ASP124 4.6 27.6 1.0 O A:HOH576 4.7 45.0 1.0 CA A:HIS122 4.7 17.3 1.0 CG A:ASP124 4.9 23.6 1.0

Zinc binding site 2 out of 2 in the Structure of New Delhi Metallo-Beta-Lactamase 12 (Ndm-12)


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 12 (Ndm-12) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:22.2 occ:1.00 SG A:CYS208 2.3 20.1 1.0 NE2 A:HIS250 2.3 19.8 1.0 OD2 A:ASP124 2.3 27.6 1.0 O A:HOH404 2.4 35.7 1.0 O A:HOH555 2.4 33.7 1.0 CD2 A:HIS250 3.1 19.0 1.0 CG A:ASP124 3.2 23.6 1.0 CB A:CYS208 3.4 19.4 1.0 CE1 A:HIS250 3.4 20.4 1.0 OD1 A:ASP124 3.5 29.5 1.0 ZN A:ZN301 3.8 23.3 1.0 NE2 A:HIS189 4.2 22.9 1.0 CB A:SER249 4.2 17.9 1.0 CG A:HIS250 4.3 19.8 1.0 ND1 A:HIS250 4.4 19.7 1.0 O A:HOH549 4.5 38.3 1.0 CB A:ASP124 4.5 20.1 1.0 CA A:CYS208 4.6 18.5 1.0 OG A:SER249 4.6 20.2 1.0 CE1 A:HIS189 4.6 23.5 1.0 NE2 A:HIS120 4.7 18.1 1.0 O A:HOH585 4.8 41.8 1.0 CE1 A:HIS120 5.0 20.9 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