Zinc in PDB 6v1m: Structure of Ndm-1 Bound to QPX7728 at 1.05 A

All present enzymatic activity of Structure of Ndm-1 Bound to QPX7728 at 1.05 A:
3.5.2.6;

The structure of Structure of Ndm-1 Bound to QPX7728 at 1.05 A, PDB code: 6v1m was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.26 / 1.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.400, 60.240, 42.060, 90.00, 98.46, 90.00
R / Rfree (%)	14.1 / 15.8

The structure of Structure of Ndm-1 Bound to QPX7728 at 1.05 A also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Zinc atom in the Structure of Ndm-1 Bound to QPX7728 at 1.05 A (pdb code 6v1m). 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 Ndm-1 Bound to QPX7728 at 1.05 A, PDB code: 6v1m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Ndm-1 Bound to QPX7728 at 1.05 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Ndm-1 Bound to QPX7728 at 1.05 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:9.8 occ:0.96 O14 A:QNA303 1.9 9.9 1.0 NE2 A:HIS189 2.0 10.2 1.0 ND1 A:HIS122 2.0 10.4 1.0 NE2 A:HIS120 2.1 9.1 1.0 O13 A:QNA303 2.7 12.1 1.0 B12 A:QNA303 2.8 11.0 1.0 CD2 A:HIS189 3.0 10.4 1.0 CG A:HIS122 3.0 9.9 1.0 CE1 A:HIS122 3.0 11.5 1.0 CE1 A:HIS189 3.0 10.7 1.0 CD2 A:HIS120 3.0 8.8 1.0 CE1 A:HIS120 3.0 9.7 1.0 CB A:HIS122 3.3 9.0 1.0 O11 A:QNA303 3.7 11.2 1.0 C15 A:QNA303 4.1 12.2 1.0 SG A:CYS208 4.1 9.0 1.0 OD1 A:ASP124 4.1 8.7 1.0 NE2 A:HIS122 4.1 11.9 1.0 ND1 A:HIS189 4.1 11.1 1.0 ND1 A:HIS120 4.1 9.6 1.0 CD2 A:HIS122 4.1 11.1 1.0 CG A:HIS189 4.1 11.0 1.0 CG A:HIS120 4.2 8.5 1.0 ZN A:ZN302 4.2 9.2 0.9 CG2 A:THR190 4.2 11.9 1.0 CB A:CYS208 4.4 10.2 1.0 O A:HOH578 4.7 22.5 1.0 CA A:HIS122 4.8 8.4 1.0 C10 A:QNA303 4.8 12.1 1.0 O01 A:QNA303 4.8 11.2 1.0 OD2 A:ASP124 4.8 9.1 1.0 CG A:ASP124 4.9 8.1 1.0

Zinc binding site 2 out of 2 in the Structure of Ndm-1 Bound to QPX7728 at 1.05 A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Ndm-1 Bound to QPX7728 at 1.05 A within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:9.2 occ:0.88 NE2 A:HIS250 2.1 9.7 1.0 O11 A:QNA303 2.1 11.2 1.0 OD2 A:ASP124 2.2 9.1 1.0 O01 A:QNA303 2.2 11.2 1.0 SG A:CYS208 2.3 9.0 1.0 C10 A:QNA303 2.9 12.1 1.0 O14 A:QNA303 3.0 9.9 1.0 CE1 A:HIS250 3.0 10.2 1.0 CD2 A:HIS250 3.0 10.2 1.0 C02 A:QNA303 3.1 12.7 1.0 B12 A:QNA303 3.2 11.0 1.0 CG A:ASP124 3.3 8.1 1.0 C04 A:QNA303 3.3 13.3 1.0 CB A:CYS208 3.3 10.2 1.0 OD1 A:ASP124 3.7 8.7 1.0 C15 A:QNA303 4.1 12.2 1.0 C09 A:QNA303 4.1 12.8 1.0 ND1 A:HIS250 4.1 10.6 1.0 CG A:HIS250 4.2 10.5 1.0 O13 A:QNA303 4.2 12.1 1.0 ZN A:ZN301 4.2 9.8 1.0 CB A:SER249 4.2 9.6 1.0 O03 A:QNA303 4.3 14.1 1.0 C16 A:QNA303 4.4 13.1 1.0 NE2 A:HIS189 4.4 10.2 1.0 CE1 A:HIS189 4.4 10.7 1.0 C17 A:QNA303 4.5 12.9 1.0 CA A:CYS208 4.5 10.4 1.0 CB A:ASP124 4.5 8.2 1.0 OG A:SER249 4.5 9.1 1.0 C05 A:QNA303 4.6 15.5 1.0

S.J.Hecker, K.R.Reddy, O.Lomovskaya, D.C.Griffith, D.Rubio-Aparicio, K.Nelson, R.Tsivkovski, D.Sun, M.Sabet, Z.Tarazi, J.Parkinson, M.Totrov, S.H.Boyer, T.W.Glinka, O.A.Pemberton, Y.Chen, M.N.Dudley. Discovery of Cyclic Boronic Acid QPX7728, An Ultra-Broad-Spectrum Inhibitor of Serine and Metallo Beta-Lactamases. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32150407
DOI: 10.1021/ACS.JMEDCHEM.9B01976