Fluorine in PDB 6d1f: Crystal Structure of Ndm-1 Complexed with Compound 8

All present enzymatic activity of Crystal Structure of Ndm-1 Complexed with Compound 8:
3.5.2.6;

The structure of Crystal Structure of Ndm-1 Complexed with Compound 8, PDB code: 6d1f 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)	27.32 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.510, 60.100, 41.750, 90.00, 97.97, 90.00
R / Rfree (%)	14.5 / 17.9

The structure of Crystal Structure of Ndm-1 Complexed with Compound 8 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Ndm-1 Complexed with Compound 8 (pdb code 6d1f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Ndm-1 Complexed with Compound 8, PDB code: 6d1f:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Ndm-1 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:20.1 occ:0.86 F12 A:P9T303 0.0 20.1 0.9 C11 A:P9T303 1.3 17.7 0.9 C13 A:P9T303 2.3 18.5 0.9 C10 A:P9T303 2.5 15.7 0.9 C05 A:P9T303 2.8 12.2 0.9 C04 A:P9T303 3.0 14.0 0.9 O A:HOH497 3.4 12.9 1.0 O A:HOH623 3.5 28.3 1.0 O07 A:P9T303 3.5 9.9 0.9 C14 A:P9T303 3.5 19.3 0.9 ND2 A:ASN220 3.5 13.1 1.0 O A:HOH630 3.6 16.3 1.0 C17 A:P9T303 3.7 16.7 0.9 P06 A:P9T303 3.7 10.4 0.9 CG A:HIS122 3.7 9.6 1.0 ND1 A:HIS122 3.9 10.2 1.0 CD2 A:HIS122 3.9 10.9 1.0 O A:HOH538 4.1 21.4 1.0 CE1 A:HIS122 4.1 11.3 1.0 NE2 A:HIS122 4.1 11.8 1.0 C16 A:P9T303 4.1 18.0 0.9 CB A:HIS122 4.2 8.2 1.0 O09 A:P9T303 4.2 9.7 0.9 C03 A:P9T303 4.4 15.2 0.9 F15 A:P9T303 4.6 22.3 0.9 CG A:ASN220 4.6 13.3 1.0 O18 A:P9T303 4.8 17.1 0.9 ZN A:ZN301 4.9 8.8 0.9

Fluorine binding site 2 out of 2 in the Crystal Structure of Ndm-1 Complexed with Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Ndm-1 Complexed with Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:22.3 occ:0.86 F15 A:P9T303 0.0 22.3 0.9 C14 A:P9T303 1.4 19.3 0.9 C13 A:P9T303 2.3 18.5 0.9 C16 A:P9T303 2.4 18.0 0.9 O A:HOH500 3.1 22.2 1.0 O A:HOH682 3.2 21.2 1.0 C11 A:P9T303 3.6 17.7 0.9 C17 A:P9T303 3.6 16.7 0.9 O A:HOH538 4.0 21.4 1.0 C10 A:P9T303 4.1 15.7 0.9 OD1 A:ASN220 4.1 15.1 1.0 ND2 A:ASN220 4.4 13.1 1.0 CG A:ASN220 4.5 13.3 1.0 F12 A:P9T303 4.6 20.1 0.9 O18 A:P9T303 4.7 17.1 0.9

O.A.Pemberton, P.Jaishankar, A.Akhtar, J.L.Adams, L.N.Shaw, A.R.Renslo, Y.Chen. Heteroaryl Phosphonates As Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. V. 62 8480 2019.
ISSN: ISSN 0022-2623
PubMed: 31483651
DOI: 10.1021/ACS.JMEDCHEM.9B00728