Fluorine in PDB 5hjr: Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate

All present enzymatic activity of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate:
3.2.1.84;

The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate, PDB code: 5hjr was solved by A.T.Caputo, P.Roversi, D.S.Alonzi, J.L.Kiappes, N.Zitzmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	103.48 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	103.512, 174.664, 63.714, 90.00, 91.31, 90.00
R / Rfree (%)	17.7 / 20.2

The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Fluorine atom in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate (pdb code 5hjr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate, PDB code: 5hjr:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:F1021 b:67.8 occ:1.00 F A:5GF1021 0.0 67.8 1.0 C5 A:5GF1021 1.4 57.2 1.0 O5 A:5GF1021 2.1 60.6 1.0 C6 A:5GF1021 2.3 50.0 1.0 C4 A:5GF1021 2.4 46.0 1.0 H3 A:5GF1021 2.4 45.6 1.0 HZ A:PHE673 2.5 42.3 1.0 H62 A:5GF1021 2.5 49.7 1.0 H61 A:5GF1021 2.8 49.9 1.0 O4 A:5GF1021 2.9 40.5 1.0 C3 A:5GF1021 2.9 44.6 1.0 HZ3 A:TRP423 3.3 43.0 1.0 CE3 A:TRP423 3.3 42.2 1.0 C1 A:5GF1021 3.3 59.3 1.0 HZ2 A:TRP525 3.3 48.4 1.0 CZ3 A:TRP423 3.3 43.5 1.0 H4 A:5GF1021 3.3 46.6 1.0 HE3 A:TRP423 3.3 41.2 1.0 CZ A:PHE673 3.4 43.5 1.0 HO4 A:5GF1021 3.4 40.0 1.0 O6 A:5GF1021 3.5 47.0 1.0 C2 A:5GF1021 3.6 48.7 1.0 HO6 A:5GF1021 3.8 47.1 1.0 H1 A:5GF1021 4.0 60.1 1.0 CZ2 A:TRP525 4.0 48.0 1.0 HE1 A:PHE673 4.1 41.3 1.0 CE1 A:PHE673 4.1 43.0 1.0 O3 A:5GF1021 4.1 44.4 1.0 HE2 A:PHE673 4.1 46.0 1.0 CH2 A:TRP423 4.1 44.2 1.0 CD2 A:TRP423 4.1 41.5 1.0 CE2 A:PHE673 4.2 45.9 1.0 O2 A:5GF1021 4.2 49.5 1.0 HH2 A:TRP525 4.2 48.3 1.0 HD2 A:HIS700 4.3 49.3 1.0 HE2 A:HIS698 4.4 36.3 1.0 CH2 A:TRP525 4.5 48.0 1.0 H2 A:5GF1021 4.5 48.3 1.0 HH2 A:TRP423 4.6 43.8 1.0 HO3 A:5GF1021 4.6 43.5 1.0 OD2 A:ASP640 4.6 60.2 1.0 OD2 A:ASP564 4.7 62.0 1.0 HB2 A:TRP423 4.7 42.0 1.0 CE2 A:TRP423 4.8 45.9 1.0 CZ2 A:TRP423 4.8 45.7 1.0 OD1 A:ASP640 4.9 56.5 1.0 OD2 A:ASP451 4.9 43.3 1.0 CE2 A:TRP525 5.0 49.3 1.0

Fluorine binding site 2 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Covalent Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:F1023 b:54.2 occ:1.00 F C:5GF1023 0.0 54.2 1.0 C5 C:5GF1023 1.4 50.7 1.0 O5 C:5GF1023 2.1 50.9 1.0 C6 C:5GF1023 2.4 47.6 1.0 C4 C:5GF1023 2.5 45.9 1.0 H3 C:5GF1023 2.6 49.7 1.0 H61 C:5GF1023 2.6 47.0 1.0 HZ C:PHE673 2.6 31.5 1.0 H62 C:5GF1023 2.6 47.7 1.0 O4 C:5GF1023 2.8 40.5 1.0 C3 C:5GF1023 3.0 48.9 1.0 HO4 C:5GF1023 3.3 40.5 1.0 C1 C:5GF1023 3.3 54.6 1.0 HZ2 C:TRP525 3.3 41.2 1.0 H4 C:5GF1023 3.4 45.8 1.0 HZ3 C:TRP423 3.4 36.0 1.0 CE3 C:TRP423 3.4 33.5 1.0 CZ3 C:TRP423 3.5 35.6 1.0 HE3 C:TRP423 3.5 33.8 1.0 CZ C:PHE673 3.5 32.4 1.0 O6 C:5GF1023 3.6 47.9 1.0 C2 C:5GF1023 3.6 50.5 1.0 HO6 C:5GF1023 3.9 48.3 1.0 H1 C:5GF1023 3.9 55.6 1.0 CZ2 C:TRP525 4.0 42.6 1.0 HE1 C:PHE673 4.1 37.2 1.0 CH2 C:TRP423 4.2 36.3 1.0 CD2 C:TRP423 4.2 31.3 1.0 CE1 C:PHE673 4.2 36.5 1.0 O3 C:5GF1023 4.2 53.7 1.0 O2 C:5GF1023 4.3 45.7 1.0 HE2 C:PHE673 4.3 33.3 1.0 CE2 C:PHE673 4.3 34.0 1.0 HE2 C:HIS698 4.4 37.1 1.0 OD2 C:ASP564 4.5 54.7 1.0 HD2 C:HIS700 4.5 39.0 1.0 H2 C:5GF1023 4.5 51.3 1.0 HH2 C:TRP525 4.6 42.9 1.0 HH2 C:TRP423 4.7 36.9 1.0 HO3 C:5GF1023 4.7 54.1 1.0 OD2 C:ASP640 4.7 53.8 1.0 CH2 C:TRP525 4.7 42.8 1.0 HE1 C:TRP525 4.7 42.1 1.0 HB2 C:TRP423 4.8 31.9 1.0 CE2 C:TRP423 4.8 36.8 1.0 HO2 C:5GF1023 4.8 44.7 1.0 OD1 C:ASP640 4.9 46.0 1.0 CZ2 C:TRP423 4.9 36.7 1.0 CE2 C:TRP525 4.9 43.1 1.0 OD2 C:ASP451 4.9 35.3 1.0 O C:HOH1105 4.9 32.5 1.0

A.T.Caputo, D.S.Alonzi, L.Marti, I.B.Reca, J.L.Kiappes, W.B.Struwe, A.Cross, S.Basu, E.D.Lowe, B.Darlot, A.Santino, P.Roversi, N.Zitzmann. Structures of Mammalian Er Alpha-Glucosidase II Capture the Binding Modes of Broad-Spectrum Iminosugar Antivirals. Proc.Natl.Acad.Sci.Usa V. 113 E4630 2016.
ISSN: ESSN 1091-6490
PubMed: 27462106
DOI: 10.1073/PNAS.1604463113