Fluorine in PDB 7naj: Crystal Structure of the Tir Domain From Human SARM1 in Complex with Ara-2'F-Adpr

The structure of Crystal Structure of the Tir Domain From Human SARM1 in Complex with Ara-2'F-Adpr, PDB code: 7naj was solved by Y.Shi, T.Ve, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.50 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.511, 117.063, 33.043, 90, 90, 90
R / Rfree (%)	20 / 22.7

The binding sites of Fluorine atom in the Crystal Structure of the Tir Domain From Human SARM1 in Complex with Ara-2'F-Adpr (pdb code 7naj). 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 the Tir Domain From Human SARM1 in Complex with Ara-2'F-Adpr, PDB code: 7naj:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Tir Domain From Human SARM1 in Complex with Ara-2'F-Adpr


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 the Tir Domain From Human SARM1 in Complex with Ara-2'F-Adpr within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:32.2 occ:1.00 F A:1LK801 0.0 32.2 1.0 C1 A:1LK801 1.4 34.7 1.0 H1 A:1LK801 2.0 41.7 1.0 C2 A:1LK801 2.4 32.8 1.0 C A:1LK801 2.4 28.7 1.0 H2 A:1LK801 2.5 39.3 1.0 H4 A:1LK801 2.6 34.4 1.0 HB3 A:ASP594 2.6 27.2 1.0 HD21 A:LEU607 2.8 42.4 1.0 HD22 A:LEU607 3.0 42.4 1.0 OE2 A:GLU642 3.0 28.4 1.0 O A:HOH921 3.0 26.4 1.0 O8 A:1LK801 3.1 33.6 1.0 HZ A:PHE565 3.1 29.6 1.0 CD2 A:LEU607 3.3 35.3 1.0 HE1 A:PHE592 3.5 39.2 1.0 CB A:ASP594 3.5 22.7 1.0 O A:1LK801 3.5 33.2 1.0 C3 A:1LK801 3.6 31.2 1.0 OD2 A:ASP594 3.7 29.9 1.0 H10 A:1LK801 3.7 40.3 1.0 HD23 A:LEU607 3.8 42.4 1.0 CG A:ASP594 3.8 28.6 1.0 CD A:GLU642 3.8 29.7 1.0 CZ A:PHE565 3.9 24.7 1.0 HB2 A:ASP594 4.0 27.2 1.0 OE1 A:GLU642 4.0 26.0 1.0 H A:ASP594 4.1 26.9 1.0 HD13 A:LEU607 4.2 51.2 1.0 H3 A:1LK801 4.3 37.4 1.0 HE1 A:PHE565 4.3 29.1 1.0 HD11 A:LEU607 4.4 51.2 1.0 CE1 A:PHE592 4.4 32.7 1.0 H6 A:1LK801 4.5 43.0 1.0 CE1 A:PHE565 4.5 24.3 1.0 CG A:LEU607 4.6 31.3 1.0 CA A:ASP594 4.6 21.1 1.0 C4 A:1LK801 4.6 35.8 1.0 CD1 A:LEU607 4.6 42.7 1.0 N A:ASP594 4.6 22.5 1.0 HA A:ASP594 4.6 25.4 1.0 HA A:SER567 4.7 29.0 1.0 OD1 A:ASP594 4.7 25.2 1.0 HE2 A:PHE565 4.7 26.5 1.0 CE2 A:PHE565 4.7 22.1 1.0 O A:ILE566 4.8 22.3 1.0 H5 A:1LK801 4.8 43.0 1.0 HE1 A:TYR568 4.8 28.5 1.0 HD22 A:LEU598 4.9 39.9 1.0 HZ A:PHE592 5.0 34.0 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Tir Domain From Human SARM1 in Complex with Ara-2'F-Adpr


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 the Tir Domain From Human SARM1 in Complex with Ara-2'F-Adpr within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:34.4 occ:1.00 F B:1LK801 0.0 34.4 1.0 C1 B:1LK801 1.4 36.6 1.0 H1 B:1LK801 2.0 43.9 1.0 C2 B:1LK801 2.4 33.6 1.0 C B:1LK801 2.4 36.5 1.0 H4 B:1LK801 2.6 43.7 1.0 H2 B:1LK801 2.6 40.3 1.0 HB3 B:ASP594 2.7 28.0 1.0 HD22 B:LEU607 2.8 48.7 1.0 HD21 B:LEU607 2.9 48.7 1.0 O B:HOH918 3.0 23.1 1.0 O8 B:1LK801 3.0 33.7 1.0 OE2 B:GLU642 3.1 29.4 1.0 HZ B:PHE565 3.2 26.6 1.0 CD2 B:LEU607 3.3 40.6 1.0 HE1 B:PHE592 3.5 34.9 1.0 O B:1LK801 3.5 35.6 1.0 CB B:ASP594 3.5 23.3 1.0 C3 B:1LK801 3.6 38.6 1.0 OD2 B:ASP594 3.6 30.8 1.0 CG B:ASP594 3.8 28.9 1.0 H10 B:1LK801 3.8 40.4 1.0 HD23 B:LEU607 3.9 48.7 1.0 CZ B:PHE565 3.9 22.2 1.0 CD B:GLU642 3.9 35.6 1.0 HB2 B:ASP594 4.0 28.0 1.0 OE1 B:GLU642 4.1 29.5 1.0 HD11 B:LEU607 4.1 52.2 1.0 H B:ASP594 4.2 28.5 1.0 HD13 B:LEU607 4.2 52.2 1.0 H3 B:1LK801 4.3 46.3 1.0 HE1 B:PHE565 4.3 31.9 1.0 CE1 B:PHE592 4.4 29.1 1.0 H5 B:1LK801 4.4 58.7 1.0 CD1 B:LEU607 4.5 43.5 1.0 CG B:LEU607 4.5 40.5 1.0 C4 B:1LK801 4.5 49.0 1.0 CE1 B:PHE565 4.5 26.6 1.0 CA B:ASP594 4.6 27.7 1.0 HA B:ASP594 4.6 33.3 1.0 N B:ASP594 4.6 23.8 1.0 OD1 B:ASP594 4.7 24.4 1.0 HA B:SER567 4.7 27.5 1.0 HE1 B:TYR568 4.7 26.7 1.0 H6 B:1LK801 4.8 58.7 1.0 CE2 B:PHE565 4.8 23.2 1.0 HE2 B:PHE565 4.8 27.8 1.0 O B:ILE566 4.8 23.1 1.0 HD22 B:LEU598 4.9 42.4 1.0 HZ B:PHE592 5.0 30.3 1.0 HB3 B:LEU607 5.0 39.4 1.0

Y.Shi, P.S.Kerry, J.D.Nanson, T.Bosanac, Y.Sasaki, R.Krauss, F.K.Saikot, S.E.Adams, T.Mosaiab, V.Masic, X.Mao, F.Rose, E.Vasquez, M.Furrer, K.Cunnea, A.Brearley, W.Gu, Z.Luo, L.Brillault, M.J.Landsberg, A.Diantonio, B.Kobe, J.Milbrandt, R.O.Hughes, T.Ve. Structural Basis of SARM1 Activation, Substrate Recognition, and Inhibition By Small Molecules. Mol.Cell V. 82 1643 2022.
ISSN: ISSN 1097-2765
PubMed: 35334231
DOI: 10.1016/J.MOLCEL.2022.03.007