Fluorine in PDB 7dzi: Intermediate of Fabp with A Delay Time of 300 Ns

The structure of Intermediate of Fabp with A Delay Time of 300 Ns, PDB code: 7dzi was solved by H.Li, L.-J.Yu, X.Liu, J.-R.Shen, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.75 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.44, 66.26, 68.91, 90, 90, 90
R / Rfree (%)	18.3 / 21.4

The binding sites of Fluorine atom in the Intermediate of Fabp with A Delay Time of 300 Ns (pdb code 7dzi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Intermediate of Fabp with A Delay Time of 300 Ns, PDB code: 7dzi:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Intermediate of Fabp with A Delay Time of 300 Ns


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Intermediate of Fabp with A Delay Time of 300 Ns within 5.0Å range: probe atom residue distance (Å) B Occ A:F63 b:29.2 occ:0.79 F14 A:HP963 0.0 29.2 0.8 F14 A:HP963 0.1 24.8 0.2 C10 A:HP963 1.3 23.8 0.8 C10 A:HP963 1.3 23.8 0.2 C11 A:HP963 2.3 21.4 0.8 C9 A:HP963 2.4 23.3 0.2 C9 A:HP963 2.4 23.6 0.8 C11 A:HP963 2.4 21.1 0.2 C5 A:PLM201 3.4 41.3 1.0 C6 A:PLM201 3.6 35.5 1.0 CD1 A:ILE52 3.6 26.9 1.0 C6 A:HP963 3.6 18.7 0.8 C8 A:HP963 3.6 24.0 0.8 C8 A:HP963 3.6 22.4 0.2 C6 A:HP963 3.6 19.6 0.2 CE A:PLM201 3.7 42.6 1.0 C8 A:PLM201 3.7 35.9 1.0 C7 A:PLM201 3.8 35.0 1.0 CG A:PLM201 4.1 46.5 1.0 C7 A:HP963 4.1 18.4 0.8 C7 A:HP963 4.1 20.0 0.2 CF A:PLM201 4.2 43.6 1.0 C4 A:PLM201 4.5 36.4 1.0 CD2 A:PHE50 4.6 20.4 1.0 CE2 A:PHE50 4.7 23.4 1.0 OD1 A:ASN111 4.8 28.6 1.0 CG1 A:ILE52 4.8 20.4 1.0 CD A:PLM201 4.8 42.4 1.0 C3 A:HP963 4.8 24.7 0.8 C3 A:HP963 4.9 22.8 0.2 OG1 A:THR102 5.0 20.5 1.0 CC A:PLM201 5.0 43.0 1.0

Fluorine binding site 2 out of 4 in the Intermediate of Fabp with A Delay Time of 300 Ns


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Intermediate of Fabp with A Delay Time of 300 Ns within 5.0Å range: probe atom residue distance (Å) B Occ A:F63 b:24.8 occ:0.21 F14 A:HP963 0.0 24.8 0.2 F14 A:HP963 0.1 29.2 0.8 C10 A:HP963 1.3 23.8 0.2 C10 A:HP963 1.3 23.8 0.8 C11 A:HP963 2.3 21.4 0.8 C9 A:HP963 2.4 23.3 0.2 C11 A:HP963 2.4 21.1 0.2 C9 A:HP963 2.4 23.6 0.8 C5 A:PLM201 3.5 41.3 1.0 C6 A:HP963 3.6 18.7 0.8 C8 A:HP963 3.6 24.0 0.8 C6 A:HP963 3.6 19.6 0.2 C8 A:HP963 3.6 22.4 0.2 CE A:PLM201 3.6 42.6 1.0 CD1 A:ILE52 3.7 26.9 1.0 C6 A:PLM201 3.7 35.5 1.0 C8 A:PLM201 3.7 35.9 1.0 C7 A:PLM201 3.9 35.0 1.0 CG A:PLM201 4.0 46.5 1.0 C7 A:HP963 4.1 18.4 0.8 C7 A:HP963 4.1 20.0 0.2 CF A:PLM201 4.1 43.6 1.0 C4 A:PLM201 4.6 36.4 1.0 CD A:PLM201 4.7 42.4 1.0 CD2 A:PHE50 4.7 20.4 1.0 CE2 A:PHE50 4.8 23.4 1.0 OD1 A:ASN111 4.8 28.6 1.0 C3 A:HP963 4.8 24.7 0.8 C3 A:HP963 4.9 22.8 0.2 CG1 A:ILE52 4.9 20.4 1.0 CC A:PLM201 4.9 43.0 1.0 OG1 A:THR102 5.0 20.5 1.0

Fluorine binding site 3 out of 4 in the Intermediate of Fabp with A Delay Time of 300 Ns


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Intermediate of Fabp with A Delay Time of 300 Ns within 5.0Å range: probe atom residue distance (Å) B Occ B:F63 b:28.6 occ:0.35 F14 B:HP963 0.0 28.6 0.3 F14 B:HP963 0.3 31.8 0.7 C10 B:HP963 1.3 31.6 0.3 C10 B:HP963 1.4 32.4 0.7 C11 B:HP963 2.3 29.3 0.3 C9 B:HP963 2.4 30.4 0.3 C9 B:HP963 2.4 30.7 0.7 C11 B:HP963 2.5 27.3 0.7 CE B:PLM201 3.4 50.4 1.0 C5 B:PLM201 3.5 47.3 1.0 C6 B:HP963 3.6 28.7 0.3 C8 B:HP963 3.6 28.2 0.3 C8 B:HP963 3.7 27.8 0.7 C6 B:PLM201 3.7 43.9 1.0 CG B:PLM201 3.7 60.3 1.0 C6 B:HP963 3.7 27.9 0.7 C8 B:PLM201 3.9 42.2 1.0 CD1 B:ILE52 3.9 29.6 1.0 C7 B:PLM201 3.9 39.7 1.0 C7 B:HP963 4.1 28.2 0.3 CF B:PLM201 4.1 53.0 1.0 C7 B:HP963 4.2 27.4 0.7 C4 B:PLM201 4.5 48.0 1.0 CD B:PLM201 4.5 53.7 1.0 CE B:MET113 4.6 30.9 0.6 OD1 B:ASN111 4.6 26.9 1.0 C3 B:HP963 4.8 32.4 0.3 OG1 B:THR102 4.9 23.4 1.0 OG B:SER100 4.9 26.5 1.0 CG1 B:ILE52 4.9 25.2 1.0 CD2 B:PHE50 4.9 27.8 1.0 C3 B:HP963 4.9 32.9 0.7 CE2 B:PHE50 4.9 30.0 1.0 O13 B:HP963 5.0 34.8 0.3

Fluorine binding site 4 out of 4 in the Intermediate of Fabp with A Delay Time of 300 Ns


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Intermediate of Fabp with A Delay Time of 300 Ns within 5.0Å range: probe atom residue distance (Å) B Occ B:F63 b:31.8 occ:0.65 F14 B:HP963 0.0 31.8 0.7 F14 B:HP963 0.3 28.6 0.3 C10 B:HP963 1.3 31.6 0.3 C10 B:HP963 1.3 32.4 0.7 C11 B:HP963 2.2 29.3 0.3 C11 B:HP963 2.3 27.3 0.7 C9 B:HP963 2.4 30.7 0.7 C9 B:HP963 2.4 30.4 0.3 CE B:PLM201 3.4 50.4 1.0 C5 B:PLM201 3.4 47.3 1.0 C6 B:HP963 3.5 28.7 0.3 CD1 B:ILE52 3.6 29.6 1.0 C6 B:HP963 3.6 27.9 0.7 C8 B:HP963 3.6 27.8 0.7 C6 B:PLM201 3.6 43.9 1.0 C8 B:HP963 3.6 28.2 0.3 CG B:PLM201 3.9 60.3 1.0 C8 B:PLM201 3.9 42.2 1.0 C7 B:PLM201 4.0 39.7 1.0 C7 B:HP963 4.1 28.2 0.3 C7 B:HP963 4.1 27.4 0.7 CF B:PLM201 4.2 53.0 1.0 C4 B:PLM201 4.4 48.0 1.0 CD B:PLM201 4.5 53.7 1.0 CG1 B:ILE52 4.6 25.2 1.0 CD2 B:PHE50 4.6 27.8 1.0 C3 B:HP963 4.7 32.4 0.3 CE2 B:PHE50 4.7 30.0 1.0 C3 B:HP963 4.8 32.9 0.7 O13 B:HP963 4.8 34.8 0.3 OD1 B:ASN111 4.8 26.9 1.0 CE B:MET113 4.9 30.9 0.6 O13 B:HP963 4.9 34.8 0.7

X.Liu, P.Liu, H.Li, Z.Xu, L.Jia, Y.Xia, M.Yu, W.Tang, X.Zhu, C.Chen, Y.Zhang, E.Nango, R.Tanaka, F.Luo, K.Kato, Y.Nakajima, S.Kishi, H.Yu, N.Matsubara, S.Owada, K.Tono, S.Iwata, L.J.Yu, J.R.Shen, J.Wang. Excited-State Intermediates in A Designer Protein Encoding A Phototrigger Caught By An X-Ray Free-Electron Laser. Nat.Chem. V. 14 1054 2022.
ISSN: ESSN 1755-4349
PubMed: 35851837
DOI: 10.1038/S41557-022-00992-3