Fluorine in PDB 7dzf: Intermediate of Fabp with A Delay Time of 10 Ns

The structure of Intermediate of Fabp with A Delay Time of 10 Ns, PDB code: 7dzf 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)	19.91 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.76, 66.84, 69.23, 90, 90, 90
R / Rfree (%)	17.4 / 20.2

The binding sites of Fluorine atom in the Intermediate of Fabp with A Delay Time of 10 Ns (pdb code 7dzf). 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 10 Ns, PDB code: 7dzf:
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 10 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 10 Ns within 5.0Å range: probe atom residue distance (Å) B Occ A:F63 b:28.4 occ:0.54 F14 A:HP963 0.0 28.4 0.5 F14 A:HP963 0.5 29.4 0.5 C10 A:HP963 1.3 21.8 0.5 C10 A:HP963 1.5 24.4 0.5 C9 A:HP963 2.3 20.9 0.5 C11 A:HP963 2.3 23.1 0.5 C9 A:HP963 2.4 21.1 0.5 C11 A:HP963 2.7 21.4 0.5 C6 A:PLM201 3.3 37.1 1.0 C5 A:PLM201 3.6 40.2 1.0 C6 A:HP963 3.6 20.5 0.5 C8 A:HP963 3.6 21.6 0.5 C8 A:HP963 3.6 20.9 0.5 C8 A:PLM201 3.7 35.9 1.0 CD1 A:ILE52 3.7 27.5 1.0 C7 A:PLM201 3.9 34.0 1.0 C6 A:HP963 3.9 20.8 0.5 CE A:PLM201 3.9 41.4 1.0 C7 A:HP963 4.1 19.4 0.5 CG A:PLM201 4.2 52.2 1.0 C7 A:HP963 4.3 19.7 0.5 CF A:PLM201 4.5 49.3 1.0 CD2 A:PHE50 4.6 14.7 0.7 CE2 A:PHE50 4.6 18.1 0.7 C4 A:PLM201 4.7 36.7 1.0 OD1 A:ASN111 4.7 25.0 1.0 C3 A:HP963 4.8 23.6 0.5 CG1 A:ILE52 4.9 21.1 1.0 OG1 A:THR102 4.9 18.2 1.0 CD A:PLM201 4.9 45.2 1.0 CC A:PLM201 5.0 46.4 1.0

Fluorine binding site 2 out of 4 in the Intermediate of Fabp with A Delay Time of 10 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 10 Ns within 5.0Å range: probe atom residue distance (Å) B Occ A:F63 b:29.4 occ:0.46 F14 A:HP963 0.0 29.4 0.5 F14 A:HP963 0.5 28.4 0.5 C10 A:HP963 1.3 21.8 0.5 C10 A:HP963 1.3 24.4 0.5 C11 A:HP963 2.1 23.1 0.5 C9 A:HP963 2.4 20.9 0.5 C11 A:HP963 2.4 21.4 0.5 C9 A:HP963 2.5 21.1 0.5 C6 A:HP963 3.4 20.5 0.5 CE A:PLM201 3.5 41.4 1.0 C8 A:HP963 3.6 20.9 0.5 C6 A:HP963 3.6 20.8 0.5 C8 A:HP963 3.6 21.6 0.5 CG A:PLM201 3.7 52.2 1.0 C6 A:PLM201 3.8 37.1 1.0 CD1 A:ILE52 3.8 27.5 1.0 C8 A:PLM201 3.9 35.9 1.0 C7 A:HP963 4.0 19.4 0.5 CF A:PLM201 4.1 49.3 1.0 C7 A:HP963 4.1 19.7 0.5 C5 A:PLM201 4.1 40.2 1.0 C7 A:PLM201 4.2 34.0 1.0 C3 A:HP963 4.6 23.6 0.5 CD A:PLM201 4.6 45.2 1.0 O13 A:HP963 4.7 21.7 0.5 CC A:PLM201 4.8 46.4 1.0 CD2 A:PHE50 4.9 14.7 0.7 C3 A:HP963 4.9 21.7 0.5 CE2 A:PHE50 4.9 18.1 0.7

Fluorine binding site 3 out of 4 in the Intermediate of Fabp with A Delay Time of 10 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 10 Ns within 5.0Å range: probe atom residue distance (Å) B Occ B:F63 b:32.9 occ:0.56 F14 B:HP963 0.0 32.9 0.6 F14 B:HP963 0.2 32.0 0.4 C10 B:HP963 1.3 31.9 0.6 C10 B:HP963 1.4 31.8 0.4 C11 B:HP963 2.3 27.8 0.4 C11 B:HP963 2.3 27.9 0.6 C9 B:HP963 2.4 27.9 0.6 C9 B:HP963 2.5 28.0 0.4 C6 B:PLM201 3.1 41.9 1.0 CD1 B:ILE52 3.6 31.0 1.0 C6 B:HP963 3.6 28.9 0.6 CE B:PLM201 3.6 50.0 1.0 C8 B:HP963 3.6 26.9 0.6 C6 B:HP963 3.6 29.0 0.4 C8 B:HP963 3.8 25.9 0.4 C5 B:PLM201 3.8 49.4 1.0 C8 B:PLM201 4.0 41.8 1.0 C7 B:PLM201 4.1 39.5 1.0 C7 B:HP963 4.1 25.3 0.6 CG B:PLM201 4.1 62.1 1.0 C7 B:HP963 4.2 26.2 0.4 CF B:PLM201 4.4 52.3 1.0 CD B:PLM201 4.5 50.9 1.0 C4 B:PLM201 4.6 48.8 1.0 CE B:MET113 4.7 26.3 0.5 CG1 B:ILE52 4.8 24.2 1.0 CD2 B:PHE50 4.8 24.5 0.4 C3 B:HP963 4.8 32.8 0.6 CD2 B:PHE50 4.8 23.0 0.6 C3 B:HP963 4.8 32.6 0.4 CE2 B:PHE50 4.8 29.6 0.4 OD1 B:ASN111 4.9 25.9 1.0 CE2 B:PHE50 4.9 30.0 0.6 O13 B:HP963 5.0 31.3 0.6

Fluorine binding site 4 out of 4 in the Intermediate of Fabp with A Delay Time of 10 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 10 Ns within 5.0Å range: probe atom residue distance (Å) B Occ B:F63 b:32.0 occ:0.44 F14 B:HP963 0.0 32.0 0.4 F14 B:HP963 0.2 32.9 0.6 C10 B:HP963 1.3 31.9 0.6 C10 B:HP963 1.3 31.8 0.4 C9 B:HP963 2.2 27.9 0.6 C11 B:HP963 2.4 27.8 0.4 C9 B:HP963 2.4 28.0 0.4 C11 B:HP963 2.4 27.9 0.6 C6 B:PLM201 3.1 41.9 1.0 C8 B:HP963 3.5 26.9 0.6 C6 B:HP963 3.6 28.9 0.6 C6 B:HP963 3.6 29.0 0.4 C8 B:HP963 3.6 25.9 0.4 CE B:PLM201 3.7 50.0 1.0 CD1 B:ILE52 3.8 31.0 1.0 C5 B:PLM201 3.8 49.4 1.0 C8 B:PLM201 4.0 41.8 1.0 C7 B:HP963 4.0 25.3 0.6 C7 B:PLM201 4.1 39.5 1.0 C7 B:HP963 4.1 26.2 0.4 CG B:PLM201 4.1 62.1 1.0 CF B:PLM201 4.5 52.3 1.0 CE B:MET113 4.6 26.3 0.5 C4 B:PLM201 4.6 48.8 1.0 CD B:PLM201 4.7 50.9 1.0 OD1 B:ASN111 4.7 25.9 1.0 C3 B:HP963 4.8 32.8 0.6 C3 B:HP963 4.9 32.6 0.4 OG1 B:THR102 4.9 20.6 1.0 CD2 B:PHE50 4.9 24.5 0.4 CE2 B:PHE50 4.9 29.6 0.4 CD2 B:PHE50 4.9 23.0 0.6 CE2 B:PHE50 4.9 30.0 0.6 CG1 B:ILE52 5.0 24.2 1.0 OG B:SER100 5.0 23.2 1.0

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