Fluorine in PDB 7dzg: Intermediate of Fabp with A Delay Time of 30 Ns

The structure of Intermediate of Fabp with A Delay Time of 30 Ns, PDB code: 7dzg 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)	19.87 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.67, 66.7, 69.07, 90, 90, 90
R / Rfree (%)	17.9 / 20.2

The binding sites of Fluorine atom in the Intermediate of Fabp with A Delay Time of 30 Ns (pdb code 7dzg). 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 30 Ns, PDB code: 7dzg:
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 30 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 30 Ns within 5.0Å range: probe atom residue distance (Å) B Occ A:F63 b:26.3 occ:0.71 F14 A:HP963 0.0 26.3 0.7 F14 A:HP963 0.6 25.6 0.3 C10 A:HP963 1.3 23.6 0.7 C10 A:HP963 1.5 22.5 0.3 C9 A:HP963 2.3 21.7 0.3 C11 A:HP963 2.3 22.2 0.7 C9 A:HP963 2.4 21.8 0.7 C11 A:HP963 2.7 22.6 0.3 C5 A:PLM201 3.5 44.9 1.0 C6 A:PLM201 3.5 39.6 1.0 C6 A:HP963 3.6 20.9 0.7 C8 A:HP963 3.6 22.5 0.7 C8 A:HP963 3.6 22.2 0.3 CE A:PLM201 3.6 41.4 1.0 CD1 A:ILE52 3.7 26.1 1.0 C8 A:PLM201 3.7 37.0 1.0 C7 A:PLM201 3.8 38.3 1.0 C6 A:HP963 3.9 19.6 0.3 C7 A:HP963 4.1 20.5 0.7 CF A:PLM201 4.2 47.4 1.0 C7 A:HP963 4.2 20.8 0.3 CG A:PLM201 4.3 47.9 1.0 C4 A:PLM201 4.6 37.5 1.0 CE2 A:PHE50 4.7 23.5 1.0 CD2 A:PHE50 4.7 20.7 1.0 OD1 A:ASN111 4.7 28.6 1.0 C3 A:HP963 4.8 23.0 0.7 CD A:PLM201 4.8 43.2 1.0 CG1 A:ILE52 4.9 20.1 1.0 OG1 A:THR102 4.9 21.1 1.0

Fluorine binding site 2 out of 4 in the Intermediate of Fabp with A Delay Time of 30 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 30 Ns within 5.0Å range: probe atom residue distance (Å) B Occ A:F63 b:25.6 occ:0.29 F14 A:HP963 0.0 25.6 0.3 F14 A:HP963 0.6 26.3 0.7 C10 A:HP963 1.3 22.5 0.3 C10 A:HP963 1.4 23.6 0.7 C11 A:HP963 2.2 22.2 0.7 C9 A:HP963 2.4 21.7 0.3 C11 A:HP963 2.4 22.6 0.3 C9 A:HP963 2.5 21.8 0.7 CE A:PLM201 3.2 41.4 1.0 C6 A:HP963 3.5 20.9 0.7 C6 A:HP963 3.6 19.6 0.3 C8 A:HP963 3.6 22.2 0.3 C8 A:HP963 3.6 22.5 0.7 CF A:PLM201 3.7 47.4 1.0 CG A:PLM201 3.7 47.9 1.0 C8 A:PLM201 3.9 37.0 1.0 CD1 A:ILE52 3.9 26.1 1.0 C7 A:HP963 4.0 20.5 0.7 C6 A:PLM201 4.0 39.6 1.0 C5 A:PLM201 4.1 44.9 1.0 C7 A:HP963 4.1 20.8 0.3 C7 A:PLM201 4.2 38.3 1.0 CD A:PLM201 4.5 43.2 1.0 C3 A:HP963 4.6 23.0 0.7 O13 A:HP963 4.8 25.5 0.7 C3 A:HP963 4.9 21.6 0.3 CC A:PLM201 4.9 43.9 1.0

Fluorine binding site 3 out of 4 in the Intermediate of Fabp with A Delay Time of 30 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 30 Ns within 5.0Å range: probe atom residue distance (Å) B Occ B:F63 b:31.0 occ:0.81 F14 B:HP963 0.0 31.0 0.8 F14 B:HP963 0.1 30.6 0.2 C10 B:HP963 1.3 31.9 0.8 C10 B:HP963 1.4 30.6 0.2 C11 B:HP963 2.3 29.0 0.8 C9 B:HP963 2.4 28.9 0.8 C11 B:HP963 2.4 29.5 0.2 C9 B:HP963 2.4 29.4 0.2 C6 B:PLM201 3.5 43.0 1.0 C5 B:PLM201 3.5 45.0 1.0 C6 B:HP963 3.6 28.4 0.8 CE B:PLM201 3.6 52.5 1.0 C8 B:HP963 3.6 28.6 0.8 CD1 B:ILE52 3.7 29.0 1.0 C6 B:HP963 3.7 29.0 0.2 C8 B:HP963 3.7 28.6 0.2 C8 B:PLM201 3.8 43.3 1.0 C7 B:PLM201 3.9 40.1 1.0 CG B:PLM201 4.0 63.2 1.0 C7 B:HP963 4.1 27.9 0.8 C7 B:HP963 4.2 28.3 0.2 CF B:PLM201 4.4 54.9 1.0 C4 B:PLM201 4.5 44.0 1.0 CD B:PLM201 4.6 52.4 1.0 OD1 B:ASN111 4.8 28.4 1.0 CG1 B:ILE52 4.8 24.5 1.0 CE B:MET113 4.8 30.8 0.5 C3 B:HP963 4.8 31.6 0.8 CD2 B:PHE50 4.8 25.3 1.0 CE2 B:PHE50 4.9 28.9 1.0 C3 B:HP963 4.9 31.1 0.2 OG1 B:THR102 5.0 22.7 1.0 O13 B:HP963 5.0 33.1 0.8

Fluorine binding site 4 out of 4 in the Intermediate of Fabp with A Delay Time of 30 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 30 Ns within 5.0Å range: probe atom residue distance (Å) B Occ B:F63 b:30.6 occ:0.19 F14 B:HP963 0.0 30.6 0.2 F14 B:HP963 0.1 31.0 0.8 C10 B:HP963 1.3 31.9 0.8 C10 B:HP963 1.3 30.6 0.2 C11 B:HP963 2.3 29.0 0.8 C9 B:HP963 2.3 28.9 0.8 C11 B:HP963 2.4 29.5 0.2 C9 B:HP963 2.4 29.4 0.2 C6 B:PLM201 3.5 43.0 1.0 C5 B:PLM201 3.5 45.0 1.0 C6 B:HP963 3.5 28.4 0.8 C8 B:HP963 3.6 28.6 0.8 C6 B:HP963 3.6 29.0 0.2 CE B:PLM201 3.6 52.5 1.0 C8 B:HP963 3.6 28.6 0.2 CD1 B:ILE52 3.7 29.0 1.0 C8 B:PLM201 3.8 43.3 1.0 C7 B:PLM201 3.9 40.1 1.0 CG B:PLM201 4.0 63.2 1.0 C7 B:HP963 4.1 27.9 0.8 C7 B:HP963 4.1 28.3 0.2 CF B:PLM201 4.4 54.9 1.0 C4 B:PLM201 4.5 44.0 1.0 CD B:PLM201 4.6 52.4 1.0 C3 B:HP963 4.8 31.6 0.8 CD2 B:PHE50 4.8 25.3 1.0 CG1 B:ILE52 4.8 24.5 1.0 OD1 B:ASN111 4.8 28.4 1.0 CE B:MET113 4.8 30.8 0.5 CE2 B:PHE50 4.8 28.9 1.0 C3 B:HP963 4.9 31.1 0.2 O13 B:HP963 4.9 33.1 0.8 OG1 B:THR102 4.9 22.7 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