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

Protein crystallography data

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

Fluorine Binding Sites:

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 7dzg

Go back to Fluorine Binding Sites List in 7dzg
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 7dzg

Go back to Fluorine Binding Sites List in 7dzg
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 7dzg

Go back to Fluorine Binding Sites List in 7dzg
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 7dzg

Go back to Fluorine Binding Sites List in 7dzg
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

Reference:

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
Page generated: Fri Aug 2 06:32:09 2024

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