Fluorine in PDB 7qz9: Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp

The structure of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp, PDB code: 7qz9 was solved by A.M.W.H.Thunnissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.39 / 2.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.377, 34.969, 68.107, 90, 97.54, 90
R / Rfree (%)	22.9 / 29

The binding sites of Fluorine atom in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp (pdb code 7qz9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp, PDB code: 7qz9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp within 5.0Å range: probe atom residue distance (Å) B Occ A:F67 b:109.2 occ:1.00 FAD A:I3D67 0.0 109.2 1.0 CH2 A:I3D67 1.4 114.2 1.0 CZ2 A:I3D67 2.4 107.3 1.0 CZ3 A:I3D67 2.4 126.8 1.0 HZ2 A:I3D67 2.6 129.0 1.0 FAE A:I3D67 2.8 110.9 1.0 CE2 A:I3D67 3.6 114.0 1.0 CE3 A:I3D67 3.7 130.4 1.0 HB2 A:LYS77 3.8 117.3 1.0 CD2 A:I3D67 4.1 126.5 1.0 HD3 A:LYS77 4.4 111.5 1.0 HE3 A:I3D67 4.6 156.8 1.0 HD2 A:LYS77 4.7 111.5 1.0 CB A:LYS77 4.7 97.5 1.0 HB3 A:LYS77 4.8 117.3 1.0 NE1 A:I3D67 4.9 117.0 1.0 CD A:LYS77 5.0 92.7 1.0

Fluorine binding site 2 out of 8 in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp within 5.0Å range: probe atom residue distance (Å) B Occ A:F67 b:110.9 occ:1.00 FAE A:I3D67 0.0 110.9 1.0 CZ3 A:I3D67 1.4 126.8 1.0 CE3 A:I3D67 2.4 130.4 1.0 CH2 A:I3D67 2.4 114.2 1.0 HE3 A:I3D67 2.6 156.8 1.0 FAD A:I3D67 2.8 109.2 1.0 HA A:ARG76 3.2 116.9 1.0 O A:ARG75 3.5 107.5 1.0 CZ2 A:I3D67 3.7 107.3 1.0 CD2 A:I3D67 3.7 126.5 1.0 H A:LYS77 3.7 130.8 1.0 CA A:ARG76 3.9 97.2 1.0 HB2 A:LYS77 3.9 117.3 1.0 N A:LYS77 3.9 108.8 1.0 C A:ARG75 3.9 113.9 1.0 C A:ARG76 4.0 116.0 1.0 N A:ARG76 4.1 109.1 1.0 CE2 A:I3D67 4.2 114.0 1.0 HB3 A:ARG75 4.4 135.2 1.0 HZ2 A:I3D67 4.5 129.0 1.0 HD3 A:ARG76 4.6 168.3 1.0 HB2 A:ARG75 4.7 135.2 1.0 CB A:LYS77 4.7 97.5 1.0 H A:ARG76 4.7 131.2 1.0 O A:ARG76 4.7 117.5 1.0 CA A:LYS77 4.8 89.3 1.0 HH11 A:ARG76 4.8 153.3 1.0 HA A:LYS77 4.9 107.5 1.0 CB A:ARG75 4.9 112.5 1.0 HB3 A:LYS77 4.9 117.3 1.0 CG A:I3D67 5.0 116.0 1.0

Fluorine binding site 3 out of 8 in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp within 5.0Å range: probe atom residue distance (Å) B Occ A:F96 b:106.3 occ:1.00 FAD A:I3D96 0.0 106.3 1.0 CH2 A:I3D96 1.4 81.0 1.0 CZ2 A:I3D96 2.3 84.7 1.0 CZ3 A:I3D96 2.4 74.2 1.0 HZ2 A:I3D96 2.6 101.8 1.0 FAE A:I3D96 2.7 64.9 1.0 HB1 B:ALA11 2.8 76.5 1.0 HA B:GLN12 3.1 71.2 1.0 HB3 B:ALA11 3.2 76.5 1.0 HG3 B:GLN12 3.3 87.5 1.0 N B:GLN12 3.4 80.9 1.0 C B:ALA11 3.4 76.0 1.0 CB B:ALA11 3.4 63.5 1.0 HG21 B:VAL15 3.5 75.5 1.0 CE2 A:I3D96 3.6 79.8 1.0 O B:ALA11 3.6 64.8 1.0 CE3 A:I3D96 3.7 75.6 1.0 H B:GLN12 3.7 97.3 1.0 CA B:GLN12 3.7 59.1 1.0 HG23 B:VAL15 3.7 75.5 1.0 HG2 B:GLN12 3.8 87.5 1.0 CG B:GLN12 3.9 72.7 1.0 CA B:ALA11 4.0 59.0 1.0 CG2 B:VAL15 4.1 62.8 1.0 CD2 A:I3D96 4.1 75.0 1.0 HB2 B:ALA11 4.3 76.5 1.0 HB B:VAL15 4.4 71.8 1.0 CB B:GLN12 4.4 67.0 1.0 HA B:ALA11 4.5 71.1 1.0 HE3 A:I3D96 4.5 91.0 1.0 O B:MET8 4.6 81.0 1.0 HE2 A:MET8 4.8 126.7 1.0 CB B:VAL15 4.8 59.6 1.0 HG22 B:VAL15 4.8 75.5 1.0 NE1 A:I3D96 4.9 96.1 1.0 C B:GLN12 4.9 55.7 1.0 H B:VAL15 5.0 58.9 1.0

Fluorine binding site 4 out of 8 in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp within 5.0Å range: probe atom residue distance (Å) B Occ A:F96 b:64.9 occ:1.00 FAE A:I3D96 0.0 64.9 1.0 CZ3 A:I3D96 1.4 74.2 1.0 CH2 A:I3D96 2.4 81.0 1.0 CE3 A:I3D96 2.4 75.6 1.0 HG21 B:VAL15 2.6 75.5 1.0 HE3 A:I3D96 2.7 91.0 1.0 FAD A:I3D96 2.7 106.3 1.0 HG11 A:VAL99 3.1 93.4 1.0 HG11 B:VAL15 3.2 91.1 1.0 HB B:VAL15 3.4 71.8 1.0 CG2 B:VAL15 3.5 62.8 1.0 HA B:GLN12 3.5 71.2 1.0 CZ2 A:I3D96 3.6 84.7 1.0 CD2 A:I3D96 3.7 75.0 1.0 CB B:VAL15 3.8 59.6 1.0 HG23 B:VAL15 3.9 75.5 1.0 HG2 B:GLN12 3.9 87.5 1.0 CG1 B:VAL15 3.9 75.7 1.0 CG1 A:VAL99 3.9 77.6 1.0 HG12 A:VAL99 4.0 93.4 1.0 CE2 A:I3D96 4.2 79.8 1.0 HG22 B:VAL15 4.2 75.5 1.0 HG21 A:VAL99 4.3 76.3 1.0 HG12 B:VAL15 4.3 91.1 1.0 CA B:GLN12 4.4 59.1 1.0 HG3 B:GLN12 4.5 87.5 1.0 HZ2 A:I3D96 4.5 101.8 1.0 HB A:VAL99 4.5 88.0 1.0 CG B:GLN12 4.6 72.7 1.0 HG13 A:VAL99 4.6 93.4 1.0 HG13 B:VAL15 4.6 91.1 1.0 CB A:VAL99 4.7 73.1 1.0 O B:ALA11 4.9 64.8 1.0 CG2 A:VAL99 5.0 63.4 1.0 CB B:GLN12 5.0 67.0 1.0 CG A:I3D96 5.0 84.9 1.0

Fluorine binding site 5 out of 8 in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp within 5.0Å range: probe atom residue distance (Å) B Occ B:F67 b:69.0 occ:1.00 FAD B:I3D67 0.0 69.0 1.0 CH2 B:I3D67 1.4 74.1 1.0 CZ2 B:I3D67 2.3 76.0 1.0 CZ3 B:I3D67 2.4 66.3 1.0 HZ2 B:I3D67 2.6 91.5 1.0 FAE B:I3D67 2.8 71.2 1.0 HB2 B:LYS77 3.3 67.7 1.0 CE2 B:I3D67 3.6 66.7 1.0 CE3 B:I3D67 3.7 69.8 1.0 HD2 B:LYS77 4.0 80.4 1.0 CD2 B:I3D67 4.1 75.0 1.0 CB B:LYS77 4.3 56.2 1.0 HD3 B:LYS77 4.3 80.4 1.0 CD B:LYS77 4.5 66.8 1.0 HE3 B:I3D67 4.6 84.0 1.0 H B:LYS77 4.6 58.3 1.0 HB3 B:LYS77 4.6 67.7 1.0 N B:LYS77 4.8 48.4 1.0 NE1 B:I3D67 4.8 68.3 1.0 CG B:LYS77 5.0 68.1 1.0

Fluorine binding site 6 out of 8 in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp within 5.0Å range: probe atom residue distance (Å) B Occ B:F67 b:71.2 occ:1.00 FAE B:I3D67 0.0 71.2 1.0 CZ3 B:I3D67 1.4 66.3 1.0 CE3 B:I3D67 2.4 69.8 1.0 CH2 B:I3D67 2.4 74.1 1.0 HE3 B:I3D67 2.6 84.0 1.0 FAD B:I3D67 2.8 69.0 1.0 HA B:ARG76 3.2 63.3 1.0 HB3 B:ARG75 3.3 103.7 1.0 O B:ARG75 3.4 78.9 1.0 C B:ARG75 3.6 69.4 1.0 CD2 B:I3D67 3.6 75.0 1.0 CZ2 B:I3D67 3.6 76.0 1.0 C B:ARG76 3.7 55.5 1.0 CA B:ARG76 3.7 52.6 1.0 H B:LYS77 3.7 58.3 1.0 N B:ARG76 3.7 76.2 1.0 N B:LYS77 3.8 48.4 1.0 HB2 B:ARG75 3.8 103.7 1.0 CB B:ARG75 3.9 86.2 1.0 HB2 B:LYS77 4.0 67.7 1.0 CE2 B:I3D67 4.1 66.7 1.0 H B:ARG76 4.2 91.7 1.0 O B:ARG76 4.2 64.0 1.0 CA B:ARG75 4.5 104.2 1.0 HZ2 B:I3D67 4.5 91.5 1.0 HA B:LYS77 4.6 62.8 1.0 CA B:LYS77 4.6 52.1 1.0 HD3 B:ARG75 4.6 121.0 1.0 CB B:LYS77 4.7 56.2 1.0 CG B:I3D67 4.9 71.7 1.0 HD3 B:ARG76 4.9 118.4 1.0 HD2 B:ARG75 5.0 121.0 1.0

Fluorine binding site 7 out of 8 in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp within 5.0Å range: probe atom residue distance (Å) B Occ B:F96 b:91.5 occ:1.00 FAD B:I3D96 0.0 91.5 1.0 CH2 B:I3D96 1.4 84.8 1.0 CZ2 B:I3D96 2.4 110.4 1.0 CZ3 B:I3D96 2.4 86.8 1.0 HZ2 B:I3D96 2.6 132.7 1.0 HA A:GLN12 2.7 104.1 1.0 FAE B:I3D96 2.7 86.2 1.0 HB1 A:ALA11 2.8 88.8 1.0 HG21 A:VAL15 2.9 94.3 1.0 C A:ALA11 3.0 96.0 1.0 N A:GLN12 3.1 95.5 1.0 HB3 A:ALA11 3.1 88.8 1.0 O A:ALA11 3.2 77.8 1.0 HG23 A:VAL15 3.2 94.3 1.0 CB A:ALA11 3.3 73.8 1.0 CA A:GLN12 3.3 86.5 1.0 HG3 A:GLN12 3.4 108.9 1.0 H A:GLN12 3.4 114.8 1.0 CG2 A:VAL15 3.4 78.4 1.0 CE3 B:I3D96 3.6 100.2 1.0 CE2 B:I3D96 3.7 98.0 1.0 HG2 A:GLN12 3.7 108.9 1.0 HB A:VAL15 3.7 97.0 1.0 CA A:ALA11 3.7 92.1 1.0 CG A:GLN12 3.9 90.5 1.0 CD2 B:I3D96 4.1 101.5 1.0 CB A:VAL15 4.1 80.7 1.0 HB2 A:ALA11 4.2 88.8 1.0 CB A:GLN12 4.2 95.4 1.0 HG22 A:VAL15 4.2 94.3 1.0 HA A:ALA11 4.2 110.7 1.0 H A:VAL15 4.5 91.6 1.0 O A:MET8 4.5 77.1 1.0 HE3 B:I3D96 4.5 120.5 1.0 C A:GLN12 4.5 80.0 1.0 HG11 A:VAL15 4.6 101.0 1.0 HB3 A:GLN12 4.8 114.7 1.0 HB2 A:GLN12 4.8 114.7 1.0 N A:ALA11 4.9 66.4 1.0 NE1 B:I3D96 4.9 91.3 1.0 O A:GLN12 4.9 74.8 1.0 CG1 A:VAL15 5.0 84.0 1.0

Fluorine binding site 8 out of 8 in the Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Transcriptional Regulator Lmrr with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp within 5.0Å range: probe atom residue distance (Å) B Occ B:F96 b:86.2 occ:1.00 FAE B:I3D96 0.0 86.2 1.0 CZ3 B:I3D96 1.4 86.8 1.0 CH2 B:I3D96 2.4 84.8 1.0 CE3 B:I3D96 2.4 100.2 1.0 HE3 B:I3D96 2.6 120.5 1.0 HG21 A:VAL15 2.7 94.3 1.0 FAD B:I3D96 2.7 91.5 1.0 HG11 A:VAL15 2.8 101.0 1.0 HG11 B:VAL99 3.1 98.2 1.0 HB A:VAL15 3.2 97.0 1.0 HA A:GLN12 3.4 104.1 1.0 CG2 A:VAL15 3.5 78.4 1.0 CG1 A:VAL15 3.5 84.0 1.0 CB A:VAL15 3.6 80.7 1.0 CZ2 B:I3D96 3.6 110.4 1.0 CD2 B:I3D96 3.7 101.5 1.0 HG2 A:GLN12 3.8 108.9 1.0 HG12 A:VAL15 3.9 101.0 1.0 HG23 A:VAL15 3.9 94.3 1.0 CG1 B:VAL99 3.9 81.7 1.0 HG21 B:VAL99 4.0 109.1 1.0 HG12 B:VAL99 4.0 98.2 1.0 HB B:VAL99 4.1 103.3 1.0 CE2 B:I3D96 4.2 98.0 1.0 HG22 A:VAL15 4.2 94.3 1.0 HG13 A:VAL15 4.3 101.0 1.0 CA A:GLN12 4.3 86.5 1.0 CB B:VAL99 4.5 85.9 1.0 CG A:GLN12 4.5 90.5 1.0 HG3 A:GLN12 4.5 108.9 1.0 HZ2 B:I3D96 4.5 132.7 1.0 HG13 B:VAL99 4.7 98.2 1.0 CG2 B:VAL99 4.7 90.7 1.0 HA B:I3D96 4.9 103.6 1.0 CB A:GLN12 4.9 95.4 1.0 O A:ALA11 4.9 77.8 1.0 HD11 B:ILE103 4.9 125.7 1.0 N A:GLN12 4.9 95.5 1.0 HB3 A:GLN12 5.0 114.7 1.0 CG B:I3D96 5.0 96.3 1.0

J.Shao, B.P.Kuiper, A.W.H.Thunnissen, R.H.Cool, L.Zhou, C.Huang, B.W.Dijkstra, J.Broos. The Role of Tryptophan in Pi Interactions in Proteins: An Experimental Approach. J.Am.Chem.Soc. V. 144 13815 2022.
ISSN: ESSN 1520-5126
PubMed: 35868012
DOI: 10.1021/JACS.2C04986