Fluorine in PDB 7qz8: Transcriptional Regulator Lmrr with Bound Daunomycin and with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp

The structure of Transcriptional Regulator Lmrr with Bound Daunomycin and with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp, PDB code: 7qz8 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)	70.51 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.146, 35.744, 71.154, 90, 97.69, 90
R / Rfree (%)	24.1 / 31.7

The binding sites of Fluorine atom in the Transcriptional Regulator Lmrr with Bound Daunomycin and with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp (pdb code 7qz8). 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 Bound Daunomycin and with Trp-67 and Trp-96 Replaced By the Unnatural Amino Acid 5,6-Difluorotrp, PDB code: 7qz8:
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 Bound Daunomycin and 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 Bound Daunomycin and 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:67.3 occ:1.00 FAD A:I3D67 0.0 67.3 1.0 CH2 A:I3D67 1.4 73.6 1.0 CZ2 A:I3D67 2.4 63.6 1.0 CZ3 A:I3D67 2.4 73.8 1.0 HZ2 A:I3D67 2.6 76.9 1.0 FAE A:I3D67 2.8 67.2 1.0 HB2 A:LYS77 3.3 72.6 1.0 CE2 A:I3D67 3.6 70.6 1.0 CE3 A:I3D67 3.7 66.7 1.0 HD2 A:LYS77 3.8 73.8 1.0 CD2 A:I3D67 4.2 70.2 1.0 CB A:LYS77 4.3 60.1 1.0 HB3 A:LYS77 4.5 72.6 1.0 HE3 A:I3D67 4.6 80.5 1.0 H A:LYS77 4.6 71.3 1.0 CD A:LYS77 4.7 61.1 1.0 NE1 A:I3D67 4.9 80.7 1.0 CG A:LYS77 4.9 56.8 1.0 HD3 A:LYS77 4.9 73.8 1.0 HG3 A:LYS77 5.0 68.6 1.0

Fluorine binding site 2 out of 8 in the Transcriptional Regulator Lmrr with Bound Daunomycin and 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 Bound Daunomycin and 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:67.2 occ:1.00 FAE A:I3D67 0.0 67.2 1.0 CZ3 A:I3D67 1.4 73.8 1.0 CH2 A:I3D67 2.4 73.6 1.0 CE3 A:I3D67 2.4 66.7 1.0 HE3 A:I3D67 2.6 80.5 1.0 FAD A:I3D67 2.8 67.3 1.0 HA A:ARG76 3.0 85.4 1.0 H A:LYS77 3.1 71.3 1.0 HB2 A:LYS77 3.3 72.6 1.0 N A:LYS77 3.4 59.0 1.0 O A:ARG75 3.5 69.9 1.0 CZ2 A:I3D67 3.6 63.6 1.0 CA A:ARG76 3.6 70.7 1.0 C A:ARG76 3.7 64.3 1.0 CD2 A:I3D67 3.7 70.2 1.0 C A:ARG75 3.9 88.0 1.0 N A:ARG76 3.9 73.8 1.0 HB3 A:ARG75 3.9 97.9 1.0 CB A:LYS77 4.1 60.1 1.0 CE2 A:I3D67 4.1 70.6 1.0 CA A:LYS77 4.2 55.3 1.0 HA A:LYS77 4.3 66.9 1.0 HB3 A:LYS77 4.4 72.6 1.0 O A:ARG76 4.5 62.6 1.0 HB2 A:ARG75 4.5 97.9 1.0 H A:ARG76 4.5 89.0 1.0 HZ2 A:I3D67 4.5 76.9 1.0 CB A:ARG75 4.6 81.1 1.0 CA A:ARG75 4.9 87.5 1.0 CG A:I3D67 5.0 67.5 1.0

Fluorine binding site 3 out of 8 in the Transcriptional Regulator Lmrr with Bound Daunomycin and 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 Bound Daunomycin and 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:65.4 occ:1.00 FAD A:I3D96 0.0 65.4 1.0 CH2 A:I3D96 1.4 74.7 1.0 CZ2 A:I3D96 2.3 77.3 1.0 CZ3 A:I3D96 2.4 70.1 1.0 HZ2 A:I3D96 2.6 93.2 1.0 HG21 B:VAL15 2.7 78.5 1.0 FAE A:I3D96 2.8 63.9 1.0 HA B:GLN12 2.9 78.1 1.0 HB1 B:ALA11 2.9 74.5 1.0 O B:ALA11 3.0 59.1 1.0 C B:ALA11 3.1 63.9 1.0 HG23 B:VAL15 3.2 78.5 1.0 O19 A:DM1201 3.3 80.7 1.0 N B:GLN12 3.3 65.6 1.0 CG2 B:VAL15 3.4 65.0 1.0 HB3 B:ALA11 3.4 74.5 1.0 C19 A:DM1201 3.5 73.2 1.0 CB B:ALA11 3.5 61.7 1.0 CA B:GLN12 3.5 64.6 1.0 HO17 A:DM1201 3.6 105.2 1.0 CE2 A:I3D96 3.6 78.1 1.0 CE3 A:I3D96 3.7 65.3 1.0 HG3 B:GLN12 3.7 74.1 1.0 H B:GLN12 3.8 79.3 1.0 C20 A:DM1201 3.8 72.8 1.0 HG2 B:GLN12 3.8 74.1 1.0 H1 A:DM1201 3.9 84.1 1.0 CA B:ALA11 3.9 68.0 1.0 HB B:VAL15 4.0 70.8 1.0 C1 A:DM1201 4.0 69.6 1.0 HG22 B:VAL15 4.1 78.5 1.0 C18 A:DM1201 4.1 78.7 1.0 CD2 A:I3D96 4.1 73.1 1.0 CG B:GLN12 4.1 61.3 1.0 CB B:VAL15 4.3 58.6 1.0 HA B:ALA11 4.3 82.1 1.0 O17 A:DM1201 4.4 87.2 1.0 HB2 B:ALA11 4.4 74.5 1.0 CB B:GLN12 4.4 58.9 1.0 HE3 A:I3D96 4.6 78.9 1.0 C5 A:DM1201 4.6 79.7 1.0 C17 A:DM1201 4.6 81.7 1.0 H B:VAL15 4.6 64.6 1.0 C B:GLN12 4.7 55.5 1.0 HG11 B:VAL15 4.7 70.2 1.0 C7 A:DM1201 4.8 83.7 1.0 O B:MET8 4.8 66.5 1.0 C2 A:DM1201 4.8 71.3 1.0 NE1 A:I3D96 4.9 81.6 1.0

Fluorine binding site 4 out of 8 in the Transcriptional Regulator Lmrr with Bound Daunomycin and 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 Bound Daunomycin and 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:63.9 occ:1.00 FAE A:I3D96 0.0 63.9 1.0 CZ3 A:I3D96 1.4 70.1 1.0 CE3 A:I3D96 2.4 65.3 1.0 CH2 A:I3D96 2.4 74.7 1.0 HG21 B:VAL15 2.6 78.5 1.0 HE3 A:I3D96 2.6 78.9 1.0 FAD A:I3D96 2.8 65.4 1.0 HG11 B:VAL15 2.9 70.2 1.0 HG11 A:VAL99 3.2 65.3 1.0 HB B:VAL15 3.3 70.8 1.0 CG2 B:VAL15 3.4 65.0 1.0 HA B:GLN12 3.4 78.1 1.0 CG1 B:VAL15 3.6 58.0 1.0 CB B:VAL15 3.6 58.6 1.0 CD2 A:I3D96 3.6 73.1 1.0 CZ2 A:I3D96 3.6 77.3 1.0 HG12 A:VAL99 3.7 65.3 1.0 HG2 B:GLN12 3.8 74.1 1.0 HG12 B:VAL15 3.9 70.2 1.0 CG1 A:VAL99 3.9 54.0 1.0 C5 A:DM1201 3.9 79.7 1.0 HG23 B:VAL15 3.9 78.5 1.0 C6 A:DM1201 4.0 87.7 1.0 C20 A:DM1201 4.1 72.8 1.0 HG22 B:VAL15 4.1 78.5 1.0 CE2 A:I3D96 4.1 78.1 1.0 H213 A:DM1201 4.2 100.4 1.0 O6 A:DM1201 4.3 86.7 1.0 C7 A:DM1201 4.3 83.7 1.0 HB A:VAL99 4.3 77.6 1.0 C4 A:DM1201 4.3 86.3 1.0 C19 A:DM1201 4.3 73.2 1.0 CA B:GLN12 4.4 64.6 1.0 HG21 A:VAL99 4.4 73.6 1.0 HG13 B:VAL15 4.4 70.2 1.0 C18 A:DM1201 4.4 78.7 1.0 HZ2 A:I3D96 4.5 93.2 1.0 C1 A:DM1201 4.6 69.6 1.0 CB A:VAL99 4.6 64.2 1.0 CG B:GLN12 4.6 61.3 1.0 HG13 A:VAL99 4.7 65.3 1.0 O B:ALA11 4.7 59.1 1.0 HA A:I3D96 4.7 76.9 1.0 O4 A:DM1201 4.8 93.0 1.0 HG3 B:GLN12 4.8 74.1 1.0 C3 A:DM1201 4.9 74.5 1.0 O19 A:DM1201 4.9 80.7 1.0 CG A:I3D96 4.9 75.9 1.0 CB B:GLN12 4.9 58.9 1.0 O B:GLN12 5.0 47.5 1.0 C21 A:DM1201 5.0 83.2 1.0 C2 A:DM1201 5.0 71.3 1.0 CG2 A:VAL99 5.0 60.9 1.0

Fluorine binding site 5 out of 8 in the Transcriptional Regulator Lmrr with Bound Daunomycin and 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 Bound Daunomycin and 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:120.5 occ:1.00 FAD B:I3D67 0.0 120.5 1.0 CH2 B:I3D67 1.4 122.9 1.0 CZ2 B:I3D67 2.4 125.4 1.0 CZ3 B:I3D67 2.4 130.4 1.0 HZ2 B:I3D67 2.6 151.0 1.0 FAE B:I3D67 2.8 139.2 1.0 HB2 B:LYS77 3.0 122.6 1.0 HD2 B:LYS77 3.2 118.8 1.0 CE2 B:I3D67 3.6 128.0 1.0 CE3 B:I3D67 3.7 132.0 1.0 CB B:LYS77 3.9 101.7 1.0 CD B:LYS77 4.0 98.6 1.0 CD2 B:I3D67 4.1 123.0 1.0 HG3 B:LYS77 4.2 115.8 1.0 CG B:LYS77 4.3 96.1 1.0 HB3 B:LYS77 4.4 122.6 1.0 HE3 B:I3D67 4.5 159.0 1.0 HD3 B:LYS77 4.6 118.8 1.0 HZ2 B:LYS77 4.7 125.3 1.0 HA B:LYS77 4.8 131.2 1.0 CA B:LYS77 4.9 108.9 1.0 NE1 B:I3D67 4.9 127.0 1.0 H B:LYS77 4.9 126.7 1.0 HE3 B:LYS77 4.9 125.1 1.0 N B:LYS77 5.0 105.2 1.0 CE B:LYS77 5.0 103.8 1.0

Fluorine binding site 6 out of 8 in the Transcriptional Regulator Lmrr with Bound Daunomycin and 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 Bound Daunomycin and 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:139.2 occ:1.00 FAE B:I3D67 0.0 139.2 1.0 CZ3 B:I3D67 1.4 130.4 1.0 CE3 B:I3D67 2.4 132.0 1.0 CH2 B:I3D67 2.4 122.9 1.0 HE3 B:I3D67 2.6 159.0 1.0 HB2 B:LYS77 2.7 122.6 1.0 FAD B:I3D67 2.8 120.5 1.0 H B:LYS77 2.9 126.7 1.0 N B:LYS77 3.0 105.2 1.0 CB B:LYS77 3.5 101.7 1.0 CA B:LYS77 3.6 108.9 1.0 HA B:LYS77 3.6 131.2 1.0 CD2 B:I3D67 3.6 123.0 1.0 CZ2 B:I3D67 3.7 125.4 1.0 HB3 B:LYS77 4.0 122.6 1.0 CE2 B:I3D67 4.2 128.0 1.0 HZ2 B:I3D67 4.5 151.0 1.0 HG3 B:LYS77 4.5 115.8 1.0 CG B:LYS77 4.6 96.1 1.0 HD2 B:LYS77 4.7 118.8 1.0 CG B:I3D67 5.0 120.2 1.0

Fluorine binding site 7 out of 8 in the Transcriptional Regulator Lmrr with Bound Daunomycin and 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 Bound Daunomycin and 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:63.4 occ:1.00 FAD B:I3D96 0.0 63.4 1.0 CH2 B:I3D96 1.4 71.2 1.0 CZ3 B:I3D96 2.4 74.6 1.0 CZ2 B:I3D96 2.4 74.2 1.0 HZ2 B:I3D96 2.6 89.6 1.0 FAE B:I3D96 2.7 68.6 1.0 HG21 A:VAL15 2.8 73.8 1.0 HA A:GLN12 3.0 66.7 1.0 HB1 A:ALA11 3.1 70.2 1.0 O17 A:DM1201 3.4 87.2 1.0 HG3 A:GLN12 3.4 70.5 1.0 HG2 A:GLN12 3.5 70.5 1.0 HB3 A:ALA11 3.5 70.2 1.0 C A:ALA11 3.5 52.6 1.0 N A:GLN12 3.5 59.8 1.0 HG23 A:VAL15 3.6 73.8 1.0 O A:ALA11 3.6 53.2 1.0 CE2 B:I3D96 3.6 67.7 1.0 CE3 B:I3D96 3.6 71.4 1.0 CG2 A:VAL15 3.6 61.1 1.0 C17 A:DM1201 3.7 81.7 1.0 CA A:GLN12 3.7 55.1 1.0 CB A:ALA11 3.7 58.0 1.0 HO17 A:DM1201 3.8 105.2 1.0 CG A:GLN12 3.8 58.3 1.0 H A:GLN12 3.9 72.3 1.0 H151 A:DM1201 3.9 101.6 1.0 O19 A:DM1201 4.0 80.7 1.0 HB A:VAL15 4.1 60.0 1.0 CD2 B:I3D96 4.1 74.8 1.0 C18 A:DM1201 4.2 78.7 1.0 CA A:ALA11 4.2 56.3 1.0 C19 A:DM1201 4.3 73.2 1.0 HG22 A:VAL15 4.3 73.8 1.0 C16 A:DM1201 4.4 86.8 1.0 CB A:GLN12 4.4 62.0 1.0 HO12 A:DM1201 4.4 120.1 1.0 CB A:VAL15 4.5 49.6 1.0 HE3 B:I3D96 4.5 86.2 1.0 HB2 A:ALA11 4.6 70.2 1.0 C15 A:DM1201 4.7 84.2 1.0 HA A:ALA11 4.7 68.0 1.0 HG11 A:VAL15 4.8 64.5 1.0 HE21 A:GLN12 4.9 81.2 1.0 H A:VAL15 4.9 57.9 1.0 NE1 B:I3D96 4.9 74.4 1.0 C A:GLN12 4.9 51.5 1.0 HB3 A:GLN12 5.0 75.0 1.0

Fluorine binding site 8 out of 8 in the Transcriptional Regulator Lmrr with Bound Daunomycin and 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 Bound Daunomycin and 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:68.6 occ:1.00 FAE B:I3D96 0.0 68.6 1.0 CZ3 B:I3D96 1.4 74.6 1.0 CH2 B:I3D96 2.4 71.2 1.0 CE3 B:I3D96 2.4 71.4 1.0 HE3 B:I3D96 2.6 86.2 1.0 FAD B:I3D96 2.7 63.4 1.0 HG21 A:VAL15 2.7 73.8 1.0 HG11 A:VAL15 2.9 64.5 1.0 HO12 A:DM1201 3.0 120.1 1.0 HG11 B:VAL99 3.1 78.6 1.0 HB A:VAL15 3.3 60.0 1.0 HA A:GLN12 3.4 66.7 1.0 HG2 A:GLN12 3.4 70.5 1.0 CG2 A:VAL15 3.6 61.1 1.0 CZ2 B:I3D96 3.6 74.2 1.0 CD2 B:I3D96 3.6 74.8 1.0 CG1 A:VAL15 3.7 53.3 1.0 CB A:VAL15 3.7 49.6 1.0 CG1 B:VAL99 3.9 65.0 1.0 H151 A:DM1201 3.9 101.6 1.0 O12 A:DM1201 3.9 99.7 1.0 C16 A:DM1201 3.9 86.8 1.0 HG12 B:VAL99 3.9 78.6 1.0 C17 A:DM1201 3.9 81.7 1.0 HG21 B:VAL99 4.0 71.2 1.0 HG12 A:VAL15 4.0 64.5 1.0 CE2 B:I3D96 4.1 67.7 1.0 HG22 A:VAL15 4.1 73.8 1.0 HG23 A:VAL15 4.1 73.8 1.0 C9 A:DM1201 4.3 93.9 1.0 CG A:GLN12 4.3 58.3 1.0 C18 A:DM1201 4.3 78.7 1.0 HB B:VAL99 4.3 76.2 1.0 C15 A:DM1201 4.4 84.2 1.0 CA A:GLN12 4.4 55.1 1.0 HG3 A:GLN12 4.4 70.5 1.0 HG13 A:VAL15 4.5 64.5 1.0 HZ2 B:I3D96 4.5 89.6 1.0 O17 A:DM1201 4.5 87.2 1.0 CB B:VAL99 4.6 63.0 1.0 HG13 B:VAL99 4.6 78.6 1.0 C8 A:DM1201 4.6 81.3 1.0 C7 A:DM1201 4.6 83.7 1.0 CG2 B:VAL99 4.8 58.9 1.0 C12 A:DM1201 4.8 95.6 1.0 HA B:I3D96 4.8 76.9 1.0 CB A:GLN12 4.8 62.0 1.0 HB3 A:GLN12 4.9 75.0 1.0 HD11 B:ILE103 4.9 69.8 1.0 HE21 A:GLN12 4.9 81.2 1.0 CG B:I3D96 5.0 72.5 1.0 O10 A:DM1201 5.0 104.1 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