Fluorine in PDB 5tth: Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State

The structure of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State, PDB code: 5tth was solved by D.Elnatan, M.Betegon, Y.Liu, D.A.Agard, Northeast Structural Genomicsconsortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.086, 95.711, 126.558, 90.00, 134.59, 90.00
R / Rfree (%)	22.8 / 26.1

The structure of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State (pdb code 5tth). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State, PDB code: 5tth:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:65.0 occ:1.00 F1 A:BEF902 0.0 65.0 1.0 BE A:BEF902 1.5 66.1 1.0 MG A:MG903 1.8 48.0 1.0 F3 A:BEF902 2.4 72.8 1.0 F2 A:BEF902 2.6 57.3 1.0 O3B A:ADP901 2.6 60.8 1.0 O2B A:ADP901 2.9 54.4 1.0 O2A A:ADP901 3.0 50.5 1.0 PB A:ADP901 3.2 57.0 1.0 OE1 A:GLU130 3.3 0.1 1.0 O3A A:ADP901 3.7 53.3 1.0 OD1 A:ASN134 3.8 77.4 1.0 CA A:GLY219 3.9 67.1 1.0 PA A:ADP901 4.0 56.5 1.0 N A:GLY219 4.0 68.9 1.0 CA A:GLY214 4.0 77.2 1.0 NH1 A:ARG417 4.4 87.7 1.0 NH2 A:ARG417 4.5 82.0 1.0 CZ A:ARG417 4.6 83.4 1.0 CD A:GLU130 4.6 94.1 1.0 O1B A:ADP901 4.6 52.0 1.0 N A:GLN215 4.7 83.5 1.0 CG A:ASN134 4.8 74.7 1.0 C A:GLY219 5.0 65.6 1.0 C A:GLY214 5.0 80.2 1.0 O1A A:ADP901 5.0 53.4 1.0 N A:GLY214 5.0 76.7 1.0 ND2 A:ASN134 5.0 74.4 1.0

Fluorine binding site 2 out of 6 in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:57.3 occ:1.00 F2 A:BEF902 0.0 57.3 1.0 BE A:BEF902 1.6 66.1 1.0 F3 A:BEF902 2.5 72.8 1.0 O3B A:ADP901 2.6 60.8 1.0 F1 A:BEF902 2.6 65.0 1.0 N A:GLY219 2.8 68.9 1.0 N A:VAL218 3.0 75.7 1.0 N A:GLY217 3.2 79.6 1.0 O3A A:ADP901 3.5 53.3 1.0 CA A:GLY219 3.6 67.1 1.0 PB A:ADP901 3.6 57.0 1.0 CB A:PHE216 3.7 78.9 1.0 C A:VAL218 3.7 70.2 1.0 CA A:VAL218 3.8 73.6 1.0 N A:PHE216 3.8 83.8 1.0 CG2 A:VAL218 3.8 76.0 1.0 CA A:GLY217 3.9 79.7 1.0 C A:PHE216 3.9 81.2 1.0 C A:GLY217 3.9 78.7 1.0 CA A:PHE216 4.0 81.5 1.0 O2A A:ADP901 4.0 50.5 1.0 PA A:ADP901 4.2 56.5 1.0 MG A:MG903 4.3 48.0 1.0 O2B A:ADP901 4.3 54.4 1.0 NH1 A:ARG417 4.4 87.7 1.0 CD2 A:PHE216 4.4 76.5 1.0 CB A:VAL218 4.4 75.3 1.0 O1A A:ADP901 4.4 53.4 1.0 CG A:PHE216 4.5 78.9 1.0 OE1 A:GLU130 4.5 0.1 1.0 O A:VAL218 4.8 69.5 1.0 O1B A:ADP901 4.8 52.0 1.0 N A:GLN215 4.9 83.5 1.0 O A:PHE216 4.9 83.4 1.0 C A:GLY219 4.9 65.6 1.0

Fluorine binding site 3 out of 6 in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:72.8 occ:1.00 F3 A:BEF902 0.0 72.8 1.0 BE A:BEF902 1.5 66.1 1.0 F1 A:BEF902 2.4 65.0 1.0 F2 A:BEF902 2.5 57.3 1.0 O3B A:ADP901 2.5 60.8 1.0 NH2 A:ARG417 2.7 82.0 1.0 NH1 A:ARG417 3.0 87.7 1.0 N A:GLN215 3.0 83.5 1.0 CZ A:ARG417 3.2 83.4 1.0 N A:PHE216 3.3 83.8 1.0 CA A:GLY214 3.4 77.2 1.0 C A:GLY214 3.7 80.2 1.0 CD2 A:PHE216 3.8 76.5 1.0 PB A:ADP901 3.9 57.0 1.0 CA A:GLN215 4.0 90.2 1.0 C A:GLN215 4.1 88.6 1.0 CB A:PHE216 4.1 78.9 1.0 MG A:MG903 4.2 48.0 1.0 O2B A:ADP901 4.2 54.4 1.0 CA A:PHE216 4.2 81.5 1.0 CG A:PHE216 4.3 78.9 1.0 NE A:ARG417 4.3 81.6 1.0 N A:GLY217 4.4 79.6 1.0 CB A:GLN215 4.5 97.0 1.0 N A:GLY214 4.6 76.7 1.0 CE2 A:PHE216 4.6 79.0 1.0 OE1 A:GLU130 4.6 0.1 1.0 O A:ILE213 4.7 80.9 1.0 O3A A:ADP901 4.7 53.3 1.0 C A:PHE216 4.8 81.2 1.0 O A:GLY214 4.9 83.8 1.0 O1B A:ADP901 4.9 52.0 1.0

Fluorine binding site 4 out of 6 in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State within 5.0Å range: probe atom residue distance (Å) B Occ B:F802 b:55.7 occ:1.00 F1 B:BEF802 0.0 55.7 1.0 BE B:BEF802 1.5 55.7 1.0 MG B:MG803 2.0 38.0 1.0 F2 B:BEF802 2.5 55.7 1.0 F3 B:BEF802 2.6 58.3 1.0 O3B B:ADP801 2.6 55.2 1.0 O2B B:ADP801 2.9 54.3 1.0 PB B:ADP801 3.1 54.6 1.0 O2A B:ADP801 3.2 52.6 1.0 OE1 B:GLU130 3.2 1.0 1.0 O3A B:ADP801 3.8 50.2 1.0 OD1 B:ASN134 3.8 86.0 1.0 CA B:GLY219 3.9 90.1 1.0 N B:GLY219 4.1 90.7 1.0 PA B:ADP801 4.1 50.9 1.0 CA B:GLY214 4.1 88.6 1.0 CD B:GLU130 4.4 96.0 1.0 O1B B:ADP801 4.6 55.3 1.0 N B:GLN215 4.6 89.2 1.0 CG B:ASN134 4.8 87.6 1.0 C B:GLY214 5.0 88.2 1.0 ND2 B:ASN134 5.0 87.9 1.0 C B:GLY219 5.0 92.7 1.0

Fluorine binding site 5 out of 6 in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State within 5.0Å range: probe atom residue distance (Å) B Occ B:F802 b:55.7 occ:1.00 F2 B:BEF802 0.0 55.7 1.0 BE B:BEF802 1.5 55.7 1.0 F3 B:BEF802 2.4 58.3 1.0 O3B B:ADP801 2.5 55.2 1.0 F1 B:BEF802 2.5 55.7 1.0 N B:GLY219 2.7 90.7 1.0 N B:VAL218 3.3 93.0 1.0 CA B:GLY219 3.3 90.1 1.0 N B:GLY217 3.5 93.1 1.0 O3A B:ADP801 3.6 50.2 1.0 PB B:ADP801 3.6 54.6 1.0 CB B:PHE216 3.6 80.2 1.0 C B:VAL218 3.7 91.6 1.0 CG2 B:VAL218 3.8 85.1 1.0 O2A B:ADP801 3.9 52.6 1.0 CA B:VAL218 3.9 90.9 1.0 N B:PHE216 4.0 87.7 1.0 OE1 B:GLU130 4.1 1.0 1.0 CA B:PHE216 4.1 85.2 1.0 C B:PHE216 4.1 89.0 1.0 C B:GLY217 4.2 96.5 1.0 CA B:GLY217 4.2 96.6 1.0 PA B:ADP801 4.2 50.9 1.0 MG B:MG803 4.2 38.0 1.0 CD2 B:PHE216 4.3 74.3 1.0 O2B B:ADP801 4.4 54.3 1.0 CB B:VAL218 4.5 86.7 1.0 CG B:PHE216 4.5 77.2 1.0 O1A B:ADP801 4.5 49.3 1.0 C B:GLY219 4.7 92.7 1.0 O B:VAL218 4.8 93.7 1.0 O1B B:ADP801 4.9 55.3 1.0 N B:GLN215 4.9 89.2 1.0

Fluorine binding site 6 out of 6 in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State within 5.0Å range: probe atom residue distance (Å) B Occ B:F802 b:58.3 occ:1.00 F3 B:BEF802 0.0 58.3 1.0 BE B:BEF802 1.5 55.7 1.0 F2 B:BEF802 2.4 55.7 1.0 F1 B:BEF802 2.6 55.7 1.0 O3B B:ADP801 2.6 55.2 1.0 N B:PHE216 3.2 87.7 1.0 N B:GLN215 3.2 89.2 1.0 CD2 B:PHE216 3.4 74.3 1.0 CB B:PHE216 3.7 80.2 1.0 CG B:PHE216 3.9 77.2 1.0 CA B:GLY214 3.9 88.6 1.0 CA B:GLN215 4.0 91.6 1.0 PB B:ADP801 4.0 54.6 1.0 CA B:PHE216 4.0 85.2 1.0 CB B:GLN215 4.0 92.3 1.0 C B:GLN215 4.1 91.3 1.0 C B:GLY214 4.1 88.2 1.0 N B:GLY217 4.3 93.1 1.0 CE2 B:PHE216 4.3 71.9 1.0 O2B B:ADP801 4.5 54.3 1.0 OE1 B:GLU130 4.5 1.0 1.0 MG B:MG803 4.5 38.0 1.0 C B:PHE216 4.7 89.0 1.0 O B:ILE213 4.7 79.1 1.0 O3A B:ADP801 4.8 50.2 1.0 O1B B:ADP801 5.0 55.3 1.0 N B:GLY214 5.0 86.4 1.0 N B:GLY219 5.0 90.7 1.0

D.Elnatan, M.Betegon, Y.Liu, T.Ramelot, M.A.Kennedy, D.A.Agard. Symmetry Broken and Rebroken During the Atp Hydrolysis Cycle of the Mitochondrial HSP90 TRAP1. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28742020
DOI: 10.7554/ELIFE.25235