Fluorine in PDB 8hsr: Thermus Thermophilus Rho-Engaged Rnap Elongation Complex

All present enzymatic activity of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex:
2.7.7.6;

The structure of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex also contains other interesting chemical elements:

Magnesium	(Mg)	7 atoms
Zinc	(Zn)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex (pdb code 8hsr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex, PDB code: 8hsr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:43.0 occ:1.00 F1 A:BEF1002 0.0 43.0 1.0 BE A:BEF1002 1.5 43.0 1.0 MG A:MG1001 2.0 35.8 1.0 O3A A:ADP1000 2.0 45.4 1.0 O1B A:ADP1000 2.3 45.4 1.0 F3 A:BEF1002 2.5 43.0 1.0 PB A:ADP1000 2.5 45.4 1.0 F2 A:BEF1002 2.6 43.0 1.0 O2B A:ADP1000 2.8 45.4 1.0 PA A:ADP1000 3.5 45.4 1.0 O1A A:ADP1000 3.7 45.4 1.0 O3B A:ADP1000 4.0 45.4 1.0 O5' A:ADP1000 4.1 45.4 1.0 N A:LYS187 4.2 0.7 1.0 OG1 A:THR191 4.2 0.7 1.0 NH1 A:ARG218 4.2 0.7 1.0 OE1 A:GLU217 4.3 0.7 1.0 NH2 B:ARG373 4.3 0.8 1.0 OE2 A:GLU217 4.4 0.7 1.0 CA A:LYS187 4.4 0.7 1.0 O2A A:ADP1000 4.6 45.4 1.0 C5' A:ADP1000 4.7 45.4 1.0 N A:ALA188 4.8 0.8 1.0 N A:GLY189 4.8 0.8 1.0 CD A:GLU217 4.8 0.7 1.0 NZ A:LYS190 4.9 0.8 1.0 OE2 A:GLU221 4.9 0.7 1.0

Fluorine binding site 2 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:43.0 occ:1.00 F2 A:BEF1002 0.0 43.0 1.0 O2B A:ADP1000 1.3 45.4 1.0 BE A:BEF1002 1.6 43.0 1.0 O3A A:ADP1000 2.2 45.4 1.0 PB A:ADP1000 2.2 45.4 1.0 N A:ALA188 2.3 0.8 1.0 F3 A:BEF1002 2.5 43.0 1.0 F1 A:BEF1002 2.6 43.0 1.0 N A:LYS187 2.9 0.7 1.0 N A:GLY189 3.0 0.8 1.0 CA A:LYS187 3.0 0.7 1.0 C A:LYS187 3.1 0.7 1.0 O5' A:ADP1000 3.2 45.4 1.0 O3B A:ADP1000 3.3 45.4 1.0 NZ A:LYS190 3.3 0.8 1.0 O1B A:ADP1000 3.3 45.4 1.0 PA A:ADP1000 3.3 45.4 1.0 CA A:ALA188 3.3 0.8 1.0 C A:ALA188 3.5 0.8 1.0 N A:LYS190 3.8 0.8 1.0 C A:PRO186 3.8 0.8 1.0 CA A:GLY189 3.9 0.8 1.0 CB A:ALA188 4.0 0.8 1.0 MG A:MG1001 4.0 35.8 1.0 O2A A:ADP1000 4.1 45.4 1.0 C5' A:ADP1000 4.2 45.4 1.0 O A:PRO185 4.2 0.8 1.0 CE A:LYS190 4.3 0.8 1.0 O A:LYS187 4.3 0.7 1.0 CA A:PRO186 4.3 0.8 1.0 C A:GLY189 4.4 0.8 1.0 O1A A:ADP1000 4.4 45.4 1.0 CG A:LYS190 4.5 0.8 1.0 CB A:LYS187 4.5 0.7 1.0 O A:ALA188 4.6 0.8 1.0 CB A:LYS190 4.6 0.8 1.0 O A:PRO186 4.7 0.8 1.0 NH2 B:ARG373 4.7 0.8 1.0 CA A:LYS190 4.8 0.8 1.0

Fluorine binding site 3 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:43.0 occ:1.00 F3 A:BEF1002 0.0 43.0 1.0 BE A:BEF1002 1.5 43.0 1.0 O2B A:ADP1000 2.3 45.4 1.0 F2 A:BEF1002 2.5 43.0 1.0 F1 A:BEF1002 2.5 43.0 1.0 NZ A:LYS190 2.9 0.8 1.0 N A:LYS187 3.2 0.7 1.0 PB A:ADP1000 3.3 45.4 1.0 O1B A:ADP1000 3.3 45.4 1.0 CA A:PRO186 3.5 0.8 1.0 CE A:LYS190 3.6 0.8 1.0 O3A A:ADP1000 3.7 45.4 1.0 C A:PRO186 3.8 0.8 1.0 CB A:PRO186 4.2 0.8 1.0 CA A:LYS187 4.2 0.7 1.0 MG A:MG1001 4.2 35.8 1.0 CD2 A:LEU327 4.3 0.8 1.0 O A:PRO185 4.4 0.8 1.0 N A:ALA188 4.4 0.8 1.0 CG A:LEU327 4.4 0.8 1.0 N A:PRO186 4.6 0.8 1.0 O3B A:ADP1000 4.6 45.4 1.0 CD1 A:LEU327 4.7 0.8 1.0 C A:LYS187 4.9 0.7 1.0 OE2 A:GLU217 4.9 0.7 1.0 C A:PRO185 4.9 0.8 1.0 CD A:LYS190 4.9 0.8 1.0

Fluorine binding site 4 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:40.5 occ:1.00 F1 B:BEF502 0.0 40.5 1.0 OE2 B:GLU217 1.2 0.7 1.0 BE B:BEF502 1.5 40.5 1.0 O1A B:ADP501 2.1 43.9 1.0 CD B:GLU217 2.3 0.7 1.0 NH1 B:ARG218 2.3 0.7 1.0 F3 B:BEF502 2.5 40.5 1.0 OE2 B:GLU221 2.5 0.7 1.0 F2 B:BEF502 2.6 40.5 1.0 OE1 B:GLU221 3.0 0.7 1.0 MG C:MG1001 3.0 45.7 1.0 CD B:GLU221 3.0 0.7 1.0 OE1 B:GLU217 3.2 0.7 1.0 NH2 C:ARG373 3.2 0.8 1.0 CG B:GLU217 3.2 0.7 1.0 PA B:ADP501 3.4 43.9 1.0 CZ B:ARG218 3.6 0.7 1.0 O3A B:ADP501 3.6 43.9 1.0 CZ C:ARG373 3.7 0.8 1.0 NE C:ARG373 3.8 0.8 1.0 O1B B:ADP501 4.1 43.9 1.0 O5' B:ADP501 4.2 43.9 1.0 NH2 B:ARG218 4.2 0.7 1.0 NH1 B:ARG276 4.3 0.8 1.0 CG B:GLU221 4.5 0.7 1.0 NE B:ARG218 4.5 0.7 1.0 NH1 C:ARG373 4.5 0.8 1.0 PB B:ADP501 4.6 43.9 1.0 CD B:ARG218 4.6 0.7 1.0 O2A B:ADP501 4.6 43.9 1.0 CG B:ARG218 4.6 0.7 1.0 CB B:GLU217 4.7 0.7 1.0 CG2 B:THR191 4.7 0.7 1.0 CD C:ARG373 4.8 0.8 1.0 O3' B:ADP501 5.0 43.9 1.0

Fluorine binding site 5 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:40.5 occ:1.00 F2 B:BEF502 0.0 40.5 1.0 BE B:BEF502 1.6 40.5 1.0 OE1 B:GLU217 2.1 0.7 1.0 O1B B:ADP501 2.4 43.9 1.0 NH1 B:ARG276 2.4 0.8 1.0 OE2 B:GLU217 2.4 0.7 1.0 CD B:GLU217 2.4 0.7 1.0 F3 B:BEF502 2.5 40.5 1.0 F1 B:BEF502 2.6 40.5 1.0 O1A B:ADP501 3.2 43.9 1.0 PB B:ADP501 3.4 43.9 1.0 O3A B:ADP501 3.5 43.9 1.0 CZ B:ARG276 3.7 0.8 1.0 CG B:GLU217 3.7 0.7 1.0 NH1 B:ARG218 3.8 0.7 1.0 PA B:ADP501 3.8 43.9 1.0 O3B B:ADP501 3.9 43.9 1.0 O C:GLY344 4.0 0.7 1.0 NH2 C:ARG373 4.1 0.8 1.0 CD B:ARG276 4.3 0.8 1.0 NE B:ARG276 4.4 0.8 1.0 CZ B:ARG218 4.5 0.7 1.0 O2A B:ADP501 4.5 43.9 1.0 NH2 B:ARG276 4.6 0.8 1.0 MG C:MG1001 4.6 45.7 1.0 CB B:GLU217 4.6 0.7 1.0 NH2 B:ARG218 4.6 0.7 1.0 OG B:SER273 4.7 0.8 1.0 O2B B:ADP501 4.8 43.9 1.0 O B:ASP216 4.9 0.8 1.0

Fluorine binding site 6 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:40.5 occ:1.00 F3 B:BEF502 0.0 40.5 1.0 BE B:BEF502 1.5 40.5 1.0 O1A B:ADP501 2.1 43.9 1.0 CD B:GLU217 2.5 0.7 1.0 F2 B:BEF502 2.5 40.5 1.0 F1 B:BEF502 2.5 40.5 1.0 OE2 B:GLU217 2.7 0.7 1.0 NH1 B:ARG276 2.7 0.8 1.0 CG B:GLU217 2.8 0.7 1.0 OE1 B:GLU217 2.9 0.7 1.0 PA B:ADP501 3.2 43.9 1.0 CG2 B:THR191 3.4 0.7 1.0 OD2 B:ASP272 3.4 0.8 1.0 O2A B:ADP501 3.6 43.9 1.0 CZ B:ARG276 3.7 0.8 1.0 CB B:GLU217 3.8 0.7 1.0 NH2 B:ARG276 3.9 0.8 1.0 O3A B:ADP501 4.0 43.9 1.0 OD1 B:ASP272 4.0 0.8 1.0 CG B:ASP272 4.1 0.8 1.0 O1B B:ADP501 4.2 43.9 1.0 OG B:SER273 4.3 0.8 1.0 MG C:MG1001 4.4 45.7 1.0 O3B B:ADP501 4.4 43.9 1.0 OE2 B:GLU221 4.4 0.7 1.0 OE1 B:GLU221 4.5 0.7 1.0 PB B:ADP501 4.5 43.9 1.0 O5' B:ADP501 4.6 43.9 1.0 CD B:GLU221 4.7 0.7 1.0 CB B:THR191 4.7 0.7 1.0 NH1 B:ARG218 4.7 0.7 1.0 CA B:GLU217 4.9 0.7 1.0 NE B:ARG276 4.9 0.8 1.0 OG1 B:THR191 4.9 0.7 1.0

Fluorine binding site 7 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F1004 b:40.5 occ:1.00 F1 C:BEF1004 0.0 40.5 1.0 BE C:BEF1004 1.5 40.5 1.0 OE1 C:GLU217 1.9 0.7 1.0 O2B C:ADP1002 2.3 43.3 1.0 NH1 C:ARG218 2.4 0.7 1.0 F3 C:BEF1004 2.5 40.5 1.0 F2 C:BEF1004 2.6 40.5 1.0 CD C:GLU217 2.7 0.7 1.0 MG C:MG1003 2.8 31.2 1.0 OE2 C:GLU217 2.9 0.7 1.0 OE1 C:GLU221 3.1 0.7 1.0 CZ C:ARG218 3.4 0.7 1.0 OE2 C:GLU221 3.6 0.7 1.0 NH1 C:ARG276 3.6 0.8 1.0 PB C:ADP1002 3.7 43.3 1.0 CD C:GLU221 3.7 0.7 1.0 O D:GLY344 3.7 0.7 1.0 NH2 C:ARG218 4.0 0.7 1.0 CG C:GLU217 4.1 0.7 1.0 CG C:ARG218 4.2 0.7 1.0 NH2 C:ARG276 4.2 0.8 1.0 NE C:ARG218 4.2 0.7 1.0 CZ C:ARG276 4.3 0.8 1.0 O1B C:ADP1002 4.3 43.3 1.0 CB C:GLU217 4.4 0.7 1.0 CA C:GLU217 4.4 0.7 1.0 O1A C:ADP1002 4.4 43.3 1.0 CD C:ARG218 4.4 0.7 1.0 N C:ARG218 4.4 0.7 1.0 OG1 C:THR191 4.6 0.7 1.0 O3A C:ADP1002 4.6 43.3 1.0 O3B C:ADP1002 4.6 43.3 1.0 C D:GLY344 5.0 0.7 1.0 C C:GLU217 5.0 0.7 1.0

Fluorine binding site 8 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F1004 b:40.5 occ:1.00 F2 C:BEF1004 0.0 40.5 1.0 BE C:BEF1004 1.6 40.5 1.0 O2B C:ADP1002 2.2 43.3 1.0 F3 C:BEF1004 2.5 40.5 1.0 NH2 C:ARG276 2.6 0.8 1.0 O D:GLY344 2.6 0.7 1.0 F1 C:BEF1004 2.6 40.5 1.0 CZ C:ARG276 3.2 0.8 1.0 PB C:ADP1002 3.2 43.3 1.0 O3B C:ADP1002 3.3 43.3 1.0 NH1 C:ARG218 3.3 0.7 1.0 NH2 C:ARG218 3.4 0.7 1.0 NH1 C:ARG276 3.5 0.8 1.0 C D:GLY344 3.5 0.7 1.0 CA D:GLY344 3.6 0.7 1.0 CZ C:ARG218 3.6 0.7 1.0 OE2 C:GLU217 3.9 0.7 1.0 O3A C:ADP1002 4.1 43.3 1.0 MG C:MG1003 4.1 31.2 1.0 NE C:ARG276 4.1 0.8 1.0 OE1 C:GLU217 4.1 0.7 1.0 O1B C:ADP1002 4.5 43.3 1.0 CD C:GLU217 4.5 0.7 1.0 CB C:PRO186 4.6 0.8 1.0 N D:THR345 4.7 0.7 1.0 NE C:ARG218 4.8 0.7 1.0 N C:LYS187 4.9 0.7 1.0

Fluorine binding site 9 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F1004 b:40.5 occ:1.00 F3 C:BEF1004 0.0 40.5 1.0 BE C:BEF1004 1.5 40.5 1.0 OE2 C:GLU217 1.8 0.7 1.0 F2 C:BEF1004 2.5 40.5 1.0 O2B C:ADP1002 2.5 43.3 1.0 F1 C:BEF1004 2.5 40.5 1.0 CD C:GLU217 2.6 0.7 1.0 OE1 C:GLU217 2.8 0.7 1.0 NH1 C:ARG276 3.0 0.8 1.0 CZ C:ARG276 3.2 0.8 1.0 OG C:SER273 3.2 0.8 1.0 PB C:ADP1002 3.2 43.3 1.0 O3B C:ADP1002 3.4 43.3 1.0 MG C:MG1003 3.5 31.2 1.0 NH2 C:ARG276 3.6 0.8 1.0 O1B C:ADP1002 3.6 43.3 1.0 OD1 C:ASP272 3.7 0.8 1.0 NE C:ARG276 3.7 0.8 1.0 CG C:GLU217 4.0 0.7 1.0 CD C:ARG276 4.2 0.8 1.0 CG C:ASP272 4.5 0.8 1.0 OD2 C:ASP272 4.6 0.8 1.0 CB C:SER273 4.6 0.8 1.0 O C:ASP216 4.6 0.8 1.0 NH1 C:ARG218 4.6 0.7 1.0 O3A C:ADP1002 4.7 43.3 1.0 O D:GLY344 4.7 0.7 1.0 OG1 C:THR191 4.9 0.7 1.0

Fluorine binding site 10 out of 18 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:F1002 b:43.3 occ:1.00 F1 D:BEF1002 0.0 43.3 1.0 BE D:BEF1002 1.5 43.3 1.0 MG D:MG1001 1.9 35.9 1.0 O2A D:ADP1000 2.1 44.2 1.0 O1B D:ADP1000 2.4 44.2 1.0 F3 D:BEF1002 2.5 43.3 1.0 F2 D:BEF1002 2.6 43.3 1.0 PA D:ADP1000 3.1 44.2 1.0 PB D:ADP1000 3.2 44.2 1.0 O3A D:ADP1000 3.2 44.2 1.0 NH1 D:ARG218 3.3 0.7 1.0 O2B D:ADP1000 3.4 44.2 1.0 OE1 D:GLU217 3.4 0.7 1.0 O1A D:ADP1000 3.9 44.2 1.0 OE2 D:GLU217 4.1 0.7 1.0 OG1 D:THR191 4.2 0.7 1.0 CD D:GLU217 4.2 0.7 1.0 OE2 D:GLU221 4.2 0.7 1.0 CZ D:ARG218 4.2 0.7 1.0 O E:GLY344 4.4 0.7 1.0 O5' D:ADP1000 4.5 44.2 1.0 CA E:GLY344 4.5 0.7 1.0 NH2 D:ARG218 4.5 0.7 1.0 NH2 D:ARG276 4.5 0.8 1.0 O3B D:ADP1000 4.6 44.2 1.0 NH2 E:ARG373 4.7 0.8 1.0 N D:LYS187 4.9 0.7 1.0 C E:GLY344 4.9 0.7 1.0

Y.Murayama, H.Ehara, M.Aoki, M.Goto, T.Yokoyama, S.I.Sekine. Structural Basis of the Transcription Termination Factor Rho Engagement with Transcribing Rna Polymerase From Thermus Thermophilus. Sci Adv V. 9 E7093 2023.
ISSN: ESSN 2375-2548
PubMed: 36753546
DOI: 10.1126/SCIADV.ADE7093