Fluorine in PDB 5jji: Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules

The structure of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules, PDB code: 5jji was solved by N.D.Thomsen, M.R.Lawson, L.B.Witkowsky, S.Qu, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.43 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.997, 198.567, 111.448, 90.00, 104.36, 90.00
R / Rfree (%)	21.9 / 24.6

The structure of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules (pdb code 5jji). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules, PDB code: 5jji:
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 Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:30.3 occ:1.00 F1 A:BEF1002 0.0 30.3 1.0 BE A:BEF1002 1.6 32.8 1.0 F3 A:BEF1002 2.5 33.2 1.0 F2 A:BEF1002 2.6 36.5 1.0 O2B A:ADP1000 2.6 31.9 1.0 NH1 B:ARG366 2.6 30.8 1.0 NH2 A:ARG212 2.7 34.3 1.0 NH1 A:ARG212 3.1 30.6 1.0 NH2 B:ARG366 3.3 34.6 1.0 CZ A:ARG212 3.3 32.7 1.0 CZ B:ARG366 3.4 31.7 1.0 CA B:GLY337 3.7 32.4 1.0 CB A:PRO180 3.7 50.4 1.0 N A:LYS181 3.9 41.1 1.0 O B:GLY337 3.9 45.2 1.0 CA A:PRO180 3.9 44.8 1.0 PB A:ADP1000 4.0 32.9 1.0 O B:LYS336 4.0 54.6 1.0 C B:GLY337 4.0 36.4 1.0 MG A:MG1001 4.4 46.0 1.0 O A:HOH1103 4.4 30.6 1.0 C A:PRO180 4.4 40.4 1.0 NE A:ARG212 4.6 30.8 1.0 N B:GLY337 4.6 26.8 1.0 NE B:ARG366 4.6 34.6 1.0 O3B A:ADP1000 4.6 33.0 1.0 O1B A:ADP1000 4.7 33.4 1.0 CG A:PRO180 4.7 37.4 1.0 C B:LYS336 4.7 41.6 1.0 CA A:LYS181 4.8 48.6 1.0 O1A A:ADP1000 5.0 50.2 1.0

Fluorine binding site 2 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:36.5 occ:1.00 F2 A:BEF1002 0.0 36.5 1.0 BE A:BEF1002 1.6 32.8 1.0 F3 A:BEF1002 2.6 33.2 1.0 F1 A:BEF1002 2.6 30.3 1.0 NZ A:LYS184 2.7 32.5 1.0 O2B A:ADP1000 2.9 31.9 1.0 CA A:PRO180 3.2 44.8 1.0 O3B A:ADP1000 3.3 33.0 1.0 PB A:ADP1000 3.4 32.9 1.0 CD1 A:LEU320 3.5 34.1 1.0 CE A:LYS184 3.6 33.0 1.0 CB A:PRO180 3.7 50.4 1.0 O A:HOH1112 4.0 40.3 1.0 N A:LYS181 4.0 41.1 1.0 N A:PRO180 4.0 30.9 1.0 O1B A:ADP1000 4.0 33.4 1.0 C A:PRO180 4.1 40.4 1.0 MG A:MG1001 4.1 46.0 1.0 CG A:PRO180 4.2 37.4 1.0 O A:PRO179 4.2 36.6 1.0 C A:PRO179 4.4 36.2 1.0 NH1 B:ARG366 4.7 30.8 1.0 CD A:PRO180 4.7 38.5 1.0 CG A:LEU320 4.8 35.6 1.0 CA B:GLY337 4.9 32.4 1.0 CD2 A:LEU320 4.9 30.9 1.0 NH1 A:ARG212 4.9 30.6 1.0 O3A A:ADP1000 4.9 54.1 1.0

Fluorine binding site 3 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:33.2 occ:1.00 F3 A:BEF1002 0.0 33.2 1.0 BE A:BEF1002 1.5 32.8 1.0 MG A:MG1001 2.0 46.0 1.0 O2B A:ADP1000 2.4 31.9 1.0 F1 A:BEF1002 2.5 30.3 1.0 F2 A:BEF1002 2.6 36.5 1.0 O A:HOH1103 2.8 30.6 1.0 O A:HOH1112 2.8 40.3 1.0 O A:HOH1106 2.9 29.9 1.0 NH1 A:ARG212 2.9 30.6 1.0 O1B A:ADP1000 3.0 33.4 1.0 PB A:ADP1000 3.1 32.9 1.0 OG1 A:THR185 3.9 39.2 1.0 NH2 B:ARG366 3.9 34.6 1.0 CZ A:ARG212 4.0 32.7 1.0 O3B A:ADP1000 4.0 33.0 1.0 OE2 A:GLU211 4.1 67.1 1.0 NH2 A:ARG212 4.2 34.3 1.0 O1A A:ADP1000 4.3 50.2 1.0 O3A A:ADP1000 4.5 54.1 1.0 OE2 A:GLU215 4.5 45.6 1.0 NZ A:LYS184 4.5 32.5 1.0 NH1 B:ARG366 4.6 30.8 1.0 CZ B:ARG366 4.7 31.7 1.0 O B:GLY337 4.8 45.2 1.0 CD A:GLU211 4.9 59.3 1.0 CE A:LYS184 4.9 33.0 1.0 PA A:ADP1000 5.0 34.1 1.0 CB A:THR185 5.0 34.9 1.0

Fluorine binding site 4 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:29.1 occ:1.00 F1 B:BEF503 0.0 29.1 1.0 BE B:BEF503 1.6 20.4 1.0 F3 B:BEF503 2.5 30.6 1.0 F2 B:BEF503 2.6 23.4 1.0 O2B B:ADP501 2.6 27.9 1.0 NH1 C:ARG366 2.7 26.8 1.0 NH2 B:ARG212 3.0 21.6 1.0 CA C:GLY337 3.4 27.4 1.0 O C:HOH1133 3.5 29.9 1.0 NH1 B:ARG212 3.5 30.7 1.0 CB B:PRO180 3.5 20.6 1.0 N B:LYS181 3.6 31.6 1.0 CZ C:ARG366 3.6 26.3 1.0 NH2 C:ARG366 3.6 21.4 1.0 CA B:PRO180 3.7 34.5 1.0 CZ B:ARG212 3.7 24.1 1.0 O C:GLY337 4.0 32.4 1.0 PB B:ADP501 4.0 27.5 1.0 O C:LYS336 4.0 38.0 1.0 C C:GLY337 4.0 26.1 1.0 C B:PRO180 4.1 27.7 1.0 N C:GLY337 4.2 23.1 1.0 MG B:MG502 4.4 39.0 1.0 CA B:LYS181 4.5 35.7 1.0 C C:LYS336 4.5 30.0 1.0 CG B:PRO180 4.5 20.3 1.0 O3B B:ADP501 4.6 27.6 1.0 O B:HOH602 4.7 29.9 1.0 O1B B:ADP501 4.7 33.5 1.0 NE C:ARG366 4.7 37.5 1.0 O B:HOH635 4.8 36.6 1.0 N B:PRO180 5.0 27.8 1.0 NE B:ARG212 5.0 30.1 1.0 O B:HOH642 5.0 29.9 1.0

Fluorine binding site 5 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:23.4 occ:1.00 F2 B:BEF503 0.0 23.4 1.0 BE B:BEF503 1.6 20.4 1.0 F3 B:BEF503 2.6 30.6 1.0 F1 B:BEF503 2.6 29.1 1.0 NZ B:LYS184 2.7 24.7 1.0 O2B B:ADP501 2.8 27.9 1.0 O B:HOH635 3.1 36.6 1.0 O3B B:ADP501 3.3 27.6 1.0 CA B:PRO180 3.3 34.5 1.0 PB B:ADP501 3.4 27.5 1.0 CD2 B:LEU320 3.5 34.1 1.0 O B:HOH642 3.5 29.9 1.0 O C:HOH1133 3.6 29.9 1.0 CE B:LYS184 3.6 27.1 1.0 CB B:PRO180 3.9 20.6 1.0 N B:LYS181 3.9 31.6 1.0 O1B B:ADP501 3.9 33.5 1.0 MG B:MG502 4.0 39.0 1.0 N B:PRO180 4.1 27.8 1.0 C B:PRO180 4.2 27.7 1.0 O B:PRO179 4.2 29.4 1.0 CG B:PRO180 4.4 20.3 1.0 C B:PRO179 4.5 27.4 1.0 CG B:LEU320 4.7 24.8 1.0 CD B:PRO180 4.8 35.9 1.0 O3A B:ADP501 4.9 34.3 1.0 O B:HOH643 4.9 40.6 1.0 NH1 C:ARG366 4.9 26.8 1.0 CD B:LYS184 5.0 28.2 1.0 CA C:GLY337 5.0 27.4 1.0

Fluorine binding site 6 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:30.6 occ:1.00 F3 B:BEF503 0.0 30.6 1.0 BE B:BEF503 1.5 20.4 1.0 MG B:MG502 2.0 39.0 1.0 O2B B:ADP501 2.5 27.9 1.0 F1 B:BEF503 2.5 29.1 1.0 F2 B:BEF503 2.6 23.4 1.0 O B:HOH642 2.7 29.9 1.0 O B:HOH602 2.9 29.9 1.0 NH1 B:ARG212 2.9 30.7 1.0 O B:HOH615 3.0 29.9 1.0 O1B B:ADP501 3.1 33.5 1.0 PB B:ADP501 3.2 27.5 1.0 O C:HOH1133 3.2 29.9 1.0 O B:HOH635 3.5 36.6 1.0 CZ B:ARG212 3.9 24.1 1.0 OG1 B:THR185 4.0 35.8 1.0 NH2 B:ARG212 4.1 21.6 1.0 NH2 C:ARG366 4.1 21.4 1.0 OE2 B:GLU211 4.1 51.2 1.0 O3B B:ADP501 4.1 27.6 1.0 O2A B:ADP501 4.3 41.0 1.0 NH1 C:ARG366 4.5 26.8 1.0 O3A B:ADP501 4.5 34.3 1.0 OE2 B:GLU215 4.6 49.4 1.0 O C:GLY337 4.7 32.4 1.0 CZ C:ARG366 4.7 26.3 1.0 CD B:GLU211 4.7 54.6 1.0 NZ B:LYS184 4.8 24.7 1.0 OE1 B:GLU211 4.8 55.9 1.0

Fluorine binding site 7 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:F1002 b:53.3 occ:1.00 F1 C:BEF1002 0.0 53.3 1.0 BE C:BEF1002 1.6 32.3 1.0 F3 C:BEF1002 2.5 30.3 1.0 F2 C:BEF1002 2.6 36.0 1.0 O3B C:ADP1000 2.6 39.7 1.0 NH1 D:ARG366 2.7 32.8 1.0 NH2 C:ARG212 3.0 32.9 1.0 CA D:GLY337 3.3 30.6 1.0 O C:HOH1146 3.4 29.9 1.0 NH1 C:ARG212 3.4 30.9 1.0 CZ D:ARG366 3.5 37.8 1.0 NH2 D:ARG366 3.5 30.1 1.0 N C:LYS181 3.6 40.5 1.0 CZ C:ARG212 3.6 31.6 1.0 CB C:PRO180 3.7 34.4 1.0 O D:GLY337 3.7 50.5 1.0 CA C:PRO180 3.8 41.6 1.0 C D:GLY337 3.9 41.6 1.0 PB C:ADP1000 4.0 41.1 1.0 C C:PRO180 4.2 39.8 1.0 O D:LYS336 4.2 39.0 1.0 N D:GLY337 4.3 26.8 1.0 MG C:MG1001 4.4 45.6 1.0 CA C:LYS181 4.5 38.4 1.0 O1B C:ADP1000 4.6 31.1 1.0 O C:HOH1105 4.7 31.1 1.0 C D:LYS336 4.7 27.6 1.0 O2B C:ADP1000 4.7 39.6 1.0 NE D:ARG366 4.8 42.5 1.0 CG C:PRO180 4.8 39.5 1.0 O C:HOH1155 4.8 29.9 1.0 O C:HOH1145 4.9 29.9 1.0 NE C:ARG212 4.9 29.9 1.0

Fluorine binding site 8 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:F1002 b:36.0 occ:1.00 F2 C:BEF1002 0.0 36.0 1.0 BE C:BEF1002 1.6 32.3 1.0 F3 C:BEF1002 2.6 30.3 1.0 F1 C:BEF1002 2.6 53.3 1.0 NZ C:LYS184 2.8 29.2 1.0 O C:HOH1155 2.8 29.9 1.0 O3B C:ADP1000 2.9 39.7 1.0 O C:HOH1146 3.4 29.9 1.0 O1B C:ADP1000 3.4 31.1 1.0 CD2 C:LEU320 3.4 35.0 1.0 O C:HOH1145 3.4 29.9 1.0 CA C:PRO180 3.4 41.6 1.0 CE C:LYS184 3.4 31.2 1.0 PB C:ADP1000 3.4 41.1 1.0 O2B C:ADP1000 3.9 39.6 1.0 MG C:MG1001 4.0 45.6 1.0 CB C:PRO180 4.0 34.4 1.0 N C:LYS181 4.0 40.5 1.0 N C:PRO180 4.3 32.6 1.0 C C:PRO180 4.3 39.8 1.0 O C:PRO179 4.4 29.9 1.0 CG C:PRO180 4.5 39.5 1.0 CG C:LEU320 4.5 35.3 1.0 C C:PRO179 4.7 33.3 1.0 CD C:LYS184 4.9 31.6 1.0 NH1 D:ARG366 4.9 32.8 1.0 O3A C:ADP1000 5.0 29.3 1.0 O C:HOH1122 5.0 32.4 1.0 CA D:GLY337 5.0 30.6 1.0 CD1 C:LEU320 5.0 27.6 1.0

Fluorine binding site 9 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ C:F1002 b:30.3 occ:1.00 F3 C:BEF1002 0.0 30.3 1.0 BE C:BEF1002 1.5 32.3 1.0 MG C:MG1001 1.9 45.6 1.0 O3B C:ADP1000 2.4 39.7 1.0 F1 C:BEF1002 2.5 53.3 1.0 F2 C:BEF1002 2.6 36.0 1.0 O C:HOH1145 2.7 29.9 1.0 O C:HOH1105 2.8 31.1 1.0 O C:HOH1104 2.9 34.2 1.0 NH1 C:ARG212 2.9 30.9 1.0 O2B C:ADP1000 3.0 39.6 1.0 PB C:ADP1000 3.1 41.1 1.0 O C:HOH1146 3.3 29.9 1.0 NH2 D:ARG366 3.7 30.1 1.0 O C:HOH1155 3.8 29.9 1.0 OG1 C:THR185 3.8 35.7 1.0 OE2 C:GLU211 3.9 46.0 1.0 CZ C:ARG212 3.9 31.6 1.0 NH2 C:ARG212 4.1 32.9 1.0 O1B C:ADP1000 4.1 31.1 1.0 O2A C:ADP1000 4.1 47.4 1.0 NH1 D:ARG366 4.3 32.8 1.0 O3A C:ADP1000 4.4 29.3 1.0 CZ D:ARG366 4.5 37.8 1.0 OE2 C:GLU215 4.6 42.5 1.0 CD C:GLU211 4.6 41.6 1.0 O D:GLY337 4.7 50.5 1.0 NZ C:LYS184 4.8 29.2 1.0 OE1 C:GLU211 4.8 45.1 1.0 PA C:ADP1000 4.9 33.7 1.0 CB C:THR185 4.9 28.0 1.0 N C:LYS181 5.0 40.5 1.0

Fluorine binding site 10 out of 18 in the Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Rho Transcription Termination Factor Bound to RU7 and 6 Adp-BEF3 Molecules within 5.0Å range: probe atom residue distance (Å) B Occ D:F1002 b:42.0 occ:1.00 F1 D:BEF1002 0.0 42.0 1.0 BE D:BEF1002 1.6 44.3 1.0 F3 D:BEF1002 2.5 39.9 1.0 F2 D:BEF1002 2.6 46.0 1.0 O3B D:ADP1000 2.6 54.2 1.0 NH1 E:ARG366 2.7 52.3 1.0 NH2 D:ARG212 2.8 42.6 1.0 NH1 D:ARG212 3.3 48.3 1.0 CZ E:ARG366 3.4 52.8 1.0 CA E:GLY337 3.4 48.6 1.0 NH2 E:ARG366 3.4 52.3 1.0 CZ D:ARG212 3.5 47.6 1.0 N D:LYS181 3.7 48.8 1.0 O E:GLY337 3.8 47.5 1.0 C E:GLY337 3.9 48.1 1.0 CB D:PRO180 4.0 38.9 1.0 PB D:ADP1000 4.0 41.7 1.0 O E:LYS336 4.1 51.0 1.0 CA D:PRO180 4.1 39.5 1.0 O D:HOH1111 4.3 29.9 1.0 C D:PRO180 4.3 48.0 1.0 MG D:MG1001 4.4 46.8 1.0 N E:GLY337 4.4 49.4 1.0 O D:HOH1121 4.4 43.5 1.0 CA D:LYS181 4.5 50.4 1.0 NE E:ARG366 4.6 53.8 1.0 C E:LYS336 4.6 50.5 1.0 O1B D:ADP1000 4.7 40.6 1.0 O2B D:ADP1000 4.7 58.9 1.0 NE D:ARG212 4.8 55.2 1.0 NZ D:LYS184 4.9 54.1 1.0 O2A D:ADP1000 5.0 51.8 1.0 O D:HOH1133 5.0 36.7 1.0

N.D.Thomsen, M.R.Lawson, L.B.Witkowsky, S.Qu, J.M.Berger. Molecular Mechanisms of Substrate-Controlled Ring Dynamics and Substepping in A Nucleic Acid-Dependent Hexameric Motor. Proc. Natl. Acad. Sci. V. 113 E7691 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27856760
DOI: 10.1073/PNAS.1616745113