Fluorine in PDB 3ice: Rho Transcription Termination Factor Bound to Rna and Adp-BEF3

The structure of Rho Transcription Termination Factor Bound to Rna and Adp-BEF3, PDB code: 3ice was solved by N.D.Thomsen, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.88 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	69.230, 127.030, 127.170, 60.48, 90.26, 89.77
R / Rfree (%)	27 / 29.5

The structure of Rho Transcription Termination Factor Bound to Rna and Adp-BEF3 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 Rna and Adp-BEF3 (pdb code 3ice). 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 Rna and Adp-BEF3, PDB code: 3ice:
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 Rna and Adp-BEF3


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:26.2 occ:1.00 F1 A:BEF1002 0.0 26.2 1.0 BE A:BEF1002 1.6 30.6 1.0 F3 A:BEF1002 2.5 28.4 1.0 F2 A:BEF1002 2.6 38.3 1.0 NH2 B:ARG366 2.8 22.4 1.0 NH2 A:ARG212 2.9 27.9 1.0 CA B:GLY337 3.1 39.8 1.0 O1B A:ADP1000 3.1 28.6 1.0 NH1 A:ARG212 3.2 28.5 1.0 NH1 B:ARG366 3.4 21.3 1.0 C B:GLY337 3.4 33.6 1.0 CZ A:ARG212 3.4 23.6 1.0 CZ B:ARG366 3.5 24.1 1.0 O B:LYS336 3.6 42.0 1.0 O B:GLY337 3.7 26.4 1.0 CB A:PRO180 3.8 41.0 1.0 CA A:PRO180 4.0 32.4 1.0 N B:THR338 4.1 35.6 1.0 O A:HOH1108 4.1 26.8 1.0 N B:GLY337 4.2 41.0 1.0 C B:LYS336 4.3 42.2 1.0 N A:LYS181 4.3 23.6 1.0 O A:HOH1102 4.3 32.9 1.0 PB A:ADP1000 4.4 32.0 1.0 MG A:MG1001 4.5 37.8 1.0 CG A:PRO180 4.6 46.7 1.0 O3A A:ADP1000 4.7 21.0 1.0 NE A:ARG212 4.7 30.9 1.0 C A:PRO180 4.7 24.6 1.0 O2B A:ADP1000 4.7 48.6 1.0 OE2 A:GLU211 4.8 47.5 1.0 NE B:ARG366 4.8 23.7 1.0 CA B:THR338 5.0 29.0 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:38.3 occ:1.00 F2 A:BEF1002 0.0 38.3 1.0 BE A:BEF1002 1.6 30.6 1.0 O1B A:ADP1000 2.4 28.6 1.0 F3 A:BEF1002 2.6 28.4 1.0 F1 A:BEF1002 2.6 26.2 1.0 O A:HOH1108 2.9 26.8 1.0 NZ A:LYS184 3.0 34.9 1.0 CA A:PRO180 3.2 32.4 1.0 PB A:ADP1000 3.5 32.0 1.0 O2B A:ADP1000 3.7 48.6 1.0 CB A:PRO180 3.7 41.0 1.0 N A:PRO180 3.8 27.0 1.0 CE A:LYS184 3.8 43.0 1.0 CG A:PRO180 4.0 46.7 1.0 MG A:MG1001 4.1 37.8 1.0 N A:LYS181 4.2 23.6 1.0 C A:PRO180 4.2 24.6 1.0 NH2 B:ARG366 4.3 22.4 1.0 CA B:GLY337 4.3 39.8 1.0 C A:PRO179 4.4 36.2 1.0 O A:PRO179 4.4 45.8 1.0 CD A:PRO180 4.4 41.8 1.0 O A:HOH1101 4.4 22.0 1.0 CD2 A:LEU320 4.4 27.6 1.0 O3B A:ADP1000 4.5 27.7 1.0 CG A:LEU320 4.7 29.6 1.0 O3A A:ADP1000 4.7 21.0 1.0 OE2 A:GLU211 4.8 47.5 1.0 O A:HOH1102 4.9 32.9 1.0 NH1 A:ARG212 5.0 28.5 1.0 O B:GLY337 5.0 26.4 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1002 b:28.4 occ:1.00 F3 A:BEF1002 0.0 28.4 1.0 BE A:BEF1002 1.5 30.6 1.0 MG A:MG1001 2.1 37.8 1.0 O A:HOH1102 2.5 32.9 1.0 F1 A:BEF1002 2.5 26.2 1.0 F2 A:BEF1002 2.6 38.3 1.0 O1B A:ADP1000 2.7 28.6 1.0 O2B A:ADP1000 2.8 48.6 1.0 O A:HOH1108 2.9 26.8 1.0 NH1 A:ARG212 3.0 28.5 1.0 PB A:ADP1000 3.2 32.0 1.0 OE2 A:GLU211 3.2 47.5 1.0 O A:HOH1109 3.3 40.6 1.0 O A:HOH1101 3.4 22.0 1.0 NH2 B:ARG366 3.4 22.4 1.0 O3A A:ADP1000 3.7 21.0 1.0 OG1 A:THR185 3.9 39.6 1.0 CZ A:ARG212 3.9 23.6 1.0 NH2 A:ARG212 4.2 27.9 1.0 NZ A:LYS184 4.5 34.9 1.0 CD A:GLU211 4.5 49.7 1.0 O B:GLY337 4.6 26.4 1.0 OE2 A:GLU215 4.6 41.0 1.0 CZ B:ARG366 4.6 24.1 1.0 O3B A:ADP1000 4.6 27.7 1.0 CB A:THR185 4.7 30.3 1.0 NE A:ARG212 4.9 30.9 1.0 C B:GLY337 4.9 33.6 1.0 CA B:GLY337 5.0 39.8 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1002 b:25.0 occ:1.00 F1 B:BEF1002 0.0 25.0 1.0 BE B:BEF1002 1.6 32.3 1.0 F3 B:BEF1002 2.5 29.5 1.0 F2 B:BEF1002 2.6 45.3 1.0 O1B B:ADP1000 2.8 27.5 1.0 NH2 B:ARG212 2.9 20.7 1.0 CA C:GLY337 3.1 47.0 1.0 NH2 C:ARG366 3.1 15.0 1.0 NH1 C:ARG366 3.2 22.9 1.0 O C:GLY337 3.5 54.8 1.0 CB B:PRO180 3.5 40.6 1.0 CZ C:ARG366 3.6 14.9 1.0 C C:GLY337 3.6 53.6 1.0 CA B:PRO180 3.8 28.3 1.0 O B:HOH1108 4.0 32.4 1.0 CZ B:ARG212 4.0 23.9 1.0 N B:LYS181 4.0 29.9 1.0 O C:LYS336 4.0 38.5 1.0 PB B:ADP1000 4.2 25.1 1.0 N C:GLY337 4.2 40.6 1.0 NH1 B:ARG212 4.2 24.8 1.0 C B:PRO180 4.4 26.4 1.0 MG B:MG1001 4.5 25.8 1.0 CG B:PRO180 4.5 40.9 1.0 C C:LYS336 4.5 44.9 1.0 O3A B:ADP1000 4.6 32.5 1.0 O2B B:ADP1000 4.6 31.6 1.0 N C:THR338 4.7 45.5 1.0 O B:HOH1101 4.7 16.3 1.0 NE C:ARG366 4.9 16.7 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1002 b:45.3 occ:1.00 F2 B:BEF1002 0.0 45.3 1.0 BE B:BEF1002 1.6 32.3 1.0 O1B B:ADP1000 2.4 27.5 1.0 F3 B:BEF1002 2.6 29.5 1.0 F1 B:BEF1002 2.6 25.0 1.0 O B:HOH1108 2.9 32.4 1.0 NZ B:LYS184 2.9 31.5 1.0 O2B B:ADP1000 3.3 31.6 1.0 PB B:ADP1000 3.3 25.1 1.0 CA B:PRO180 3.5 28.3 1.0 MG B:MG1001 3.6 25.8 1.0 O B:HOH1102 4.0 33.7 1.0 CB B:PRO180 4.0 40.6 1.0 CE B:LYS184 4.0 24.6 1.0 O B:PRO179 4.1 33.0 1.0 N B:PRO180 4.2 20.7 1.0 O3B B:ADP1000 4.3 23.5 1.0 N B:LYS181 4.3 29.9 1.0 C B:PRO180 4.4 26.4 1.0 CG B:PRO180 4.5 40.9 1.0 C B:PRO179 4.5 23.1 1.0 O3A B:ADP1000 4.5 32.5 1.0 NH2 C:ARG366 4.6 15.0 1.0 O B:HOH1101 4.8 16.3 1.0 CA C:GLY337 4.8 47.0 1.0 CG B:LEU320 4.9 38.1 1.0 CD B:PRO180 5.0 40.2 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1002 b:29.5 occ:1.00 F3 B:BEF1002 0.0 29.5 1.0 BE B:BEF1002 1.5 32.3 1.0 MG B:MG1001 2.0 25.8 1.0 O B:HOH1101 2.5 16.3 1.0 F1 B:BEF1002 2.5 25.0 1.0 F2 B:BEF1002 2.6 45.3 1.0 O1B B:ADP1000 2.6 27.5 1.0 O2B B:ADP1000 2.8 31.6 1.0 O B:HOH1108 3.1 32.4 1.0 PB B:ADP1000 3.1 25.1 1.0 NH2 C:ARG366 3.2 15.0 1.0 NH1 B:ARG212 3.2 24.8 1.0 O3A B:ADP1000 3.4 32.5 1.0 O B:HOH1102 3.5 33.7 1.0 NH2 B:ARG212 3.5 20.7 1.0 OE2 B:GLU211 3.6 42.0 1.0 CZ B:ARG212 3.8 23.9 1.0 OG1 B:THR185 3.8 30.4 1.0 O C:GLY337 4.3 54.8 1.0 CZ C:ARG366 4.3 14.9 1.0 OE2 B:GLU215 4.4 31.6 1.0 O3B B:ADP1000 4.5 23.5 1.0 CB B:THR185 4.5 20.5 1.0 CD B:GLU211 4.6 30.1 1.0 NH1 C:ARG366 4.6 22.9 1.0 NZ B:LYS184 4.7 31.5 1.0 PA B:ADP1000 5.0 23.6 1.0 OE1 B:GLU211 5.0 28.6 1.0 C C:GLY337 5.0 53.6 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1002 b:32.8 occ:1.00 F1 C:BEF1002 0.0 32.8 1.0 BE C:BEF1002 1.6 37.9 1.0 F3 C:BEF1002 2.5 26.9 1.0 O1B C:ADP1000 2.5 32.5 1.0 F2 C:BEF1002 2.6 47.5 1.0 NH2 C:ARG212 2.9 41.2 1.0 NH2 D:ARG366 3.1 30.4 1.0 CA D:GLY337 3.1 32.1 1.0 O D:LYS336 3.7 32.6 1.0 CB C:PRO180 3.7 39.1 1.0 C D:GLY337 3.7 38.6 1.0 CA C:PRO180 3.8 32.7 1.0 CZ C:ARG212 3.9 35.6 1.0 O D:GLY337 3.9 38.5 1.0 N C:LYS181 3.9 40.7 1.0 PB C:ADP1000 3.9 32.8 1.0 NH1 C:ARG212 3.9 40.3 1.0 CZ D:ARG366 4.1 29.6 1.0 N D:GLY337 4.1 37.3 1.0 C C:PRO180 4.2 34.7 1.0 C D:LYS336 4.3 37.0 1.0 MG C:MG1001 4.3 45.5 1.0 NH1 D:ARG366 4.3 30.2 1.0 O2B C:ADP1000 4.4 48.7 1.0 O3A C:ADP1000 4.6 54.5 1.0 N D:THR338 4.7 32.1 1.0 CG C:PRO180 4.7 49.5 1.0 O C:HOH1101 4.8 18.5 1.0 CA C:LYS181 4.8 41.4 1.0 NZ C:LYS184 5.0 22.1 1.0 O3B C:ADP1000 5.0 33.3 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1002 b:47.5 occ:1.00 F2 C:BEF1002 0.0 47.5 1.0 BE C:BEF1002 1.6 37.9 1.0 F3 C:BEF1002 2.6 26.9 1.0 F1 C:BEF1002 2.6 32.8 1.0 NZ C:LYS184 2.9 22.1 1.0 O1B C:ADP1000 2.9 32.5 1.0 O2B C:ADP1000 3.4 48.7 1.0 PB C:ADP1000 3.7 32.8 1.0 CA C:PRO180 3.7 32.7 1.0 MG C:MG1001 3.8 45.5 1.0 O C:HOH1116 3.8 46.1 1.0 CD2 C:LEU320 3.9 29.2 1.0 CG C:LEU320 4.0 18.1 1.0 CB C:PRO180 4.1 39.1 1.0 CE C:LYS184 4.1 17.6 1.0 CD1 C:LEU320 4.4 30.9 1.0 OE1 C:GLU211 4.4 55.7 1.0 CG C:PRO180 4.5 49.5 1.0 N C:LYS181 4.5 40.7 1.0 N C:PRO180 4.5 28.8 1.0 O3B C:ADP1000 4.5 33.3 1.0 CA D:GLY337 4.5 32.1 1.0 C C:PRO180 4.7 34.7 1.0 CD C:LYS184 4.8 22.5 1.0 O C:PRO179 4.9 37.4 1.0 O D:GLY337 4.9 38.5 1.0 C C:PRO179 5.0 30.9 1.0 O3A C:ADP1000 5.0 54.5 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:F1002 b:26.9 occ:1.00 F3 C:BEF1002 0.0 26.9 1.0 BE C:BEF1002 1.6 37.9 1.0 MG C:MG1001 2.0 45.5 1.0 F1 C:BEF1002 2.5 32.8 1.0 O1B C:ADP1000 2.6 32.5 1.0 F2 C:BEF1002 2.6 47.5 1.0 O2B C:ADP1000 2.7 48.7 1.0 O C:HOH1116 2.8 46.1 1.0 NH1 C:ARG212 2.9 40.3 1.0 O C:HOH1101 2.9 18.5 1.0 PB C:ADP1000 3.1 32.8 1.0 NH2 C:ARG212 3.5 41.2 1.0 O3A C:ADP1000 3.6 54.5 1.0 CZ C:ARG212 3.6 35.6 1.0 OG1 C:THR185 3.8 24.8 1.0 OE1 C:GLU211 4.0 55.7 1.0 NH2 D:ARG366 4.1 30.4 1.0 OE2 C:GLU211 4.1 53.7 1.0 CD C:GLU211 4.2 52.7 1.0 O D:GLY337 4.2 38.5 1.0 OE2 C:GLU215 4.5 50.5 1.0 O3B C:ADP1000 4.5 33.3 1.0 NZ C:LYS184 4.6 22.1 1.0 C D:GLY337 4.8 38.6 1.0 CA D:GLY337 4.8 32.1 1.0 NE C:ARG212 4.9 37.2 1.0 CB C:THR185 4.9 31.6 1.0

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


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 Rna and Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ D:F1002 b:74.4 occ:1.00 F1 D:BEF1002 0.0 74.4 1.0 BE D:BEF1002 1.5 57.7 1.0 F3 D:BEF1002 2.5 37.7 1.0 O1B D:ADP1000 2.5 60.5 1.0 F2 D:BEF1002 2.6 67.0 1.0 CB D:PRO180 3.1 63.1 1.0 CA D:PRO180 3.1 76.6 1.0 NH2 E:ARG366 3.1 65.7 1.0 CA E:GLY337 3.4 69.0 1.0 N D:LYS181 3.5 75.8 1.0 NH1 D:ARG212 3.5 59.9 1.0 C D:PRO180 3.8 80.3 1.0 O E:GLY337 3.9 68.2 1.0 NH2 D:ARG212 3.9 64.9 1.0 CG D:PRO180 3.9 69.6 1.0 PB D:ADP1000 3.9 67.0 1.0 C E:GLY337 4.0 66.8 1.0 CZ D:ARG212 4.2 59.7 1.0 NZ D:LYS184 4.2 55.2 1.0 CZ E:ARG366 4.3 57.4 1.0 N D:PRO180 4.3 65.2 1.0 MG D:MG1001 4.3 58.3 1.0 O2B D:ADP1000 4.4 59.6 1.0 O3A D:ADP1000 4.4 51.0 1.0 N E:GLY337 4.4 67.0 1.0 O E:LYS336 4.4 67.4 1.0 O D:HOH1112 4.5 43.6 1.0 OE2 D:GLU211 4.7 57.5 1.0 NH1 E:ARG366 4.7 58.2 1.0 CA D:LYS181 4.7 79.7 1.0 CD D:PRO180 4.8 67.9 1.0 C E:LYS336 4.8 70.7 1.0 O D:PRO180 5.0 78.0 1.0

N.D.Thomsen, J.M.Berger. Running in Reverse: the Structural Basis For Translocation Polarity in Hexameric Helicases. Cell(Cambridge,Mass.) V. 139 523 2009.
ISSN: ISSN 0092-8674
PubMed: 19879839
DOI: 10.1016/J.CELL.2009.08.043