Fluorine in PDB 8hsl: Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer

Enzymatic activity of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer:
2.7.7.6;

Other elements in 8hsl:

The structure of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Magnesium (Mg) 7 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer (pdb code 8hsl). 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 Rna Polymerase Bound with An Inverted Rho Hexamer, PDB code: 8hsl:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 8hsl

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Fluorine binding site 1 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:74.4
occ:1.00
 F1 A:BEF1002 0.0 74.4 1.0
BE A:BEF1002 1.5 57.7 1.0
O3B A:ADP1000 2.1 60.5 1.0
N A:LYS187 2.3 0.7 1.0
F3 A:BEF1002 2.5 37.7 1.0
F2 A:BEF1002 2.6 67.0 1.0
C A:PRO186 3.1 0.8 1.0
CA A:PRO186 3.1 0.8 1.0
CA A:LYS187 3.3 0.7 1.0
CB A:PRO186 3.4 0.8 1.0
PB A:ADP1000 3.4 67.0 1.0
O3A A:ADP1000 3.6 51.0 1.0
CB A:LYS187 3.9 0.7 1.0
NH2 A:ARG218 3.9 0.7 1.0
NH1 B:ARG373 4.2 0.8 1.0
O2B A:ADP1000 4.2 59.6 1.0
O A:PRO186 4.2 0.8 1.0
MG A:MG1001 4.3 58.3 1.0
O1B A:ADP1000 4.5 56.9 1.0
N A:PRO186 4.6 0.8 1.0
C A:LYS187 4.6 0.7 1.0
CG A:PRO186 4.7 0.8 1.0
CZ B:ARG373 4.7 0.8 1.0
CZ A:ARG218 4.8 0.7 1.0
NH1 A:ARG218 4.8 0.7 1.0
NH2 B:ARG373 4.8 0.8 1.0
N A:ALA188 4.9 0.8 1.0
CG A:LYS187 4.9 0.7 1.0
O A:PRO185 4.9 0.8 1.0
CE A:LYS190 5.0 0.8 1.0

Fluorine binding site 2 out of 18 in 8hsl

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Fluorine binding site 2 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:67.0
occ:1.00
 F2 A:BEF1002 0.0 67.0 1.0
BE A:BEF1002 1.6 57.7 1.0
F3 A:BEF1002 2.5 37.7 1.0
F1 A:BEF1002 2.6 74.4 1.0
O3B A:ADP1000 2.8 60.5 1.0
CE A:LYS190 3.3 0.8 1.0
CA A:PRO186 3.3 0.8 1.0
CD2 A:LEU327 3.6 0.8 1.0
CB A:PRO186 3.6 0.8 1.0
NZ A:LYS190 3.7 0.8 1.0
CG A:LEU327 3.9 0.8 1.0
MG A:MG1001 4.0 58.3 1.0
PB A:ADP1000 4.0 67.0 1.0
N A:LYS187 4.0 0.7 1.0
O2B A:ADP1000 4.1 59.6 1.0
C A:PRO186 4.2 0.8 1.0
CG A:PRO186 4.2 0.8 1.0
N A:PRO186 4.3 0.8 1.0
CD1 A:LEU327 4.6 0.8 1.0
CD A:LYS190 4.6 0.8 1.0
O A:PRO185 4.7 0.8 1.0
NH2 A:ARG218 4.8 0.7 1.0
C A:PRO185 4.8 0.8 1.0
CD A:PRO186 5.0 0.8 1.0
O3A A:ADP1000 5.0 51.0 1.0

Fluorine binding site 3 out of 18 in 8hsl

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Fluorine binding site 3 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:37.7
occ:1.00
 F3 A:BEF1002 0.0 37.7 1.0
BE A:BEF1002 1.5 57.7 1.0
MG A:MG1001 1.8 58.3 1.0
O3B A:ADP1000 2.1 60.5 1.0
O2B A:ADP1000 2.2 59.6 1.0
PB A:ADP1000 2.4 67.0 1.0
F2 A:BEF1002 2.5 67.0 1.0
F1 A:BEF1002 2.5 74.4 1.0
NZ A:LYS190 2.9 0.8 1.0
O3A A:ADP1000 3.0 51.0 1.0
CE A:LYS190 3.4 0.8 1.0
OG1 A:THR191 3.5 0.7 1.0
NH1 A:ARG218 3.8 0.7 1.0
O1B A:ADP1000 3.9 56.9 1.0
N A:LYS187 4.1 0.7 1.0
NH2 A:ARG218 4.3 0.7 1.0
PA A:ADP1000 4.3 51.2 1.0
NH2 B:ARG373 4.4 0.8 1.0
CZ A:ARG218 4.5 0.7 1.0
O2A A:ADP1000 4.5 70.2 1.0
CB A:THR191 4.7 0.7 1.0
NH1 B:ARG373 4.7 0.8 1.0
O1A A:ADP1000 4.8 47.3 1.0
CA A:PRO186 4.8 0.8 1.0
CD A:LYS190 4.9 0.8 1.0
CA A:LYS187 4.9 0.7 1.0
CZ B:ARG373 5.0 0.8 1.0

Fluorine binding site 4 out of 18 in 8hsl

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Fluorine binding site 4 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:70.8
occ:1.00
 F1 B:BEF1002 0.0 70.8 1.0
BE B:BEF1002 1.5 85.5 1.0
NH2 B:ARG218 2.1 0.7 1.0
F3 B:BEF1002 2.5 91.9 1.0
F2 B:BEF1002 2.6 83.2 1.0
CZ B:ARG218 3.1 0.7 1.0
CA C:GLY344 3.2 0.7 1.0
O C:GLY344 3.3 0.7 1.0
O3B B:ADP1000 3.3 93.1 1.0
NH1 B:ARG218 3.4 0.7 1.0
C C:GLY344 3.6 0.7 1.0
NH1 C:ARG373 3.8 0.8 1.0
NH2 C:ARG373 4.0 0.8 1.0
O2B B:ADP1000 4.3 88.8 1.0
N C:GLY344 4.3 0.7 1.0
NE B:ARG218 4.4 0.7 1.0
PB B:ADP1000 4.4 107.9 1.0
CB B:PRO186 4.4 0.8 1.0
CZ C:ARG373 4.4 0.8 1.0
O C:LYS343 4.4 0.6 1.0
N B:LYS187 4.6 0.7 1.0
CA B:PRO186 4.8 0.8 1.0
MG B:MG1001 4.8 95.1 1.0
C C:LYS343 4.8 0.6 1.0
N C:THR345 4.9 0.7 1.0

Fluorine binding site 5 out of 18 in 8hsl

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Fluorine binding site 5 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:83.2
occ:1.00
 F2 B:BEF1002 0.0 83.2 1.0
BE B:BEF1002 1.6 85.5 1.0
F3 B:BEF1002 2.5 91.9 1.0
O3B B:ADP1000 2.5 93.1 1.0
F1 B:BEF1002 2.6 70.8 1.0
O2B B:ADP1000 3.0 88.8 1.0
CE B:LYS190 3.1 0.8 1.0
PB B:ADP1000 3.1 107.9 1.0
CA B:PRO186 3.2 0.8 1.0
N B:LYS187 3.2 0.7 1.0
CB B:PRO186 3.5 0.8 1.0
NZ B:LYS190 3.6 0.8 1.0
C B:PRO186 3.7 0.8 1.0
O1B B:ADP1000 3.8 94.3 1.0
MG B:MG1001 4.0 95.1 1.0
CA B:LYS187 4.3 0.7 1.0
CD B:LYS190 4.4 0.8 1.0
N B:PRO186 4.4 0.8 1.0
NH2 B:ARG218 4.5 0.7 1.0
CG B:PRO186 4.5 0.8 1.0
O3A B:ADP1000 4.5 111.3 1.0
CD2 B:LEU327 4.6 0.8 1.0
O B:PRO185 4.7 0.8 1.0
NH1 B:ARG218 4.7 0.7 1.0
CG B:LYS190 4.9 0.8 1.0
O B:PRO186 4.9 0.8 1.0
C B:PRO185 5.0 0.8 1.0

Fluorine binding site 6 out of 18 in 8hsl

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Fluorine binding site 6 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:91.9
occ:1.00
 F3 B:BEF1002 0.0 91.9 1.0
BE B:BEF1002 1.5 85.5 1.0
MG B:MG1001 2.3 95.1 1.0
O2B B:ADP1000 2.3 88.8 1.0
NH1 B:ARG218 2.5 0.7 1.0
F2 B:BEF1002 2.5 83.2 1.0
F1 B:BEF1002 2.5 70.8 1.0
O3B B:ADP1000 3.1 93.1 1.0
PB B:ADP1000 3.2 107.9 1.0
OE2 B:GLU217 3.2 0.7 1.0
NH2 B:ARG218 3.3 0.7 1.0
NZ B:LYS190 3.3 0.8 1.0
CZ B:ARG218 3.3 0.7 1.0
CE B:LYS190 3.8 0.8 1.0
O3A B:ADP1000 4.0 111.3 1.0
CD B:GLU217 4.2 0.7 1.0
OG1 B:THR191 4.2 0.7 1.0
OE1 B:GLU217 4.3 0.7 1.0
O1B B:ADP1000 4.5 94.3 1.0
NE B:ARG218 4.6 0.7 1.0
O C:GLY344 4.6 0.7 1.0
OE2 B:GLU221 4.7 0.7 1.0
NH1 C:ARG373 4.7 0.8 1.0
OE1 B:GLU221 4.9 0.7 1.0

Fluorine binding site 7 out of 18 in 8hsl

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Fluorine binding site 7 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1002

b:77.2
occ:1.00
 F1 C:BEF1002 0.0 77.2 1.0
BE C:BEF1002 1.5 71.5 1.0
F3 C:BEF1002 2.5 74.8 1.0
F2 C:BEF1002 2.6 66.6 1.0
NH2 C:ARG218 2.9 0.7 1.0
O1B C:ADP1000 3.5 75.8 1.0
CB C:PRO186 3.7 0.8 1.0
N C:LYS187 3.8 0.7 1.0
O3A C:ADP1000 3.9 77.3 1.0
CA C:PRO186 3.9 0.8 1.0
CZ C:ARG218 4.0 0.7 1.0
NH1 C:ARG218 4.1 0.7 1.0
C C:PRO186 4.3 0.8 1.0
PB C:ADP1000 4.4 88.2 1.0
MG C:MG1001 4.7 72.5 1.0
CG C:PRO186 4.8 0.8 1.0
CA C:LYS187 4.8 0.7 1.0
NH2 D:ARG373 4.9 0.8 1.0
NH1 D:ARG373 4.9 0.8 1.0
O2B C:ADP1000 4.9 91.8 1.0

Fluorine binding site 8 out of 18 in 8hsl

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Fluorine binding site 8 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1002

b:66.6
occ:1.00
 F2 C:BEF1002 0.0 66.6 1.0
BE C:BEF1002 1.6 71.5 1.0
O1B C:ADP1000 2.1 75.8 1.0
F3 C:BEF1002 2.5 74.8 1.0
F1 C:BEF1002 2.6 77.2 1.0
NZ C:LYS190 3.2 0.8 1.0
PB C:ADP1000 3.2 88.2 1.0
O2B C:ADP1000 3.5 91.8 1.0
CA C:PRO186 3.7 0.8 1.0
MG C:MG1001 3.7 72.5 1.0
O3A C:ADP1000 3.8 77.3 1.0
CB C:PRO186 4.1 0.8 1.0
CD2 C:LEU327 4.2 0.8 1.0
N C:LYS187 4.3 0.7 1.0
CG C:LEU327 4.3 0.8 1.0
CE C:LYS190 4.4 0.8 1.0
O3B C:ADP1000 4.5 71.5 1.0
C C:PRO186 4.6 0.8 1.0
N C:PRO186 4.6 0.8 1.0
CD1 C:LEU327 4.6 0.8 1.0
CG C:PRO186 4.7 0.8 1.0
O C:PRO185 4.9 0.8 1.0
NH2 C:ARG218 4.9 0.7 1.0

Fluorine binding site 9 out of 18 in 8hsl

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Fluorine binding site 9 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1002

b:74.8
occ:1.00
 F3 C:BEF1002 0.0 74.8 1.0
BE C:BEF1002 1.5 71.5 1.0
MG C:MG1001 2.3 72.5 1.0
F2 C:BEF1002 2.5 66.6 1.0
F1 C:BEF1002 2.5 77.2 1.0
O3A C:ADP1000 2.9 77.3 1.0
NH1 C:ARG218 2.9 0.7 1.0
O2B C:ADP1000 3.1 91.8 1.0
O1B C:ADP1000 3.2 75.8 1.0
PB C:ADP1000 3.2 88.2 1.0
NH2 C:ARG218 3.4 0.7 1.0
CZ C:ARG218 3.6 0.7 1.0
O2A C:ADP1000 3.7 72.2 1.0
PA C:ADP1000 3.9 67.3 1.0
OG1 C:THR191 4.0 0.7 1.0
OE2 C:GLU221 4.5 0.7 1.0
OE1 C:GLU217 4.5 0.7 1.0
N C:LYS187 4.7 0.7 1.0
O5' C:ADP1000 4.7 70.9 1.0
O3B C:ADP1000 4.7 71.5 1.0
NH2 D:ARG373 4.7 0.8 1.0
NE C:ARG218 4.9 0.7 1.0

Fluorine binding site 10 out of 18 in 8hsl

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Fluorine binding site 10 out of 18 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1002

b:26.2
occ:1.00
 F1 D:BEF1002 0.0 26.2 1.0
BE D:BEF1002 1.5 30.6 1.0
F3 D:BEF1002 2.5 28.4 1.0
NH2 D:ARG218 2.5 0.7 1.0
F2 D:BEF1002 2.6 38.3 1.0
CZ D:ARG218 3.6 0.7 1.0
O1B D:ADP1000 3.7 28.6 1.0
CB D:PRO186 4.0 0.8 1.0
NH1 D:ARG218 4.1 0.7 1.0
N D:LYS187 4.3 0.7 1.0
CA D:PRO186 4.4 0.8 1.0
MG D:MG1001 4.5 37.8 1.0
CA E:GLY344 4.5 0.7 1.0
NH1 E:ARG373 4.5 0.8 1.0
NE D:ARG218 4.6 0.7 1.0
NH2 E:ARG373 4.7 0.8 1.0
C D:PRO186 4.7 0.8 1.0
PB D:ADP1000 4.8 32.0 1.0
CZ E:ARG373 4.9 0.8 1.0

Reference:

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
Page generated: Fri Aug 2 20:13:59 2024

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