Fluorine in PDB 4esv: A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates

All present enzymatic activity of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates:
3.6.4.12;

The structure of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates, PDB code: 4esv was solved by O.Itsathitphaisarn, R.A.Wing, W.K.Eliason, J.Wang, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 3.20
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	149.124, 180.321, 279.128, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 28.9

The structure of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates also contains other interesting chemical elements:

Aluminium	(Al)	10 atoms
Calcium	(Ca)	14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40;

Binding sites:

The binding sites of Fluorine atom in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates (pdb code 4esv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 40 binding sites of Fluorine where determined in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates, PDB code: 4esv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:89.6 occ:1.00 F1 A:ALF504 0.0 89.6 1.0 AL A:ALF504 1.8 84.5 1.0 F3 A:ALF504 2.5 97.1 1.0 F4 A:ALF504 2.6 97.9 1.0 O3B A:GDP502 2.7 83.1 1.0 NZ F:LYS418 2.9 72.6 1.0 CE F:LYS418 3.0 71.6 1.0 N A:SER213 3.4 84.7 1.0 NH2 F:ARG420 3.4 85.0 1.0 F2 A:ALF504 3.5 93.2 1.0 PB A:GDP502 3.8 81.8 1.0 O F:GLN388 3.9 81.1 1.0 O3A A:GDP502 3.9 85.9 1.0 CA A:SER213 4.1 86.3 1.0 NE F:ARG420 4.1 76.6 1.0 CZ F:ARG420 4.1 83.0 1.0 C A:PRO212 4.2 81.8 1.0 CA A:PRO212 4.2 75.7 1.0 CB A:PRO212 4.2 74.7 1.0 CB A:SER213 4.4 88.3 1.0 O1B A:GDP502 4.4 70.6 1.0 CD F:LYS418 4.5 69.0 1.0 C F:GLN388 4.8 75.7 1.0 CA F:GLN388 4.8 72.6 1.0 O F:GLU387 4.8 76.8 1.0 NZ A:LYS216 4.9 80.1 1.0 O F:ALA390 4.9 69.7 1.0 CA A:CA503 4.9 0.0 1.0 OG A:SER213 4.9 95.6 1.0 O2B A:GDP502 5.0 69.5 1.0

Fluorine binding site 2 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:93.2 occ:1.00 F2 A:ALF504 0.0 93.2 1.0 AL A:ALF504 1.8 84.5 1.0 F4 A:ALF504 2.5 97.9 1.0 F3 A:ALF504 2.5 97.1 1.0 O1B A:GDP502 3.0 70.6 1.0 CA A:CA503 3.0 0.0 1.0 OE1 A:GLU241 3.2 0.1 1.0 O3B A:GDP502 3.2 83.1 1.0 NZ A:LYS216 3.2 80.1 1.0 F1 A:ALF504 3.5 89.6 1.0 PB A:GDP502 3.7 81.8 1.0 OE1 A:GLN362 3.8 92.5 1.0 NE2 A:GLN362 3.8 77.9 1.0 CD A:GLU241 4.0 0.9 1.0 OE2 A:GLU241 4.1 0.6 1.0 CE2 A:TYR321 4.1 75.6 1.0 CE A:LYS216 4.2 69.3 1.0 CD2 A:TYR321 4.2 76.5 1.0 CD A:GLN362 4.2 86.2 1.0 NH2 F:ARG420 4.3 85.0 1.0 O3A A:GDP502 4.7 85.9 1.0 O F:GLN388 4.7 81.1 1.0 O2B A:GDP502 4.8 69.5 1.0 CZ A:TYR321 5.0 80.3 1.0

Fluorine binding site 3 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:97.1 occ:1.00 F3 A:ALF504 0.0 97.1 1.0 AL A:ALF504 1.8 84.5 1.0 NH2 F:ARG420 2.2 85.0 1.0 F1 A:ALF504 2.5 89.6 1.0 F2 A:ALF504 2.5 93.2 1.0 OE1 A:GLU241 2.7 0.1 1.0 CZ F:ARG420 3.0 83.0 1.0 NE F:ARG420 3.0 76.6 1.0 CA A:CA503 3.1 0.0 1.0 O3B A:GDP502 3.5 83.1 1.0 CD A:GLU241 3.5 0.9 1.0 F4 A:ALF504 3.5 97.9 1.0 O1B A:GDP502 3.6 70.6 1.0 OE2 A:GLU241 3.8 0.6 1.0 PB A:GDP502 3.9 81.8 1.0 O3A A:GDP502 3.9 85.9 1.0 O F:GLN388 4.0 81.1 1.0 NH1 F:ARG420 4.3 82.8 1.0 NZ F:LYS418 4.4 72.6 1.0 CD F:ARG420 4.4 76.2 1.0 CG A:GLU241 4.7 95.8 1.0 CE A:MET242 4.8 98.5 1.0 CE F:LYS418 5.0 71.6 1.0

Fluorine binding site 4 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ A:F504 b:97.9 occ:1.00 F4 A:ALF504 0.0 97.9 1.0 AL A:ALF504 1.8 84.5 1.0 O3B A:GDP502 2.3 83.1 1.0 F2 A:ALF504 2.5 93.2 1.0 F1 A:ALF504 2.6 89.6 1.0 NZ A:LYS216 2.7 80.1 1.0 OE1 A:GLN362 2.8 92.5 1.0 CA A:PRO212 3.1 75.7 1.0 F3 A:ALF504 3.5 97.1 1.0 CB A:PRO212 3.6 74.7 1.0 N A:SER213 3.6 84.7 1.0 PB A:GDP502 3.6 81.8 1.0 CD A:GLN362 3.8 86.2 1.0 O1B A:GDP502 3.9 70.6 1.0 C A:PRO212 3.9 81.8 1.0 CE A:LYS216 4.1 69.3 1.0 N A:PRO212 4.2 74.8 1.0 CG A:PRO212 4.2 78.0 1.0 NE2 A:GLN362 4.2 77.9 1.0 O2B A:GDP502 4.4 69.5 1.0 O A:ARG211 4.6 84.2 1.0 CA F:GLN388 4.6 72.6 1.0 O F:GLN388 4.6 81.1 1.0 O3A A:GDP502 4.7 85.9 1.0 C A:ARG211 4.7 80.0 1.0 CA A:SER213 4.8 86.3 1.0 NZ F:LYS418 4.9 72.6 1.0 CD A:PRO212 4.9 76.5 1.0 CB F:GLN388 4.9 71.9 1.0 CA A:CA503 4.9 0.0 1.0

Fluorine binding site 5 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ C:F503 b:80.6 occ:1.00 F1 C:ALF503 0.0 80.6 1.0 AL C:ALF503 1.8 70.4 1.0 F3 C:ALF503 2.5 86.8 1.0 F4 C:ALF503 2.5 66.7 1.0 O3B C:GDP501 2.6 67.3 1.0 NZ B:LYS418 2.8 65.3 1.0 N C:SER213 3.2 79.7 1.0 CA C:PRO212 3.2 72.8 1.0 CB C:PRO212 3.2 73.2 1.0 CE B:LYS418 3.3 70.3 1.0 F2 C:ALF503 3.5 88.6 1.0 C C:PRO212 3.6 74.8 1.0 PB C:GDP501 4.0 73.4 1.0 CA B:GLN388 4.0 77.7 1.0 NZ C:LYS216 4.1 74.3 1.0 O B:GLN388 4.1 83.7 1.0 OE1 C:GLN362 4.1 91.6 1.0 CG C:PRO212 4.2 78.0 1.0 NH2 B:ARG420 4.2 65.9 1.0 CA C:SER213 4.2 83.2 1.0 N C:PRO212 4.5 71.9 1.0 CD B:LYS418 4.5 65.9 1.0 O1B C:GDP501 4.5 66.6 1.0 CB B:GLN388 4.5 79.7 1.0 C B:GLN388 4.6 79.6 1.0 O3A C:GDP501 4.6 78.0 1.0 O B:GLU387 4.6 75.0 1.0 CB C:SER213 4.7 87.5 1.0 O C:PRO212 4.7 77.1 1.0

Fluorine binding site 6 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ C:F503 b:88.6 occ:1.00 F2 C:ALF503 0.0 88.6 1.0 AL C:ALF503 1.8 70.4 1.0 CA C:CA502 2.2 0.2 1.0 F4 C:ALF503 2.5 66.7 1.0 O1B C:GDP501 2.5 66.6 1.0 F3 C:ALF503 2.5 86.8 1.0 OE1 C:GLU241 2.6 0.7 1.0 O3B C:GDP501 3.1 67.3 1.0 PB C:GDP501 3.3 73.4 1.0 NH2 B:ARG420 3.4 65.9 1.0 F1 C:ALF503 3.5 80.6 1.0 CD C:GLU241 3.6 0.7 1.0 O3A C:GDP501 4.0 78.0 1.0 OE2 C:GLU241 4.0 0.3 1.0 NZ C:LYS216 4.2 74.3 1.0 OG1 C:THR217 4.2 84.6 1.0 NE B:ARG420 4.3 64.1 1.0 CZ B:ARG420 4.3 64.0 1.0 CE2 C:TYR321 4.4 71.1 1.0 CD2 C:TYR321 4.6 67.5 1.0 O2B C:GDP501 4.7 66.6 1.0 O B:GLN388 4.8 83.7 1.0 CE C:MET242 4.9 97.9 1.0 CG C:GLU241 4.9 95.5 1.0

Fluorine binding site 7 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ C:F503 b:86.8 occ:1.00 F3 C:ALF503 0.0 86.8 1.0 AL C:ALF503 1.8 70.4 1.0 F1 C:ALF503 2.5 80.6 1.0 F2 C:ALF503 2.5 88.6 1.0 NH2 B:ARG420 2.7 65.9 1.0 O3B C:GDP501 2.8 67.3 1.0 NE B:ARG420 3.1 64.1 1.0 O3A C:GDP501 3.2 78.0 1.0 CZ B:ARG420 3.3 64.0 1.0 PB C:GDP501 3.4 73.4 1.0 NZ B:LYS418 3.5 65.3 1.0 F4 C:ALF503 3.5 66.7 1.0 CE B:LYS418 3.6 70.3 1.0 O1B C:GDP501 3.6 66.6 1.0 CA C:CA502 4.1 0.2 1.0 OE1 C:GLU241 4.2 0.7 1.0 N C:SER213 4.2 79.7 1.0 CD B:ARG420 4.4 64.1 1.0 NH1 B:ARG420 4.6 64.1 1.0 CA C:SER213 4.6 83.2 1.0 O B:GLN388 4.6 83.7 1.0 CG B:ARG420 4.6 64.4 1.0 PA C:GDP501 4.8 74.7 1.0 O2B C:GDP501 4.8 66.6 1.0 CD C:GLU241 4.9 0.7 1.0 CB B:ARG420 5.0 67.3 1.0

Fluorine binding site 8 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ C:F503 b:66.7 occ:1.00 F4 C:ALF503 0.0 66.7 1.0 AL C:ALF503 1.8 70.4 1.0 F2 C:ALF503 2.5 88.6 1.0 F1 C:ALF503 2.5 80.6 1.0 OE1 C:GLN362 2.7 91.6 1.0 NZ C:LYS216 2.7 74.3 1.0 O3B C:GDP501 3.0 67.3 1.0 NE2 C:GLN362 3.3 75.4 1.0 CD C:GLN362 3.4 85.3 1.0 F3 C:ALF503 3.5 86.8 1.0 O1B C:GDP501 3.7 66.6 1.0 CE C:LYS216 3.9 68.3 1.0 PB C:GDP501 4.0 73.4 1.0 CE2 C:TYR321 4.1 71.1 1.0 OE1 C:GLU241 4.3 0.7 1.0 CA C:CA502 4.3 0.2 1.0 CB B:GLN388 4.3 79.7 1.0 O B:GLN388 4.3 83.7 1.0 CA C:PRO212 4.5 72.8 1.0 CA B:GLN388 4.6 77.7 1.0 OE2 C:GLU241 4.6 0.3 1.0 CD2 C:TYR321 4.6 67.5 1.0 NH2 B:ARG420 4.7 65.9 1.0 CZ C:TYR321 4.7 81.3 1.0 CG C:GLN362 4.8 84.5 1.0 CB C:PRO212 4.8 73.2 1.0 OH C:TYR321 4.8 95.3 1.0 NZ B:LYS418 4.9 65.3 1.0 CD C:GLU241 4.9 0.7 1.0 O2B C:GDP501 4.9 66.6 1.0 C B:GLN388 4.9 79.6 1.0 N C:SER213 4.9 79.7 1.0

Fluorine binding site 9 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:67.4 occ:1.00 F1 C:ALF504 0.0 67.4 1.0 AL C:ALF504 1.7 77.9 1.0 F4 C:ALF504 2.5 94.9 1.0 F3 C:ALF504 2.5 74.6 1.0 NZ C:LYS418 2.9 70.9 1.0 O3B D:GDP501 3.0 65.8 1.0 NH2 C:ARG420 3.0 83.4 1.0 CE C:LYS418 3.3 69.7 1.0 O D:HOH601 3.3 69.9 1.0 O C:GLN388 3.5 78.2 1.0 F2 C:ALF504 3.5 92.7 1.0 N D:SER213 3.8 78.9 1.0 CZ C:ARG420 3.9 85.7 1.0 NE C:ARG420 4.1 81.1 1.0 PB D:GDP501 4.1 80.0 1.0 CA D:PRO212 4.3 73.9 1.0 CB D:PRO212 4.3 72.9 1.0 O3A D:GDP501 4.3 81.8 1.0 C C:GLN388 4.4 69.3 1.0 CA C:GLN388 4.4 68.4 1.0 OE1 D:GLU241 4.5 95.7 1.0 O1B D:GDP501 4.5 65.2 1.0 C D:PRO212 4.5 76.0 1.0 CA D:SER213 4.6 82.2 1.0 CA D:CA502 4.6 90.6 1.0 NZ D:LYS216 4.7 76.3 1.0 CD C:LYS418 4.7 68.3 1.0 OE2 D:GLU241 4.8 0.9 1.0 O C:GLU387 4.9 71.3 1.0 O C:ALA390 4.9 67.8 1.0 OE1 D:GLN362 5.0 91.4 1.0 CD D:GLU241 5.0 98.1 1.0

Fluorine binding site 10 out of 40 in the A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of A New Twist on the Translocation Mechanism of Helicases From the Structure of Dnab with Its Substrates within 5.0Å range: probe atom residue distance (Å) B Occ C:F504 b:92.7 occ:1.00 F2 C:ALF504 0.0 92.7 1.0 AL C:ALF504 1.8 77.9 1.0 CA D:CA502 2.2 90.6 1.0 F3 C:ALF504 2.5 74.6 1.0 F4 C:ALF504 2.6 94.9 1.0 O1B D:GDP501 2.6 65.2 1.0 O3B D:GDP501 2.7 65.8 1.0 PB D:GDP501 3.2 80.0 1.0 NZ D:LYS216 3.2 76.3 1.0 OE1 D:GLU241 3.5 95.7 1.0 F1 C:ALF504 3.5 67.4 1.0 OG1 D:THR217 3.8 84.4 1.0 CE D:LYS216 3.9 66.7 1.0 O2B D:GDP501 4.2 65.6 1.0 CD2 D:TYR321 4.3 83.8 1.0 O3A D:GDP501 4.4 81.8 1.0 CE2 D:TYR321 4.5 89.3 1.0 OE1 D:GLN362 4.6 91.4 1.0 CD D:GLU241 4.6 98.1 1.0 CB D:LYS216 4.6 71.2 1.0 NH2 C:ARG420 4.6 83.4 1.0 NE2 D:GLN362 4.7 74.2 1.0 OD2 D:ASP320 4.8 99.4 1.0 OE2 D:GLU241 4.9 0.9 1.0

O.Itsathitphaisarn, R.A.Wing, W.K.Eliason, J.Wang, T.A.Steitz. The Hexameric Helicase Dnab Adopts A Nonplanar Conformation During Translocation. Cell(Cambridge,Mass.) V. 151 267 2012.
ISSN: ISSN 0092-8674
PubMed: 23022319
DOI: 10.1016/J.CELL.2012.09.014