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Fluorine in PDB 6s3m: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4

Protein crystallography data

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4, PDB code: 6s3m was solved by Y.X.Dai, W.F.Chen, F.Y.Teng, N.N.Liu, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.54 / 2.11
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 87.735, 101.974, 250.925, 90, 90, 90
R / Rfree (%) 22.4 / 26.8

Other elements in 6s3m:

The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 also contains other interesting chemical elements:

Aluminium (Al) 2 atoms
Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 (pdb code 6s3m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4, PDB code: 6s3m:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6s3m

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Fluorine binding site 1 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:40.3
occ:1.00
 F1 A:ALF1003 0.0 40.3 1.0
AL A:ALF1003 1.8 39.2 1.0
O A:HOH1133 2.3 29.6 1.0
F4 A:ALF1003 2.5 48.3 1.0
F3 A:ALF1003 2.5 35.8 1.0
O3B A:ADP1001 2.6 32.6 1.0
NH2 A:ARG462 2.8 31.8 1.0
NH1 A:ARG462 3.0 26.3 1.0
NH1 A:ARG256 3.0 37.8 1.0
NH2 A:ARG256 3.2 31.3 1.0
CZ A:ARG462 3.3 30.0 1.0
N A:GLY94 3.5 31.7 1.0
F2 A:ALF1003 3.6 42.0 1.0
CZ A:ARG256 3.6 35.2 1.0
CB A:ALA93 3.7 35.6 1.0
CA A:ALA93 3.7 33.6 1.0
OE1 A:GLN212 3.8 27.8 1.0
PB A:ADP1001 4.0 34.5 1.0
NE2 A:GLN212 4.0 26.0 1.0
C A:ALA93 4.1 36.5 1.0
CD A:GLN212 4.3 25.9 1.0
CA A:GLY94 4.4 29.6 1.0
O1B A:ADP1001 4.5 33.8 1.0
N A:GLY436 4.6 38.2 1.0
NE A:ARG462 4.6 30.1 1.0
CA A:GLY436 4.7 24.1 1.0
MG A:MG1002 4.7 33.3 1.0
NZ A:LYS97 4.9 59.2 1.0
O2B A:ADP1001 4.9 37.0 1.0
NE A:ARG256 4.9 34.6 1.0
O A:HOH1160 5.0 31.4 1.0
O A:HOH1154 5.0 28.0 1.0
C A:GLY436 5.0 24.4 1.0
OE2 A:GLU172 5.0 37.4 1.0

Fluorine binding site 2 out of 8 in 6s3m

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Fluorine binding site 2 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:42.0
occ:1.00
 F2 A:ALF1003 0.0 42.0 1.0
AL A:ALF1003 1.8 39.2 1.0
MG A:MG1002 2.0 33.3 1.0
O A:HOH1158 2.3 27.9 1.0
O A:HOH1154 2.5 28.0 1.0
F4 A:ALF1003 2.5 48.3 1.0
F3 A:ALF1003 2.5 35.8 1.0
O2B A:ADP1001 2.8 37.0 1.0
O A:HOH1133 2.9 29.6 1.0
O3B A:ADP1001 3.0 32.6 1.0
OE2 A:GLU172 3.1 37.4 1.0
PB A:ADP1001 3.1 34.5 1.0
O A:HOH1171 3.1 30.9 1.0
NZ A:LYS97 3.5 59.2 1.0
F1 A:ALF1003 3.6 40.3 1.0
O1B A:ADP1001 3.6 33.8 1.0
O A:HOH1160 3.6 31.4 1.0
CE A:LYS97 3.7 53.0 1.0
CD A:GLU172 3.8 35.6 1.0
OG1 A:THR98 3.9 43.8 1.0
OE1 A:GLU172 4.1 38.4 1.0
CA A:GLY436 4.5 24.1 1.0
O3A A:ADP1001 4.7 26.8 1.0
CG A:GLU172 4.8 31.4 1.0
NE2 A:GLN212 4.8 26.0 1.0
OE1 A:GLN212 4.9 27.8 1.0
OD1 A:ASP171 4.9 26.5 1.0
CB A:LYS97 4.9 32.4 1.0

Fluorine binding site 3 out of 8 in 6s3m

Go back to Fluorine Binding Sites List in 6s3m
Fluorine binding site 3 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:35.8
occ:1.00
 F3 A:ALF1003 0.0 35.8 1.0
AL A:ALF1003 1.8 39.2 1.0
F2 A:ALF1003 2.5 42.0 1.0
F1 A:ALF1003 2.5 40.3 1.0
O A:HOH1133 2.6 29.6 1.0
NE2 A:GLN212 2.6 26.0 1.0
O A:HOH1154 2.9 28.0 1.0
O3B A:ADP1001 3.2 32.6 1.0
NZ A:LYS97 3.2 59.2 1.0
CE A:LYS97 3.3 53.0 1.0
OE1 A:GLN212 3.4 27.8 1.0
CD A:GLN212 3.4 25.9 1.0
CA A:ALA93 3.5 33.6 1.0
O1B A:ADP1001 3.5 33.8 1.0
F4 A:ALF1003 3.6 48.3 1.0
PB A:ADP1001 3.8 34.5 1.0
N A:GLY94 3.9 31.7 1.0
CB A:ALA93 4.1 35.6 1.0
O A:PRO92 4.2 36.9 1.0
C A:ALA93 4.3 36.5 1.0
N A:ALA93 4.3 31.7 1.0
MG A:MG1002 4.4 33.3 1.0
O2B A:ADP1001 4.4 37.0 1.0
O A:HOH1158 4.5 27.9 1.0
OE2 A:GLU172 4.5 37.4 1.0
C A:PRO92 4.5 30.7 1.0
NH2 A:ARG462 4.6 31.8 1.0
CB A:ASP209 4.7 32.5 1.0
CG A:GLN212 4.8 26.2 1.0
OE1 A:GLU172 4.9 38.4 1.0
CD A:LYS97 4.9 47.3 1.0
O A:GLY91 5.0 40.9 1.0

Fluorine binding site 4 out of 8 in 6s3m

Go back to Fluorine Binding Sites List in 6s3m
Fluorine binding site 4 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:48.3
occ:1.00
 F4 A:ALF1003 0.0 48.3 1.0
AL A:ALF1003 1.8 39.2 1.0
O3B A:ADP1001 2.3 32.6 1.0
F1 A:ALF1003 2.5 40.3 1.0
F2 A:ALF1003 2.5 42.0 1.0
O A:HOH1160 2.5 31.4 1.0
MG A:MG1002 2.7 33.3 1.0
O A:HOH1133 2.7 29.6 1.0
NH2 A:ARG256 3.0 31.3 1.0
CA A:GLY436 3.1 24.1 1.0
O A:GLY436 3.2 24.5 1.0
PB A:ADP1001 3.3 34.5 1.0
C A:GLY436 3.3 24.4 1.0
O A:HOH1171 3.4 30.9 1.0
O2B A:ADP1001 3.4 37.0 1.0
F3 A:ALF1003 3.6 35.8 1.0
NH1 A:ARG462 3.7 26.3 1.0
N A:GLY436 3.8 38.2 1.0
OE2 A:GLU172 3.9 37.4 1.0
O2A A:ADP1001 4.0 27.0 1.0
CZ A:ARG256 4.1 35.2 1.0
N A:LEU437 4.3 30.1 1.0
O3A A:ADP1001 4.3 26.8 1.0
NH1 A:ARG256 4.4 37.8 1.0
O A:HOH1158 4.4 27.9 1.0
O A:HOH1168 4.4 44.9 1.0
O1B A:ADP1001 4.5 33.8 1.0
OG1 A:THR98 4.7 43.8 1.0
CZ A:ARG462 4.7 30.0 1.0
PA A:ADP1001 4.7 42.1 1.0
NH2 A:ARG462 4.7 31.8 1.0
O A:HOH1154 4.8 28.0 1.0
N A:GLY94 5.0 31.7 1.0

Fluorine binding site 5 out of 8 in 6s3m

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Fluorine binding site 5 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:46.4
occ:1.00
 F1 B:ALF1003 0.0 46.4 1.0
AL B:ALF1003 1.8 47.5 1.0
F3 B:ALF1003 2.5 45.6 1.0
F4 B:ALF1003 2.5 45.4 1.0
NH2 B:ARG462 2.8 43.9 1.0
O1B B:ADP1001 2.8 51.2 1.0
CB B:ALA93 3.1 48.6 1.0
CA B:ALA93 3.2 53.5 1.0
N B:GLY94 3.3 54.6 1.0
NH1 B:ARG256 3.3 49.0 1.0
NH1 B:ARG462 3.4 47.2 1.0
OE1 B:GLN212 3.4 49.4 1.0
CZ B:ARG462 3.5 45.4 1.0
F2 B:ALF1003 3.6 47.9 1.0
C B:ALA93 3.7 56.4 1.0
NH2 B:ARG256 3.9 45.9 1.0
NE2 B:GLN212 4.0 39.9 1.0
CZ B:ARG256 4.0 47.7 1.0
PB B:ADP1001 4.1 50.8 1.0
CD B:GLN212 4.1 43.4 1.0
CA B:GLY94 4.4 51.5 1.0
O B:HOH1163 4.4 45.6 1.0
N B:ALA93 4.5 54.2 1.0
O2B B:ADP1001 4.5 47.8 1.0
NE B:ARG462 4.8 45.3 1.0
NZ B:LYS97 4.8 45.0 1.0
O B:ALA93 4.8 42.3 1.0
OG1 B:THR461 4.9 47.7 1.0
O3B B:ADP1001 4.9 51.8 1.0

Fluorine binding site 6 out of 8 in 6s3m

Go back to Fluorine Binding Sites List in 6s3m
Fluorine binding site 6 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:47.9
occ:1.00
 F2 B:ALF1003 0.0 47.9 1.0
AL B:ALF1003 1.8 47.5 1.0
MG B:MG1002 1.9 52.3 1.0
O B:HOH1125 2.3 37.7 1.0
O B:HOH1116 2.3 52.4 1.0
F3 B:ALF1003 2.5 45.6 1.0
F4 B:ALF1003 2.6 45.4 1.0
O3B B:ADP1001 2.6 51.8 1.0
O B:HOH1142 2.7 53.4 1.0
O B:HOH1163 2.8 45.6 1.0
OE1 B:GLU172 2.9 62.4 1.0
O1B B:ADP1001 3.0 51.2 1.0
PB B:ADP1001 3.2 50.8 1.0
OG1 B:THR98 3.5 82.4 1.0
F1 B:ALF1003 3.6 46.4 1.0
O2B B:ADP1001 3.9 47.8 1.0
CD B:GLU172 3.9 60.5 1.0
CA B:GLY436 4.1 45.2 1.0
CE B:LYS97 4.4 41.2 1.0
OE2 B:GLU172 4.6 60.4 1.0
NZ B:LYS97 4.6 45.0 1.0
O1A B:ADP1001 4.6 54.3 1.0
CB B:THR98 4.6 72.4 1.0
O3A B:ADP1001 4.6 49.6 1.0
O B:GLY436 4.6 52.3 1.0
N B:GLY436 4.8 47.4 1.0
OD2 B:ASP171 4.9 60.0 1.0
CG B:GLU172 4.9 57.4 1.0
C B:GLY436 4.9 46.8 1.0
N B:THR98 5.0 58.6 1.0
NH2 B:ARG256 5.0 45.9 1.0

Fluorine binding site 7 out of 8 in 6s3m

Go back to Fluorine Binding Sites List in 6s3m
Fluorine binding site 7 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:45.6
occ:1.00
 F3 B:ALF1003 0.0 45.6 1.0
AL B:ALF1003 1.8 47.5 1.0
F1 B:ALF1003 2.5 46.4 1.0
O1B B:ADP1001 2.5 51.2 1.0
F2 B:ALF1003 2.5 47.9 1.0
O B:HOH1142 2.8 53.4 1.0
NH2 B:ARG256 2.8 45.9 1.0
NH1 B:ARG462 3.0 47.2 1.0
O B:GLY436 3.2 52.3 1.0
CA B:GLY436 3.3 45.2 1.0
C B:GLY436 3.4 46.8 1.0
MG B:MG1002 3.5 52.3 1.0
F4 B:ALF1003 3.5 45.4 1.0
O B:HOH1125 3.6 37.7 1.0
PB B:ADP1001 3.7 50.8 1.0
N B:GLY436 3.7 47.4 1.0
CZ B:ARG256 3.8 47.7 1.0
NH1 B:ARG256 3.8 49.0 1.0
O3B B:ADP1001 3.8 51.8 1.0
O1A B:ADP1001 3.9 54.3 1.0
CZ B:ARG462 4.0 45.4 1.0
NH2 B:ARG462 4.0 43.9 1.0
OE1 B:GLU172 4.1 62.4 1.0
N B:LEU437 4.3 45.0 1.0
O3A B:ADP1001 4.6 49.6 1.0
O B:LEU437 4.6 50.5 1.0
O B:HOH1163 4.7 45.6 1.0
N B:GLY94 4.7 54.6 1.0
O B:HOH1116 4.8 52.4 1.0
O2B B:ADP1001 4.8 47.8 1.0
PA B:ADP1001 4.9 51.1 1.0

Fluorine binding site 8 out of 8 in 6s3m

Go back to Fluorine Binding Sites List in 6s3m
Fluorine binding site 8 out of 8 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:45.4
occ:1.00
 F4 B:ALF1003 0.0 45.4 1.0
AL B:ALF1003 1.8 47.5 1.0
O B:HOH1163 2.2 45.6 1.0
F1 B:ALF1003 2.5 46.4 1.0
F2 B:ALF1003 2.6 47.9 1.0
NZ B:LYS97 2.9 45.0 1.0
CE B:LYS97 3.2 41.2 1.0
O1B B:ADP1001 3.2 51.2 1.0
F3 B:ALF1003 3.5 45.6 1.0
OE1 B:GLN212 3.6 49.4 1.0
O2B B:ADP1001 3.6 47.8 1.0
PB B:ADP1001 3.7 50.8 1.0
CA B:ALA93 3.9 53.5 1.0
NE2 B:GLN212 4.0 39.9 1.0
O3B B:ADP1001 4.1 51.8 1.0
O B:HOH1116 4.1 52.4 1.0
CD B:GLN212 4.1 43.4 1.0
OE1 B:GLU172 4.1 62.4 1.0
N B:GLY94 4.3 54.6 1.0
MG B:MG1002 4.3 52.3 1.0
CB B:ALA93 4.6 48.6 1.0
O B:PRO92 4.6 61.3 1.0
N B:ALA93 4.6 54.2 1.0
C B:ALA93 4.7 56.4 1.0
CD B:LYS97 4.7 58.0 1.0
O B:HOH1125 4.7 37.7 1.0
OE2 B:GLU172 4.8 60.4 1.0
O B:GLY91 4.8 54.6 1.0
CB B:ASP209 4.8 54.4 1.0
CD B:GLU172 4.8 60.5 1.0
C B:PRO92 4.9 57.3 1.0
NH2 B:ARG462 4.9 43.9 1.0

Reference:

Y.X.Dai, W.F.Chen, F.Y.Teng, N.N.Liu, X.M.Hou, S.X.Dou, S.Rety, X.G.Xi. Unraveling the Structural and Mechanistic Basis of SF1B Helicase Dimerization: Inhibitory Regulation of Thermus Oshimau PIF1 Activity To Be Published.
Page generated: Tue Jul 15 15:36:16 2025

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