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Fluorine in PDB 6hpu: Crystal Structure of Human PIF1 Helicase in Complex with Adp-ALF4

Enzymatic activity of Crystal Structure of Human PIF1 Helicase in Complex with Adp-ALF4

All present enzymatic activity of Crystal Structure of Human PIF1 Helicase in Complex with Adp-ALF4:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Human PIF1 Helicase in Complex with Adp-ALF4, PDB code: 6hpu was solved by V.M.Levdikov, S.Dehghani-Tafti, B.D.Bax, C.M.Sanders, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 91.03 / 3.96
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.850, 209.850, 78.885, 90.00, 90.00, 120.00
R / Rfree (%) 17.5 / 25.3

Other elements in 6hpu:

The structure of Crystal Structure of Human PIF1 Helicase in Complex with Adp-ALF4 also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human PIF1 Helicase in Complex with Adp-ALF4 (pdb code 6hpu). 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 Human PIF1 Helicase in Complex with Adp-ALF4, PDB code: 6hpu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6hpu

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Fluorine binding site 1 out of 8 in the Crystal Structure of Human PIF1 Helicase in Complex with 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 Human PIF1 Helicase in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:0.4
occ:1.00
 F1 A:ALF802 0.0 0.4 1.0
AL A:ALF802 1.8 0.6 1.0
F4 A:ALF802 2.5 0.6 1.0
NH2 A:ARG584 2.5 0.9 1.0
O1B A:ADP801 2.6 0.5 1.0
F3 A:ALF802 2.6 0.9 1.0
C A:GLY559 2.9 0.6 1.0
CA A:GLY559 3.2 0.1 1.0
N A:MET560 3.2 0.4 1.0
N A:GLY559 3.2 0.9 1.0
NH2 A:ARG381 3.2 0.8 1.0
O A:MET560 3.3 0.4 1.0
O A:GLY559 3.3 0.1 1.0
MG A:MG803 3.5 0.8 1.0
NH1 A:ARG381 3.5 0.3 1.0
F2 A:ALF802 3.6 0.2 1.0
CZ A:ARG584 3.6 0.2 1.0
NH1 A:ARG584 3.8 0.9 1.0
PB A:ADP801 3.8 0.1 1.0
CZ A:ARG381 3.8 0.6 1.0
O3B A:ADP801 3.9 0.5 1.0
C A:MET560 4.0 0.4 1.0
OE2 A:GLU307 4.1 0.3 1.0
CA A:MET560 4.2 0.7 1.0
O1A A:ADP801 4.2 0.2 1.0
C A:GLN558 4.5 0.1 1.0
NE2 A:GLN346 4.7 0.2 1.0
NE A:ARG584 4.8 0.2 1.0
O2B A:ADP801 4.8 0.1 1.0
O3A A:ADP801 4.8 0.6 1.0
OE1 A:GLN346 5.0 0.1 1.0

Fluorine binding site 2 out of 8 in 6hpu

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Fluorine binding site 2 out of 8 in the Crystal Structure of Human PIF1 Helicase in Complex with 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 Human PIF1 Helicase in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:0.2
occ:1.00
 F2 A:ALF802 0.0 0.2 1.0
AL A:ALF802 1.8 0.6 1.0
NZ A:LYS234 2.2 0.4 1.0
F3 A:ALF802 2.5 0.9 1.0
OE1 A:GLN346 2.5 0.1 1.0
F4 A:ALF802 2.5 0.6 1.0
O1B A:ADP801 3.1 0.5 1.0
O2B A:ADP801 3.2 0.1 1.0
CE A:LYS234 3.3 0.8 1.0
CD A:GLN346 3.4 0.1 1.0
PB A:ADP801 3.4 0.1 1.0
F1 A:ALF802 3.6 0.4 1.0
NE2 A:GLN346 3.6 0.2 1.0
OE2 A:GLU307 3.6 0.3 1.0
O3B A:ADP801 3.8 0.5 1.0
CA A:ALA230 4.0 0.1 1.0
O A:SER229 4.1 0.2 1.0
OE1 A:GLU307 4.2 0.7 1.0
CD A:GLU307 4.3 0.5 1.0
N A:GLY231 4.4 0.6 1.0
MG A:MG803 4.6 0.8 1.0
N A:ALA230 4.6 0.8 1.0
CB A:ASP343 4.6 0.3 1.0
CB A:ALA230 4.6 0.4 1.0
CD A:LYS234 4.6 0.9 1.0
C A:SER229 4.7 0.4 1.0
NH1 A:ARG584 4.7 0.9 1.0
CG A:GLN346 4.7 0.8 1.0
C A:ALA230 4.8 0.1 1.0
O3A A:ADP801 5.0 0.6 1.0

Fluorine binding site 3 out of 8 in 6hpu

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Fluorine binding site 3 out of 8 in the Crystal Structure of Human PIF1 Helicase in Complex with 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 Human PIF1 Helicase in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:0.9
occ:1.00
 F3 A:ALF802 0.0 0.9 1.0
AL A:ALF802 1.8 0.6 1.0
OE2 A:GLU307 2.1 0.3 1.0
MG A:MG803 2.2 0.8 1.0
F2 A:ALF802 2.5 0.2 1.0
F1 A:ALF802 2.6 0.4 1.0
O3B A:ADP801 2.6 0.5 1.0
O1B A:ADP801 2.9 0.5 1.0
PB A:ADP801 3.2 0.1 1.0
CD A:GLU307 3.2 0.5 1.0
CA A:GLY559 3.6 0.1 1.0
F4 A:ALF802 3.6 0.6 1.0
NZ A:LYS234 3.6 0.4 1.0
OE1 A:GLU307 3.8 0.7 1.0
O2B A:ADP801 3.9 0.1 1.0
CE A:LYS234 4.0 0.8 1.0
N A:GLY559 4.0 0.9 1.0
C A:GLY559 4.1 0.6 1.0
O A:GLY559 4.1 0.1 1.0
OG A:SER235 4.2 0.7 1.0
CG A:GLU307 4.4 0.5 1.0
O3A A:ADP801 4.7 0.6 1.0
OE1 A:GLN346 4.7 0.1 1.0
NE2 A:GLN346 4.8 0.2 1.0
OD1 A:ASP306 4.8 0.1 1.0
NH2 A:ARG584 4.9 0.9 1.0
OD2 A:ASP306 4.9 0.3 1.0
CB A:SER235 4.9 0.5 1.0
O1A A:ADP801 5.0 0.2 1.0
N A:MET560 5.0 0.4 1.0

Fluorine binding site 4 out of 8 in 6hpu

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Fluorine binding site 4 out of 8 in the Crystal Structure of Human PIF1 Helicase in Complex with 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 Human PIF1 Helicase in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F802

b:0.6
occ:1.00
 F4 A:ALF802 0.0 0.6 1.0
AL A:ALF802 1.8 0.6 1.0
NH1 A:ARG584 2.3 0.9 1.0
F2 A:ALF802 2.5 0.2 1.0
F1 A:ALF802 2.5 0.4 1.0
O1B A:ADP801 2.8 0.5 1.0
NH1 A:ARG381 2.8 0.3 1.0
OE1 A:GLN346 3.0 0.1 1.0
NH2 A:ARG584 3.0 0.9 1.0
CZ A:ARG584 3.1 0.2 1.0
CA A:ALA230 3.3 0.1 1.0
CB A:ALA230 3.3 0.4 1.0
NE2 A:GLN346 3.6 0.2 1.0
F3 A:ALF802 3.6 0.9 1.0
CD A:GLN346 3.7 0.1 1.0
N A:GLY231 3.7 0.6 1.0
CZ A:ARG381 3.8 0.6 1.0
C A:ALA230 3.9 0.1 1.0
NH2 A:ARG381 3.9 0.8 1.0
PB A:ADP801 4.0 0.1 1.0
O2B A:ADP801 4.2 0.1 1.0
NE A:ARG584 4.4 0.2 1.0
NZ A:LYS234 4.5 0.4 1.0
N A:ALA230 4.6 0.8 1.0
O A:MET560 4.6 0.4 1.0
CA A:GLY231 4.7 0.8 1.0
O3B A:ADP801 4.8 0.5 1.0
O A:ALA230 4.9 0.1 1.0
O A:SER583 4.9 0.2 1.0
N A:GLY559 5.0 0.9 1.0
NE A:ARG381 5.0 0.3 1.0

Fluorine binding site 5 out of 8 in 6hpu

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Fluorine binding site 5 out of 8 in the Crystal Structure of Human PIF1 Helicase in Complex with 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 Human PIF1 Helicase in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:79.1
occ:1.00
 F1 B:ALF802 0.0 79.1 1.0
AL B:ALF802 1.8 99.8 1.0
F3 B:ALF802 2.5 0.6 1.0
O3B B:ADP801 2.5 0.6 1.0
F4 B:ALF802 2.6 81.0 1.0
C B:GLY559 2.9 0.4 1.0
NH2 B:ARG584 3.0 0.5 1.0
CA B:GLY559 3.1 0.6 1.0
O B:GLY559 3.1 0.9 1.0
N B:GLY559 3.2 0.1 1.0
N B:MET560 3.3 0.9 1.0
NH2 B:ARG381 3.4 0.4 1.0
F2 B:ALF802 3.6 0.2 1.0
MG B:MG803 3.6 58.4 1.0
PB B:ADP801 3.7 0.6 1.0
OE2 B:GLU307 3.8 0.6 1.0
NH1 B:ARG584 3.8 0.4 1.0
NH1 B:ARG381 3.8 0.1 1.0
CZ B:ARG584 3.9 0.4 1.0
O B:MET560 3.9 0.5 1.0
O2B B:ADP801 3.9 0.3 1.0
CZ B:ARG381 4.1 0.8 1.0
O1A B:ADP801 4.1 0.5 1.0
CA B:MET560 4.3 0.5 1.0
C B:MET560 4.3 0.1 1.0
C B:GLN558 4.5 0.5 1.0
NE2 B:GLN346 4.8 0.6 1.0
O1B B:ADP801 4.8 0.5 1.0
O3A B:ADP801 4.8 0.5 1.0
N B:GLY231 5.0 0.6 1.0
CD B:GLU307 5.0 0.5 1.0

Fluorine binding site 6 out of 8 in 6hpu

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Fluorine binding site 6 out of 8 in the Crystal Structure of Human PIF1 Helicase in Complex with 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 Human PIF1 Helicase in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:0.2
occ:1.00
 F2 B:ALF802 0.0 0.2 1.0
AL B:ALF802 1.8 99.8 1.0
OE1 B:GLN346 2.5 0.2 1.0
NZ B:LYS234 2.5 0.0 1.0
F4 B:ALF802 2.5 81.0 1.0
F3 B:ALF802 2.5 0.6 1.0
O3B B:ADP801 3.1 0.6 1.0
O1B B:ADP801 3.2 0.5 1.0
CD B:GLN346 3.3 0.6 1.0
NE2 B:GLN346 3.4 0.6 1.0
PB B:ADP801 3.4 0.6 1.0
F1 B:ALF802 3.6 79.1 1.0
O2B B:ADP801 3.8 0.3 1.0
O B:SER229 3.8 80.8 1.0
CE B:LYS234 3.8 0.2 1.0
OE2 B:GLU307 3.9 0.6 1.0
N B:GLY231 3.9 0.6 1.0
CA B:ALA230 4.0 1.0 1.0
OE1 B:GLU307 4.3 0.6 1.0
MG B:MG803 4.4 58.4 1.0
C B:ALA230 4.5 0.3 1.0
CD B:GLU307 4.5 0.5 1.0
C B:SER229 4.6 89.5 1.0
CB B:ASP343 4.6 0.2 1.0
CG B:GLN346 4.7 0.0 1.0
N B:ALA230 4.7 0.2 1.0
CB B:ALA230 4.8 0.6 1.0
CA B:GLY231 4.9 0.1 1.0
NH1 B:ARG584 4.9 0.4 1.0
O B:GLY228 5.0 89.2 1.0
O3A B:ADP801 5.0 0.5 1.0
CD B:LYS234 5.0 0.4 1.0

Fluorine binding site 7 out of 8 in 6hpu

Go back to Fluorine Binding Sites List in 6hpu
Fluorine binding site 7 out of 8 in the Crystal Structure of Human PIF1 Helicase in Complex with 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 Human PIF1 Helicase in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:0.6
occ:1.00
 F3 B:ALF802 0.0 0.6 1.0
AL B:ALF802 1.8 99.8 1.0
MG B:MG803 2.1 58.4 1.0
OE2 B:GLU307 2.2 0.6 1.0
F1 B:ALF802 2.5 79.1 1.0
F2 B:ALF802 2.5 0.2 1.0
O2B B:ADP801 2.7 0.3 1.0
O3B B:ADP801 2.9 0.6 1.0
PB B:ADP801 3.2 0.6 1.0
CD B:GLU307 3.2 0.5 1.0
CA B:GLY559 3.6 0.6 1.0
F4 B:ALF802 3.6 81.0 1.0
NZ B:LYS234 3.6 0.0 1.0
OG B:SER235 3.7 0.3 1.0
OE1 B:GLU307 3.7 0.6 1.0
O1B B:ADP801 3.9 0.5 1.0
O B:GLY559 4.0 0.9 1.0
N B:GLY559 4.0 0.1 1.0
C B:GLY559 4.1 0.4 1.0
CG B:GLU307 4.4 0.3 1.0
NE2 B:GLN346 4.5 0.6 1.0
CE B:LYS234 4.6 0.2 1.0
OE1 B:GLN346 4.7 0.2 1.0
O3A B:ADP801 4.7 0.5 1.0
CB B:SER235 4.7 0.3 1.0
O1A B:ADP801 4.8 0.5 1.0
OD2 B:ASP306 4.8 92.4 1.0

Fluorine binding site 8 out of 8 in 6hpu

Go back to Fluorine Binding Sites List in 6hpu
Fluorine binding site 8 out of 8 in the Crystal Structure of Human PIF1 Helicase in Complex with 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 Human PIF1 Helicase in Complex with Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F802

b:81.0
occ:1.00
 F4 B:ALF802 0.0 81.0 1.0
AL B:ALF802 1.8 99.8 1.0
F2 B:ALF802 2.5 0.2 1.0
NH1 B:ARG584 2.6 0.4 1.0
F1 B:ALF802 2.6 79.1 1.0
O3B B:ADP801 2.7 0.6 1.0
NH1 B:ARG381 3.0 0.1 1.0
N B:GLY231 3.0 0.6 1.0
OE1 B:GLN346 3.3 0.2 1.0
CA B:ALA230 3.4 1.0 1.0
CZ B:ARG584 3.5 0.4 1.0
NH2 B:ARG584 3.5 0.5 1.0
F3 B:ALF802 3.6 0.6 1.0
C B:ALA230 3.6 0.3 1.0
CB B:ALA230 3.6 0.6 1.0
CD B:GLN346 3.9 0.6 1.0
NE2 B:GLN346 3.9 0.6 1.0
PB B:ADP801 3.9 0.6 1.0
CZ B:ARG381 4.0 0.8 1.0
CA B:GLY231 4.0 0.1 1.0
NH2 B:ARG381 4.0 0.4 1.0
O1B B:ADP801 4.1 0.5 1.0
O B:ALA230 4.7 0.5 1.0
NE B:ARG584 4.7 0.8 1.0
N B:ALA230 4.8 0.2 1.0
O2B B:ADP801 4.8 0.3 1.0
O B:SER229 4.8 80.8 1.0
NZ B:LYS234 4.8 0.0 1.0
OG B:SER583 4.9 0.9 1.0

Reference:

S.Dehghani-Tafti, V.Levdikov, A.A.Antson, B.Bax, C.M.Sanders. Structural and Functional Analysis of the Nucleotide and Dna Binding Activities of the Human PIF1 Helicase. Nucleic Acids Res. V. 47 3208 2019.
ISSN: ESSN 1362-4962
PubMed: 30698796
DOI: 10.1093/NAR/GKZ028
Page generated: Thu Aug 1 21:17:47 2024

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