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Fluorine in PDB 5fte: Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna

Enzymatic activity of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna

All present enzymatic activity of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna, PDB code: 5fte was solved by W.-F.Chen, Y.-X.Dai, X.-L.Duan, N.-N.Liu, W.Shi, M.Li, S.-X.Dou, N.Li, Y.-H.Dong, S.Rety, X.-G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.122 / 3.19
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.743, 86.743, 149.222, 90.00, 90.00, 120.00
R / Rfree (%) 22.12 / 27.93

Other elements in 5fte:

The structure of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Aluminium (Al) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna (pdb code 5fte). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna, PDB code: 5fte:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5fte

Go back to Fluorine Binding Sites List in 5fte
Fluorine binding site 1 out of 3 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna


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 PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1433

b:96.2
occ:1.00
 F1 A:AF31433 0.0 96.2 1.0
AL A:AF31433 1.7 87.1 1.0
OE2 A:GLU106 2.8 0.6 1.0
MG A:MG1434 2.8 95.0 1.0
F3 A:AF31433 3.0 0.7 1.0
F2 A:AF31433 3.0 81.7 1.0
OE1 A:GLU106 3.2 1.0 1.0
CD A:GLU106 3.2 0.5 1.0
NZ A:LYS34 3.4 89.3 1.0
OE1 A:GLN145 3.7 88.0 1.0
CD A:GLN145 3.8 90.8 1.0
O3B A:ADP1432 3.9 94.6 1.0
O1B A:ADP1432 4.0 99.8 1.0
N A:GLY365 4.1 79.3 1.0
NH2 A:ARG390 4.1 85.8 1.0
CG A:GLN364 4.1 94.1 1.0
CA A:GLY365 4.2 82.0 1.0
NE2 A:GLN145 4.2 93.7 1.0
CE A:LYS34 4.2 86.4 1.0
CG A:GLN145 4.3 95.7 1.0
NH1 A:ARG390 4.4 70.2 1.0
CG A:GLU106 4.4 0.9 1.0
CD A:GLN364 4.5 92.3 1.0
PB A:ADP1432 4.6 0.3 1.0
CZ A:ARG390 4.6 81.7 1.0
NH2 A:ARG188 4.7 0.4 1.0
NE2 A:GLN364 4.7 80.8 1.0
CG2 A:THR35 4.8 70.3 1.0
C A:GLN364 4.9 83.7 1.0
OE1 A:GLN364 5.0 0.1 1.0

Fluorine binding site 2 out of 3 in 5fte

Go back to Fluorine Binding Sites List in 5fte
Fluorine binding site 2 out of 3 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna


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 PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1433

b:81.7
occ:1.00
 F2 A:AF31433 0.0 81.7 1.0
AL A:AF31433 1.7 87.1 1.0
MG A:MG1434 1.9 95.0 1.0
O3B A:ADP1432 2.6 94.6 1.0
F3 A:AF31433 2.9 0.7 1.0
F1 A:AF31433 3.0 96.2 1.0
NH2 A:ARG188 3.0 0.4 1.0
CA A:GLY365 3.1 82.0 1.0
PB A:ADP1432 3.2 0.3 1.0
O1B A:ADP1432 3.3 99.8 1.0
O A:GLY365 3.3 1.0 1.0
O3A A:ADP1432 3.4 0.7 1.0
C A:GLY365 3.5 93.2 1.0
OG1 A:THR35 3.5 0.1 1.0
NH1 A:ARG390 3.5 70.2 1.0
NH1 A:ARG188 3.6 95.9 1.0
CZ A:ARG188 3.8 95.4 1.0
N A:GLY365 3.8 79.3 1.0
O1A A:ADP1432 3.9 89.4 1.0
CG2 A:THR35 4.1 70.3 1.0
OE1 A:GLU106 4.2 1.0 1.0
NH2 A:ARG390 4.2 85.8 1.0
PA A:ADP1432 4.3 94.8 1.0
CZ A:ARG390 4.4 81.7 1.0
CB A:THR35 4.4 87.0 1.0
N A:LEU366 4.5 87.1 1.0
NZ A:LYS34 4.5 89.3 1.0
O2B A:ADP1432 4.7 0.6 1.0
O A:LEU366 4.9 85.9 1.0
CD A:GLU106 5.0 0.5 1.0

Fluorine binding site 3 out of 3 in 5fte

Go back to Fluorine Binding Sites List in 5fte
Fluorine binding site 3 out of 3 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna


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 PIF1 Helicase From Bacteroides in Complex with Adp-ALF3 and Ssdna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1433

b:0.7
occ:1.00
 F3 A:AF31433 0.0 0.7 1.0
AL A:AF31433 1.7 87.1 1.0
NH2 A:ARG390 2.2 85.8 1.0
NH2 A:ARG188 2.2 0.4 1.0
O1B A:ADP1432 2.7 99.8 1.0
F2 A:AF31433 2.9 81.7 1.0
F1 A:AF31433 3.0 96.2 1.0
CB A:ALA30 3.1 78.6 1.0
CZ A:ARG390 3.2 81.7 1.0
CA A:ALA30 3.2 89.3 1.0
NH1 A:ARG390 3.4 70.2 1.0
CZ A:ARG188 3.5 95.4 1.0
N A:GLY31 3.5 0.5 1.0
C A:ALA30 3.8 99.9 1.0
OE1 A:GLN145 3.8 88.0 1.0
PB A:ADP1432 3.9 0.3 1.0
O3B A:ADP1432 4.2 94.6 1.0
MG A:MG1434 4.2 95.0 1.0
NZ A:LYS34 4.2 89.3 1.0
NH1 A:ARG188 4.3 95.9 1.0
NE A:ARG188 4.3 85.8 1.0
CD A:GLN145 4.4 90.8 1.0
NE2 A:GLN145 4.4 93.7 1.0
O3A A:ADP1432 4.4 0.7 1.0
NE A:ARG390 4.4 84.0 1.0
OG A:SER389 4.4 0.4 1.0
N A:ALA30 4.5 92.6 1.0
CA A:GLY31 4.7 0.8 1.0
O A:ALA30 4.8 0.1 1.0

Reference:

W.-F.Chen, Y.-X.Dai, X.-L.Duan, N.-N.Liu, W.Shi, N.Li, M.Li, S.-X.Dou, Y.-H.Dong, S.Rety, X.-G.Xi. Crystal Structures of the BSPIF1 Helicase Reveal That A Major Movement of the 2B SH3 Domain Is Required For Dna Unwinding Nucleic Acids Res. V. 44 2949 2016.
ISSN: ISSN 0305-1048
PubMed: 26809678
DOI: 10.1093/NAR/GKW033
Page generated: Thu Aug 1 09:28:22 2024

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