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Fluorine in PDB 5o6e: Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4

Enzymatic activity of Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4

All present enzymatic activity of Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4:
3.6.4.12;

Protein crystallography data

The structure of Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4, PDB code: 5o6e was solved by K.Y.Lu, W.F.Chen, S.Rety, N.N.Liu, X.G.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.21 / 3.35
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.605, 150.605, 136.339, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 25.7

Other elements in 5o6e:

The structure of Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 (pdb code 5o6e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4, PDB code: 5o6e:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5o6e

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Fluorine binding site 1 out of 8 in the Structure of SCPIF1 in Complex with Tttgggtt 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 Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:66.1
occ:1.00
 F1 A:ALF1002 0.0 66.1 1.0
AL A:ALF1002 1.8 78.3 1.0
F4 A:ALF1002 2.4 82.9 1.0
F3 A:ALF1002 2.6 91.8 1.0
O3B A:ADP1001 2.6 72.7 1.0
OE1 A:GLN381 3.1 76.3 1.0
CA A:ALA260 3.2 98.0 1.0
CB A:ALA260 3.3 0.8 1.0
NH2 A:ARG734 3.3 87.4 1.0
N A:GLY261 3.4 81.2 1.0
NE2 A:GLN381 3.5 59.7 1.0
F2 A:ALF1002 3.6 79.6 1.0
CD A:GLN381 3.7 70.9 1.0
NH1 A:ARG417 3.7 95.7 1.0
C A:ALA260 3.7 84.7 1.0
PB A:ADP1001 4.0 75.4 1.0
NZ A:LYS264 4.0 58.5 1.0
NH1 A:ARG734 4.1 78.3 1.0
NH2 A:ARG417 4.2 1.0 1.0
CZ A:ARG734 4.2 81.5 1.0
CZ A:ARG417 4.4 95.2 1.0
CA A:GLY261 4.5 81.8 1.0
O2B A:ADP1001 4.5 69.4 1.0
OE2 A:GLU342 4.5 0.7 1.0
N A:ALA260 4.5 1.0 1.0
O1B A:ADP1001 4.8 77.7 1.0
O A:ALA260 4.8 78.8 1.0
CE A:LYS264 5.0 58.6 1.0

Fluorine binding site 2 out of 8 in 5o6e

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Fluorine binding site 2 out of 8 in the Structure of SCPIF1 in Complex with Tttgggtt 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 Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:79.6
occ:1.00
 F2 A:ALF1002 0.0 79.6 1.0
AL A:ALF1002 1.8 78.3 1.0
MG A:MG1003 2.1 74.9 1.0
O2B A:ADP1001 2.3 69.4 1.0
F3 A:ALF1002 2.5 91.8 1.0
OE2 A:GLU342 2.5 0.7 1.0
F4 A:ALF1002 2.6 82.9 1.0
O3B A:ADP1001 3.2 72.7 1.0
PB A:ADP1001 3.2 75.4 1.0
OG A:SER265 3.4 0.8 1.0
CA A:GLY709 3.5 81.4 1.0
F1 A:ALF1002 3.6 66.1 1.0
CD A:GLU342 3.7 0.4 1.0
O A:GLY709 3.9 85.4 1.0
C A:GLY709 4.1 85.1 1.0
CB A:SER265 4.2 95.5 1.0
N A:GLY709 4.2 75.0 1.0
O2A A:ADP1001 4.4 85.7 1.0
O1B A:ADP1001 4.4 77.7 1.0
NH2 A:ARG417 4.4 1.0 1.0
OE1 A:GLU342 4.4 0.1 1.0
O3A A:ADP1001 4.5 77.0 1.0
CG A:GLU342 4.6 98.2 1.0
NZ A:LYS264 4.8 58.5 1.0
CE A:LYS264 4.9 58.6 1.0
PA A:ADP1001 5.0 81.5 1.0

Fluorine binding site 3 out of 8 in 5o6e

Go back to Fluorine Binding Sites List in 5o6e
Fluorine binding site 3 out of 8 in the Structure of SCPIF1 in Complex with Tttgggtt 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 Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:91.8
occ:1.00
 F3 A:ALF1002 0.0 91.8 1.0
AL A:ALF1002 1.8 78.3 1.0
F2 A:ALF1002 2.5 79.6 1.0
F1 A:ALF1002 2.6 66.1 1.0
OE2 A:GLU342 3.0 0.7 1.0
NZ A:LYS264 3.1 58.5 1.0
O3B A:ADP1001 3.3 72.7 1.0
CE A:LYS264 3.3 58.6 1.0
OE1 A:GLU342 3.5 0.1 1.0
F4 A:ALF1002 3.5 82.9 1.0
CD A:GLU342 3.5 0.4 1.0
O2B A:ADP1001 3.7 69.4 1.0
MG A:MG1003 3.7 74.9 1.0
OE1 A:GLN381 3.8 76.3 1.0
NE2 A:GLN381 3.9 59.7 1.0
PB A:ADP1001 3.9 75.4 1.0
CD A:GLN381 4.2 70.9 1.0
O1B A:ADP1001 4.4 77.7 1.0
CA A:GLY377 4.8 81.9 1.0
N A:ASP378 4.8 84.7 1.0
CD A:LYS264 4.8 57.6 1.0
CG A:GLU342 4.9 98.2 1.0
CA A:ALA260 5.0 98.0 1.0
C A:GLY377 5.0 88.4 1.0

Fluorine binding site 4 out of 8 in 5o6e

Go back to Fluorine Binding Sites List in 5o6e
Fluorine binding site 4 out of 8 in the Structure of SCPIF1 in Complex with Tttgggtt 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 Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:82.9
occ:1.00
 F4 A:ALF1002 0.0 82.9 1.0
AL A:ALF1002 1.8 78.3 1.0
NH2 A:ARG417 2.3 1.0 1.0
F1 A:ALF1002 2.4 66.1 1.0
O3B A:ADP1001 2.5 72.7 1.0
F2 A:ALF1002 2.6 79.6 1.0
NH1 A:ARG417 3.0 95.7 1.0
CZ A:ARG417 3.1 95.2 1.0
NH1 A:ARG734 3.1 78.3 1.0
PB A:ADP1001 3.4 75.4 1.0
O2B A:ADP1001 3.5 69.4 1.0
F3 A:ALF1002 3.5 91.8 1.0
O A:GLY709 3.7 85.4 1.0
CA A:GLY709 3.7 81.4 1.0
C A:GLY709 3.8 85.1 1.0
NH2 A:ARG734 3.8 87.4 1.0
CZ A:ARG734 3.9 81.5 1.0
N A:GLY709 4.0 75.0 1.0
O3A A:ADP1001 4.2 77.0 1.0
OE2 A:GLU342 4.2 0.7 1.0
N A:GLY261 4.3 81.2 1.0
O2A A:ADP1001 4.3 85.7 1.0
NE A:ARG417 4.4 79.9 1.0
MG A:MG1003 4.4 74.9 1.0
N A:GLN710 4.5 86.7 1.0
O A:GLN710 4.6 84.6 1.0
CA A:GLY261 4.6 81.8 1.0
O1B A:ADP1001 4.8 77.7 1.0
PA A:ADP1001 5.0 81.5 1.0
OG A:SER265 5.0 0.8 1.0

Fluorine binding site 5 out of 8 in 5o6e

Go back to Fluorine Binding Sites List in 5o6e
Fluorine binding site 5 out of 8 in the Structure of SCPIF1 in Complex with Tttgggtt 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 Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:58.0
occ:1.00
 F1 B:ALF1002 0.0 58.0 1.0
AL B:ALF1002 1.8 67.6 1.0
NH2 B:ARG734 2.4 82.7 1.0
F4 B:ALF1002 2.5 67.3 1.0
O2B B:ADP1001 2.5 69.4 1.0
F3 B:ALF1002 2.5 80.0 1.0
CA B:ALA260 3.1 77.1 1.0
NH1 B:ARG417 3.1 65.7 1.0
CB B:ALA260 3.2 76.0 1.0
N B:GLY261 3.3 68.7 1.0
CZ B:ARG734 3.3 81.9 1.0
NH1 B:ARG734 3.5 82.5 1.0
F2 B:ALF1002 3.5 66.8 1.0
C B:ALA260 3.6 71.5 1.0
OE1 B:GLN381 3.6 76.7 1.0
NE2 B:GLN381 3.9 66.0 1.0
NH2 B:ARG417 3.9 67.0 1.0
PB B:ADP1001 4.0 73.7 1.0
CZ B:ARG417 4.0 66.8 1.0
CD B:GLN381 4.1 71.5 1.0
N B:ALA260 4.4 83.9 1.0
CA B:GLY261 4.4 70.1 1.0
O1B B:ADP1001 4.5 72.8 1.0
NE B:ARG734 4.6 78.0 1.0
NZ B:LYS264 4.7 55.8 1.0
O B:ALA260 4.7 70.9 1.0
OE2 B:GLU342 4.8 0.6 1.0
O3A B:ADP1001 4.8 76.8 1.0
O B:SER259 4.9 90.3 1.0
O3B B:ADP1001 4.9 73.5 1.0
OG B:SER733 5.0 66.9 1.0

Fluorine binding site 6 out of 8 in 5o6e

Go back to Fluorine Binding Sites List in 5o6e
Fluorine binding site 6 out of 8 in the Structure of SCPIF1 in Complex with Tttgggtt 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 Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:66.8
occ:1.00
 F2 B:ALF1002 0.0 66.8 1.0
AL B:ALF1002 1.8 67.6 1.0
MG B:MG1003 1.8 68.3 1.0
OE2 B:GLU342 2.1 0.6 1.0
F4 B:ALF1002 2.5 67.3 1.0
O1B B:ADP1001 2.5 72.8 1.0
F3 B:ALF1002 2.6 80.0 1.0
O2B B:ADP1001 3.1 69.4 1.0
PB B:ADP1001 3.3 73.7 1.0
CD B:GLU342 3.3 97.4 1.0
OG B:SER265 3.4 0.8 1.0
F1 B:ALF1002 3.5 58.0 1.0
CA B:GLY709 3.9 84.4 1.0
OE1 B:GLU342 3.9 0.9 1.0
CB B:SER265 4.4 85.8 1.0
N B:GLY709 4.4 81.9 1.0
CG B:GLU342 4.4 86.9 1.0
O3A B:ADP1001 4.5 76.8 1.0
O3B B:ADP1001 4.5 73.5 1.0
CE B:LYS264 4.5 59.9 1.0
O B:GLY709 4.6 88.8 1.0
C B:GLY709 4.6 87.9 1.0
OD1 B:ASP341 4.8 69.2 1.0
NZ B:LYS264 4.8 55.8 1.0
O1A B:ADP1001 4.8 76.7 1.0
OD2 B:ASP341 4.9 76.4 1.0
NE2 B:GLN381 5.0 66.0 1.0
NH1 B:ARG734 5.0 82.5 1.0

Fluorine binding site 7 out of 8 in 5o6e

Go back to Fluorine Binding Sites List in 5o6e
Fluorine binding site 7 out of 8 in the Structure of SCPIF1 in Complex with Tttgggtt 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 Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:80.0
occ:1.00
 F3 B:ALF1002 0.0 80.0 1.0
AL B:ALF1002 1.8 67.6 1.0
F1 B:ALF1002 2.5 58.0 1.0
F2 B:ALF1002 2.6 66.8 1.0
OE1 B:GLN381 2.9 76.7 1.0
O2B B:ADP1001 3.1 69.4 1.0
NE2 B:GLN381 3.1 66.0 1.0
OE2 B:GLU342 3.4 0.6 1.0
CD B:GLN381 3.4 71.5 1.0
NZ B:LYS264 3.4 55.8 1.0
F4 B:ALF1002 3.5 67.3 1.0
CE B:LYS264 3.6 59.9 1.0
OE1 B:GLU342 3.7 0.9 1.0
CD B:GLU342 4.0 97.4 1.0
PB B:ADP1001 4.0 73.7 1.0
O1B B:ADP1001 4.1 72.8 1.0
CA B:ALA260 4.1 77.1 1.0
MG B:MG1003 4.3 68.3 1.0
NH2 B:ARG734 4.4 82.7 1.0
CB B:ALA260 4.6 76.0 1.0
CB B:ASP378 4.6 73.3 1.0
N B:GLY261 4.7 68.7 1.0
N B:ALA260 4.7 83.9 1.0
O B:SER259 4.8 90.3 1.0
O3B B:ADP1001 4.8 73.5 1.0
CG B:GLN381 4.9 69.2 1.0
C B:ALA260 5.0 71.5 1.0

Fluorine binding site 8 out of 8 in 5o6e

Go back to Fluorine Binding Sites List in 5o6e
Fluorine binding site 8 out of 8 in the Structure of SCPIF1 in Complex with Tttgggtt 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 Structure of SCPIF1 in Complex with Tttgggtt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:67.3
occ:1.00
 F4 B:ALF1002 0.0 67.3 1.0
AL B:ALF1002 1.8 67.6 1.0
F2 B:ALF1002 2.5 66.8 1.0
F1 B:ALF1002 2.5 58.0 1.0
O2B B:ADP1001 2.7 69.4 1.0
NH2 B:ARG417 2.7 67.0 1.0
NH1 B:ARG734 3.2 82.5 1.0
MG B:MG1003 3.3 68.3 1.0
O B:GLY709 3.3 88.8 1.0
O1B B:ADP1001 3.3 72.8 1.0
PB B:ADP1001 3.4 73.7 1.0
CA B:GLY709 3.4 84.4 1.0
C B:GLY709 3.5 87.9 1.0
NH1 B:ARG417 3.5 65.7 1.0
F3 B:ALF1002 3.5 80.0 1.0
CZ B:ARG417 3.6 66.8 1.0
NH2 B:ARG734 3.7 82.7 1.0
O3A B:ADP1001 3.9 76.8 1.0
N B:GLY709 3.9 81.9 1.0
CZ B:ARG734 3.9 81.9 1.0
O1A B:ADP1001 3.9 76.7 1.0
OE2 B:GLU342 3.9 0.6 1.0
N B:GLN710 4.3 90.1 1.0
PA B:ADP1001 4.6 72.8 1.0
N B:GLY261 4.6 68.7 1.0
O B:GLN710 4.8 82.3 1.0
O3B B:ADP1001 4.8 73.5 1.0
NE B:ARG417 4.8 70.5 1.0
OG B:SER265 4.9 0.8 1.0

Reference:

K.Y.Lu, W.F.Chen, S.Rety, N.N.Liu, W.Q.Wu, Y.X.Dai, D.Li, H.Y.Ma, S.X.Dou, X.G.Xi. Insights Into the Structural and Mechanistic Basis of Multifunctional S. Cerevisiae PIF1P Helicase. Nucleic Acids Res. V. 46 1486 2018.
ISSN: ESSN 1362-4962
PubMed: 29202194
DOI: 10.1093/NAR/GKX1217
Page generated: Thu Aug 1 12:12:40 2024

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