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Fluorine in PDB 5o6b: Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4

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

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

Protein crystallography data

The structure of Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4, PDB code: 5o6b 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) 58.71 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.246, 88.373, 187.703, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.8

Other elements in 5o6b:

The structure of Structure of SCPIF1 in Complex with Gggtttt and 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 Structure of SCPIF1 in Complex with Gggtttt and Adp-ALF4 (pdb code 5o6b). 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 Gggtttt and Adp-ALF4, PDB code: 5o6b:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5o6b

Go back to Fluorine Binding Sites List in 5o6b
Fluorine binding site 1 out of 8 in the Structure of SCPIF1 in Complex with Gggtttt 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 Gggtttt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:29.1
occ:1.00
 F1 A:ALF1002 0.0 29.1 1.0
AL A:ALF1002 1.8 29.5 1.0
F4 A:ALF1002 2.5 31.3 1.0
F3 A:ALF1002 2.5 31.1 1.0
O A:HOH1150 2.6 26.9 1.0
NH2 A:ARG734 2.6 26.9 1.0
O2B A:ADP1001 2.8 26.1 1.0
NH1 A:ARG417 2.9 26.2 1.0
CA A:ALA260 3.1 32.0 1.0
CB A:ALA260 3.1 25.2 1.0
NH1 A:ARG734 3.2 27.0 1.0
N A:GLY261 3.2 30.8 1.0
CZ A:ARG734 3.3 27.3 1.0
F2 A:ALF1002 3.6 27.4 1.0
C A:ALA260 3.6 34.6 1.0
NE2 A:GLN381 3.6 30.3 1.0
NH2 A:ARG417 3.7 25.1 1.0
CZ A:ARG417 3.8 30.8 1.0
OE1 A:GLN381 3.9 29.7 1.0
CD A:GLN381 4.1 33.8 1.0
PB A:ADP1001 4.3 26.9 1.0
CA A:GLY261 4.3 26.8 1.0
N A:ALA260 4.4 33.2 1.0
NE A:ARG734 4.6 23.6 1.0
O A:ALA260 4.8 33.5 1.0
OG A:SER733 4.8 31.1 1.0
N A:GLY709 4.9 23.3 1.0
NZ A:LYS264 4.9 31.7 1.0
O3B A:ADP1001 4.9 28.2 1.0

Fluorine binding site 2 out of 8 in 5o6b

Go back to Fluorine Binding Sites List in 5o6b
Fluorine binding site 2 out of 8 in the Structure of SCPIF1 in Complex with Gggtttt 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 Gggtttt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:27.4
occ:1.00
 F2 A:ALF1002 0.0 27.4 1.0
AL A:ALF1002 1.8 29.5 1.0
MG A:MG1003 1.9 26.1 1.0
F3 A:ALF1002 2.5 31.1 1.0
F4 A:ALF1002 2.6 31.3 1.0
O A:HOH1150 2.6 26.9 1.0
O A:HOH1157 2.7 24.0 1.0
O2B A:ADP1001 2.7 26.1 1.0
O A:HOH1207 2.8 24.0 1.0
OE2 A:GLU342 2.8 26.2 1.0
O1B A:ADP1001 2.9 26.6 1.0
O A:HOH1176 3.0 34.0 1.0
O A:HOH1173 3.2 24.6 1.0
PB A:ADP1001 3.4 26.9 1.0
F1 A:ALF1002 3.6 29.1 1.0
CD A:GLU342 3.8 29.2 1.0
CA A:GLY709 3.8 19.8 1.0
OG A:SER265 4.0 29.6 1.0
OE1 A:GLU342 4.2 28.6 1.0
N A:GLY709 4.3 23.3 1.0
O3B A:ADP1001 4.3 28.2 1.0
NZ A:LYS264 4.4 31.7 1.0
CE A:LYS264 4.6 32.8 1.0
O3A A:ADP1001 4.6 28.9 1.0
O A:GLY709 4.7 27.5 1.0
C A:GLY709 4.7 27.5 1.0
NH2 A:ARG417 4.9 25.1 1.0
CG A:GLU342 4.9 30.4 1.0
NH1 A:ARG734 4.9 27.0 1.0
OE1 A:GLN381 4.9 29.7 1.0
O2A A:ADP1001 5.0 26.3 1.0

Fluorine binding site 3 out of 8 in 5o6b

Go back to Fluorine Binding Sites List in 5o6b
Fluorine binding site 3 out of 8 in the Structure of SCPIF1 in Complex with Gggtttt 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 Gggtttt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:31.1
occ:1.00
 F3 A:ALF1002 0.0 31.1 1.0
AL A:ALF1002 1.8 29.5 1.0
F2 A:ALF1002 2.5 27.4 1.0
F1 A:ALF1002 2.5 29.1 1.0
O A:HOH1150 2.6 26.9 1.0
O2B A:ADP1001 2.7 26.1 1.0
NZ A:LYS264 2.8 31.7 1.0
O A:HOH1176 2.8 34.0 1.0
NE2 A:GLN381 3.0 30.3 1.0
F4 A:ALF1002 3.6 31.3 1.0
CE A:LYS264 3.6 32.8 1.0
PB A:ADP1001 3.7 26.9 1.0
OE1 A:GLN381 3.7 29.7 1.0
CA A:ALA260 3.7 32.0 1.0
CD A:GLN381 3.8 33.8 1.0
O3B A:ADP1001 3.9 28.2 1.0
N A:GLY261 4.0 30.8 1.0
O1B A:ADP1001 4.1 26.6 1.0
O A:HOH1157 4.1 24.0 1.0
MG A:MG1003 4.2 26.1 1.0
O A:SER259 4.3 30.2 1.0
OE2 A:GLU342 4.3 26.2 1.0
N A:ALA260 4.4 33.2 1.0
C A:ALA260 4.4 34.6 1.0
CB A:ALA260 4.5 25.2 1.0
C A:SER259 4.7 29.1 1.0
CB A:ASP378 4.7 32.9 1.0
NH2 A:ARG734 4.8 26.9 1.0
O A:GLY258 4.8 33.6 1.0
OE1 A:GLU342 4.8 28.6 1.0
CD A:GLU342 5.0 29.2 1.0

Fluorine binding site 4 out of 8 in 5o6b

Go back to Fluorine Binding Sites List in 5o6b
Fluorine binding site 4 out of 8 in the Structure of SCPIF1 in Complex with Gggtttt 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 Gggtttt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:31.3
occ:1.00
 F4 A:ALF1002 0.0 31.3 1.0
AL A:ALF1002 1.8 29.5 1.0
F1 A:ALF1002 2.5 29.1 1.0
F2 A:ALF1002 2.6 27.4 1.0
O2B A:ADP1001 2.6 26.1 1.0
NH2 A:ARG417 2.7 25.1 1.0
O A:HOH1150 2.7 26.9 1.0
NH1 A:ARG734 2.8 27.0 1.0
CA A:GLY709 3.1 19.8 1.0
O A:HOH1173 3.1 24.6 1.0
C A:GLY709 3.3 27.5 1.0
O A:GLY709 3.3 27.5 1.0
CZ A:ARG417 3.5 30.8 1.0
N A:GLY709 3.5 23.3 1.0
NH1 A:ARG417 3.6 26.2 1.0
F3 A:ALF1002 3.6 31.1 1.0
MG A:MG1003 3.6 26.1 1.0
PB A:ADP1001 3.8 26.9 1.0
CZ A:ARG734 3.8 27.3 1.0
O1B A:ADP1001 4.0 26.6 1.0
NH2 A:ARG734 4.0 26.9 1.0
N A:GLN710 4.1 23.9 1.0
O2A A:ADP1001 4.1 26.3 1.0
O A:GLN710 4.2 26.3 1.0
OE2 A:GLU342 4.2 26.2 1.0
O A:HOH1207 4.3 24.0 1.0
O3A A:ADP1001 4.3 28.9 1.0
N A:GLY261 4.6 30.8 1.0
C A:GLN710 4.7 28.0 1.0
NE A:ARG417 4.8 29.9 1.0
O A:HOH1240 4.8 45.5 1.0
C A:GLN708 4.9 25.8 1.0
CA A:GLN710 5.0 21.8 1.0
PA A:ADP1001 5.0 26.1 1.0

Fluorine binding site 5 out of 8 in 5o6b

Go back to Fluorine Binding Sites List in 5o6b
Fluorine binding site 5 out of 8 in the Structure of SCPIF1 in Complex with Gggtttt 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 Gggtttt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:29.8
occ:1.00
 F1 B:ALF1002 0.0 29.8 1.0
AL B:ALF1002 1.8 32.2 1.0
F4 B:ALF1002 2.4 29.1 1.0
F3 B:ALF1002 2.5 29.9 1.0
O2B B:ADP1001 2.7 36.7 1.0
O B:HOH1129 2.7 24.8 1.0
NH2 B:ARG734 2.7 26.6 1.0
NH1 B:ARG417 3.1 38.6 1.0
CB B:ALA260 3.1 31.3 1.0
CA B:ALA260 3.1 34.7 1.0
NH1 B:ARG734 3.2 24.1 1.0
N B:GLY261 3.2 30.0 1.0
CZ B:ARG734 3.4 23.9 1.0
F2 B:ALF1002 3.5 32.4 1.0
C B:ALA260 3.6 33.2 1.0
NE2 B:GLN381 3.7 30.4 1.0
NH2 B:ARG417 3.8 32.6 1.0
CZ B:ARG417 3.9 37.7 1.0
OE1 B:GLN381 3.9 33.0 1.0
PB B:ADP1001 4.1 33.6 1.0
CD B:GLN381 4.2 30.6 1.0
CA B:GLY261 4.3 36.7 1.0
N B:ALA260 4.4 35.1 1.0
NE B:ARG734 4.7 28.3 1.0
O3B B:ADP1001 4.7 34.9 1.0
O B:ALA260 4.8 32.4 1.0
NZ B:LYS264 4.8 30.6 1.0
OG B:SER733 4.8 33.4 1.0
N B:GLY709 4.9 24.9 1.0
O3A B:ADP1001 4.9 32.8 1.0
O B:HOH1158 4.9 29.9 1.0
CA B:GLY709 5.0 25.4 1.0

Fluorine binding site 6 out of 8 in 5o6b

Go back to Fluorine Binding Sites List in 5o6b
Fluorine binding site 6 out of 8 in the Structure of SCPIF1 in Complex with Gggtttt 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 Gggtttt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:32.4
occ:1.00
 F2 B:ALF1002 0.0 32.4 1.0
AL B:ALF1002 1.8 32.2 1.0
MG B:MG1003 1.9 30.7 1.0
F3 B:ALF1002 2.5 29.9 1.0
O B:HOH1199 2.6 28.0 1.0
F4 B:ALF1002 2.6 29.1 1.0
O2B B:ADP1001 2.8 36.7 1.0
O1B B:ADP1001 2.8 31.6 1.0
O B:HOH1129 2.9 24.8 1.0
O B:HOH1161 2.9 21.5 1.0
OE1 B:GLU342 2.9 28.0 1.0
O B:HOH1158 3.0 29.9 1.0
PB B:ADP1001 3.1 33.6 1.0
F1 B:ALF1002 3.5 29.8 1.0
CD B:GLU342 3.8 33.6 1.0
CA B:GLY709 3.9 25.4 1.0
OG B:SER265 4.0 26.5 1.0
O3B B:ADP1001 4.0 34.9 1.0
NZ B:LYS264 4.3 30.6 1.0
OE2 B:GLU342 4.3 31.1 1.0
O3A B:ADP1001 4.5 32.8 1.0
CE B:LYS264 4.5 29.5 1.0
N B:GLY709 4.6 24.9 1.0
O B:GLY709 4.7 31.2 1.0
C B:GLY709 4.7 31.4 1.0
O2A B:ADP1001 4.9 34.5 1.0
CB B:SER265 4.9 25.4 1.0
CG B:GLU342 5.0 26.7 1.0
OE1 B:GLN381 5.0 33.0 1.0
NH2 B:ARG417 5.0 32.6 1.0

Fluorine binding site 7 out of 8 in 5o6b

Go back to Fluorine Binding Sites List in 5o6b
Fluorine binding site 7 out of 8 in the Structure of SCPIF1 in Complex with Gggtttt 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 Gggtttt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:29.9
occ:1.00
 F3 B:ALF1002 0.0 29.9 1.0
AL B:ALF1002 1.8 32.2 1.0
F2 B:ALF1002 2.5 32.4 1.0
F1 B:ALF1002 2.5 29.8 1.0
O B:HOH1158 2.7 29.9 1.0
NZ B:LYS264 2.8 30.6 1.0
O2B B:ADP1001 2.8 36.7 1.0
O B:HOH1129 2.8 24.8 1.0
NE2 B:GLN381 3.0 30.4 1.0
CE B:LYS264 3.4 29.5 1.0
PB B:ADP1001 3.5 33.6 1.0
F4 B:ALF1002 3.6 29.1 1.0
O3B B:ADP1001 3.7 34.9 1.0
CA B:ALA260 3.7 34.7 1.0
OE1 B:GLN381 3.7 33.0 1.0
CD B:GLN381 3.8 30.6 1.0
N B:GLY261 4.0 30.0 1.0
O1B B:ADP1001 4.1 31.6 1.0
O B:HOH1199 4.1 28.0 1.0
MG B:MG1003 4.2 30.7 1.0
OE1 B:GLU342 4.3 28.0 1.0
N B:ALA260 4.4 35.1 1.0
C B:ALA260 4.4 33.2 1.0
CB B:ALA260 4.4 31.3 1.0
O B:SER259 4.4 33.2 1.0
C B:SER259 4.7 33.7 1.0
CB B:ASP378 4.7 34.3 1.0
OE2 B:GLU342 4.8 31.1 1.0
NH2 B:ARG734 4.8 26.6 1.0
CD B:LYS264 4.9 36.0 1.0
O B:GLY258 4.9 35.2 1.0
CD B:GLU342 4.9 33.6 1.0
O3A B:ADP1001 5.0 32.8 1.0

Fluorine binding site 8 out of 8 in 5o6b

Go back to Fluorine Binding Sites List in 5o6b
Fluorine binding site 8 out of 8 in the Structure of SCPIF1 in Complex with Gggtttt 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 Gggtttt and Adp-ALF4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1002

b:29.1
occ:1.00
 F4 B:ALF1002 0.0 29.1 1.0
AL B:ALF1002 1.8 32.2 1.0
F1 B:ALF1002 2.4 29.8 1.0
O2B B:ADP1001 2.6 36.7 1.0
F2 B:ALF1002 2.6 32.4 1.0
NH1 B:ARG734 2.7 24.1 1.0
O B:HOH1129 2.8 24.8 1.0
NH2 B:ARG417 2.8 32.6 1.0
CA B:GLY709 3.0 25.4 1.0
C B:GLY709 3.2 31.4 1.0
O B:GLY709 3.4 31.2 1.0
N B:GLY709 3.5 24.9 1.0
F3 B:ALF1002 3.6 29.9 1.0
NH1 B:ARG417 3.6 38.6 1.0
CZ B:ARG417 3.7 37.7 1.0
MG B:MG1003 3.7 30.7 1.0
PB B:ADP1001 3.8 33.6 1.0
CZ B:ARG734 3.8 23.9 1.0
NH2 B:ARG734 4.0 26.6 1.0
N B:GLN710 4.0 22.5 1.0
O1B B:ADP1001 4.1 31.6 1.0
O B:GLN710 4.1 30.9 1.0
OE1 B:GLU342 4.1 28.0 1.0
O2A B:ADP1001 4.2 34.5 1.0
O B:HOH1161 4.3 21.5 1.0
O3A B:ADP1001 4.4 32.8 1.0
C B:GLN710 4.7 29.8 1.0
N B:GLY261 4.7 30.0 1.0
C B:GLN708 4.8 24.0 1.0
NE B:ARG417 4.9 34.8 1.0
CA B:GLN710 4.9 27.3 1.0
PA B:ADP1001 4.9 32.3 1.0
O3B B:ADP1001 5.0 34.9 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: Sun Dec 13 12:29:19 2020

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