Fluorine in PDB 6s3i: Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4
Protein crystallography data
The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4, PDB code: 6s3i
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)
|
59.57 /
2.46
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.195,
61.195,
260.358,
90,
90,
90
|
R / Rfree (%)
|
24.4 /
30.2
|
Other elements in 6s3i:
The structure of Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4 also contains other interesting chemical elements:
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-MGF4
(pdb code 6s3i). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4, PDB code: 6s3i:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 6s3i
Go back to
Fluorine Binding Sites List in 6s3i
Fluorine binding site 1 out
of 4 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4
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-MGF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1003
b:61.3
occ:1.00
|
F1
|
A:MF41003
|
0.0
|
61.3
|
1.0
|
MG
|
A:MF41003
|
1.8
|
72.6
|
1.0
|
MG
|
A:MG1002
|
1.9
|
62.8
|
1.0
|
HA2
|
A:GLY436
|
2.5
|
60.8
|
1.0
|
O3B
|
A:ADP1001
|
2.7
|
45.0
|
1.0
|
O
|
A:HOH1105
|
2.7
|
45.7
|
1.0
|
O1B
|
A:ADP1001
|
2.9
|
56.0
|
1.0
|
F2
|
A:MF41003
|
2.9
|
45.0
|
1.0
|
O
|
A:HOH1111
|
3.0
|
45.3
|
1.0
|
F3
|
A:MF41003
|
3.0
|
44.6
|
1.0
|
F4
|
A:MF41003
|
3.0
|
54.3
|
1.0
|
O
|
A:HOH1106
|
3.1
|
48.8
|
1.0
|
OE2
|
A:GLU172
|
3.2
|
44.6
|
1.0
|
PB
|
A:ADP1001
|
3.2
|
44.9
|
1.0
|
CA
|
A:GLY436
|
3.5
|
50.4
|
1.0
|
OG1
|
A:THR98
|
3.5
|
45.0
|
1.0
|
O
|
A:GLY436
|
3.8
|
52.0
|
1.0
|
HA3
|
A:GLY436
|
3.8
|
60.8
|
1.0
|
HH22
|
A:ARG256
|
4.0
|
85.0
|
1.0
|
C
|
A:GLY436
|
4.0
|
44.9
|
1.0
|
HH12
|
A:ARG462
|
4.1
|
66.1
|
1.0
|
O2B
|
A:ADP1001
|
4.1
|
50.2
|
1.0
|
HZ1
|
A:LYS97
|
4.2
|
55.8
|
1.0
|
O1A
|
A:ADP1001
|
4.2
|
44.8
|
1.0
|
CD
|
A:GLU172
|
4.3
|
44.6
|
1.0
|
H
|
A:GLY436
|
4.3
|
54.2
|
1.0
|
N
|
A:GLY436
|
4.3
|
44.9
|
1.0
|
H
|
A:THR98
|
4.4
|
54.1
|
1.0
|
HB
|
A:THR98
|
4.4
|
54.4
|
1.0
|
HH22
|
A:ARG462
|
4.5
|
72.7
|
1.0
|
HH12
|
A:ARG256
|
4.5
|
55.2
|
1.0
|
HZ2
|
A:LYS97
|
4.5
|
55.8
|
1.0
|
HE22
|
A:GLN212
|
4.6
|
62.0
|
1.0
|
CB
|
A:THR98
|
4.6
|
45.1
|
1.0
|
O3A
|
A:ADP1001
|
4.6
|
49.7
|
1.0
|
HE2
|
A:LYS97
|
4.7
|
53.7
|
1.0
|
H
|
A:GLY94
|
4.7
|
54.2
|
1.0
|
HB2
|
A:LYS97
|
4.7
|
54.2
|
1.0
|
NZ
|
A:LYS97
|
4.7
|
46.3
|
1.0
|
NH2
|
A:ARG256
|
4.8
|
70.6
|
1.0
|
NH1
|
A:ARG462
|
4.9
|
54.8
|
1.0
|
OE1
|
A:GLU172
|
4.9
|
44.5
|
1.0
|
HG2
|
A:GLU172
|
4.9
|
54.2
|
1.0
|
PA
|
A:ADP1001
|
5.0
|
44.3
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 6s3i
Go back to
Fluorine Binding Sites List in 6s3i
Fluorine binding site 2 out
of 4 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4
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-MGF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1003
b:45.0
occ:1.00
|
F2
|
A:MF41003
|
0.0
|
45.0
|
1.0
|
MG
|
A:MF41003
|
1.8
|
72.6
|
1.0
|
HA2
|
A:GLY436
|
2.7
|
60.8
|
1.0
|
OE1
|
A:GLN212
|
2.7
|
54.0
|
1.0
|
H
|
A:GLY436
|
2.7
|
54.2
|
1.0
|
HG3
|
A:GLN435
|
2.8
|
54.2
|
1.0
|
OE2
|
A:GLU172
|
2.8
|
44.6
|
1.0
|
F3
|
A:MF41003
|
2.8
|
44.6
|
1.0
|
F4
|
A:MF41003
|
2.8
|
54.3
|
1.0
|
F1
|
A:MF41003
|
2.9
|
61.3
|
1.0
|
HE22
|
A:GLN212
|
2.9
|
62.0
|
1.0
|
HH22
|
A:ARG462
|
3.0
|
72.7
|
1.0
|
N
|
A:GLY436
|
3.1
|
44.9
|
1.0
|
CA
|
A:GLY436
|
3.3
|
50.4
|
1.0
|
HH12
|
A:ARG462
|
3.4
|
66.1
|
1.0
|
CD
|
A:GLN212
|
3.5
|
54.6
|
1.0
|
NE2
|
A:GLN212
|
3.5
|
51.4
|
1.0
|
HG2
|
A:GLN435
|
3.5
|
54.2
|
1.0
|
NH2
|
A:ARG462
|
3.5
|
60.4
|
1.0
|
CG
|
A:GLN435
|
3.5
|
44.9
|
1.0
|
CD
|
A:GLU172
|
3.7
|
44.6
|
1.0
|
NH1
|
A:ARG462
|
3.9
|
54.8
|
1.0
|
HA3
|
A:GLY436
|
3.9
|
60.8
|
1.0
|
OE1
|
A:GLU172
|
3.9
|
44.5
|
1.0
|
C
|
A:GLN435
|
4.0
|
45.0
|
1.0
|
CZ
|
A:ARG462
|
4.0
|
66.4
|
1.0
|
HH21
|
A:ARG462
|
4.0
|
72.7
|
1.0
|
HE21
|
A:GLN435
|
4.1
|
57.8
|
1.0
|
O
|
A:HOH1105
|
4.1
|
45.7
|
1.0
|
HA
|
A:GLN435
|
4.1
|
68.5
|
1.0
|
HE21
|
A:GLN212
|
4.3
|
62.0
|
1.0
|
CD
|
A:GLN435
|
4.4
|
52.4
|
1.0
|
C
|
A:GLY436
|
4.4
|
44.9
|
1.0
|
CA
|
A:GLN435
|
4.5
|
56.8
|
1.0
|
HH11
|
A:ARG462
|
4.5
|
66.1
|
1.0
|
O1B
|
A:ADP1001
|
4.5
|
56.0
|
1.0
|
NE2
|
A:GLN435
|
4.5
|
47.9
|
1.0
|
HH12
|
A:ARG256
|
4.5
|
55.2
|
1.0
|
MG
|
A:MG1002
|
4.6
|
62.8
|
1.0
|
HB1
|
A:ALA93
|
4.6
|
54.8
|
1.0
|
CB
|
A:GLN435
|
4.6
|
53.3
|
1.0
|
HZ2
|
A:LYS97
|
4.6
|
55.8
|
1.0
|
HB2
|
A:ALA93
|
4.8
|
54.8
|
1.0
|
HA
|
A:ALA93
|
4.8
|
54.5
|
1.0
|
O
|
A:GLN435
|
4.8
|
48.0
|
1.0
|
HG22
|
A:VAL458
|
4.9
|
62.6
|
1.0
|
CG
|
A:GLN212
|
4.9
|
47.4
|
1.0
|
O
|
A:GLY436
|
5.0
|
52.0
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 6s3i
Go back to
Fluorine Binding Sites List in 6s3i
Fluorine binding site 3 out
of 4 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4
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-MGF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1003
b:44.6
occ:1.00
|
F3
|
A:MF41003
|
0.0
|
44.6
|
1.0
|
MG
|
A:MF41003
|
1.8
|
72.6
|
1.0
|
HE22
|
A:GLN212
|
1.9
|
62.0
|
1.0
|
HZ2
|
A:LYS97
|
2.1
|
55.8
|
1.0
|
HZ1
|
A:LYS97
|
2.3
|
55.8
|
1.0
|
NZ
|
A:LYS97
|
2.6
|
46.3
|
1.0
|
HA
|
A:ALA93
|
2.7
|
54.5
|
1.0
|
NE2
|
A:GLN212
|
2.8
|
51.4
|
1.0
|
F2
|
A:MF41003
|
2.8
|
45.0
|
1.0
|
F4
|
A:MF41003
|
2.9
|
54.3
|
1.0
|
F1
|
A:MF41003
|
3.0
|
61.3
|
1.0
|
HZ3
|
A:LYS97
|
3.1
|
55.8
|
1.0
|
HE21
|
A:GLN212
|
3.2
|
62.0
|
1.0
|
O1B
|
A:ADP1001
|
3.2
|
56.0
|
1.0
|
H
|
A:GLY94
|
3.4
|
54.2
|
1.0
|
O2B
|
A:ADP1001
|
3.6
|
50.2
|
1.0
|
HE2
|
A:LYS97
|
3.7
|
53.7
|
1.0
|
CA
|
A:ALA93
|
3.7
|
45.2
|
1.0
|
CE
|
A:LYS97
|
3.7
|
44.5
|
1.0
|
PB
|
A:ADP1001
|
3.8
|
44.9
|
1.0
|
CD
|
A:GLN212
|
3.8
|
54.6
|
1.0
|
HH22
|
A:ARG462
|
3.9
|
72.7
|
1.0
|
OE1
|
A:GLN212
|
3.9
|
54.0
|
1.0
|
HB1
|
A:ALA93
|
3.9
|
54.8
|
1.0
|
HB2
|
A:ALA93
|
4.0
|
54.8
|
1.0
|
CB
|
A:ALA93
|
4.1
|
45.4
|
1.0
|
N
|
A:GLY94
|
4.1
|
44.9
|
1.0
|
HE3
|
A:LYS97
|
4.2
|
53.7
|
1.0
|
O3B
|
A:ADP1001
|
4.3
|
45.0
|
1.0
|
OE2
|
A:GLU172
|
4.3
|
44.6
|
1.0
|
O
|
A:PRO92
|
4.4
|
55.8
|
1.0
|
HB2
|
A:ASP209
|
4.4
|
63.8
|
1.0
|
C
|
A:ALA93
|
4.5
|
45.0
|
1.0
|
N
|
A:ALA93
|
4.5
|
45.3
|
1.0
|
HH12
|
A:ARG256
|
4.6
|
55.2
|
1.0
|
O
|
A:HOH1106
|
4.6
|
48.8
|
1.0
|
HA2
|
A:GLY436
|
4.6
|
60.8
|
1.0
|
HB2
|
A:LYS97
|
4.6
|
54.2
|
1.0
|
HB3
|
A:ASP209
|
4.6
|
63.8
|
1.0
|
NH2
|
A:ARG462
|
4.6
|
60.4
|
1.0
|
HD3
|
A:LYS97
|
4.7
|
71.4
|
1.0
|
MG
|
A:MG1002
|
4.7
|
62.8
|
1.0
|
C
|
A:PRO92
|
4.7
|
46.2
|
1.0
|
CD
|
A:LYS97
|
4.9
|
59.3
|
1.0
|
OE1
|
A:GLU172
|
4.9
|
44.5
|
1.0
|
HH21
|
A:ARG462
|
5.0
|
72.7
|
1.0
|
HH12
|
A:ARG462
|
5.0
|
66.1
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 6s3i
Go back to
Fluorine Binding Sites List in 6s3i
Fluorine binding site 4 out
of 4 in the Crystal Structure of Helicase PIF1 From Thermus Oshimai in Complex with Ssdna (Dt)18 and Adp-MGF4
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-MGF4 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1003
b:54.3
occ:1.00
|
F4
|
A:MF41003
|
0.0
|
54.3
|
1.0
|
MG
|
A:MF41003
|
1.8
|
72.6
|
1.0
|
HH22
|
A:ARG462
|
1.8
|
72.7
|
1.0
|
HH12
|
A:ARG256
|
1.8
|
55.2
|
1.0
|
HH12
|
A:ARG462
|
2.4
|
66.1
|
1.0
|
O1B
|
A:ADP1001
|
2.5
|
56.0
|
1.0
|
NH2
|
A:ARG462
|
2.6
|
60.4
|
1.0
|
NH1
|
A:ARG256
|
2.7
|
45.7
|
1.0
|
F2
|
A:MF41003
|
2.8
|
45.0
|
1.0
|
F3
|
A:MF41003
|
2.9
|
44.6
|
1.0
|
HH22
|
A:ARG256
|
2.9
|
85.0
|
1.0
|
H
|
A:GLY94
|
3.0
|
54.2
|
1.0
|
F1
|
A:MF41003
|
3.0
|
61.3
|
1.0
|
NH1
|
A:ARG462
|
3.1
|
54.8
|
1.0
|
HB1
|
A:ALA93
|
3.1
|
54.8
|
1.0
|
HH11
|
A:ARG256
|
3.2
|
55.2
|
1.0
|
CZ
|
A:ARG462
|
3.3
|
66.4
|
1.0
|
HH21
|
A:ARG462
|
3.3
|
72.7
|
1.0
|
NH2
|
A:ARG256
|
3.5
|
70.6
|
1.0
|
CZ
|
A:ARG256
|
3.5
|
57.6
|
1.0
|
HA2
|
A:GLY436
|
3.6
|
60.8
|
1.0
|
HA
|
A:ALA93
|
3.6
|
54.5
|
1.0
|
N
|
A:GLY94
|
3.7
|
44.9
|
1.0
|
HE22
|
A:GLN212
|
3.8
|
62.0
|
1.0
|
HH11
|
A:ARG462
|
3.8
|
66.1
|
1.0
|
H
|
A:GLY436
|
3.9
|
54.2
|
1.0
|
CB
|
A:ALA93
|
3.9
|
45.4
|
1.0
|
PB
|
A:ADP1001
|
3.9
|
44.9
|
1.0
|
HA2
|
A:GLY94
|
4.1
|
54.3
|
1.0
|
CA
|
A:ALA93
|
4.1
|
45.2
|
1.0
|
HB2
|
A:ALA93
|
4.1
|
54.8
|
1.0
|
CA
|
A:GLY436
|
4.3
|
50.4
|
1.0
|
C
|
A:ALA93
|
4.3
|
45.0
|
1.0
|
HH21
|
A:ARG256
|
4.3
|
85.0
|
1.0
|
CA
|
A:GLY94
|
4.4
|
45.0
|
1.0
|
N
|
A:GLY436
|
4.5
|
44.9
|
1.0
|
OE1
|
A:GLN212
|
4.5
|
54.0
|
1.0
|
NE2
|
A:GLN212
|
4.5
|
51.4
|
1.0
|
C
|
A:GLY436
|
4.5
|
44.9
|
1.0
|
O3B
|
A:ADP1001
|
4.5
|
45.0
|
1.0
|
NE
|
A:ARG462
|
4.6
|
60.8
|
1.0
|
O1A
|
A:ADP1001
|
4.6
|
44.8
|
1.0
|
O
|
A:GLY436
|
4.6
|
52.0
|
1.0
|
HZ1
|
A:LYS97
|
4.6
|
55.8
|
1.0
|
O2B
|
A:ADP1001
|
4.7
|
50.2
|
1.0
|
HB3
|
A:ALA93
|
4.7
|
54.8
|
1.0
|
MG
|
A:MG1002
|
4.8
|
62.8
|
1.0
|
NE
|
A:ARG256
|
4.8
|
58.9
|
1.0
|
HA3
|
A:GLY94
|
4.8
|
54.3
|
1.0
|
HZ2
|
A:LYS97
|
4.9
|
55.8
|
1.0
|
CD
|
A:GLN212
|
4.9
|
54.6
|
1.0
|
O
|
A:HOH1111
|
4.9
|
45.3
|
1.0
|
HE
|
A:ARG462
|
4.9
|
73.2
|
1.0
|
O3A
|
A:ADP1001
|
5.0
|
49.7
|
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: Fri Aug 2 01:36:08 2024
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