Fluorine in PDB 5vhc: DHX36 with An N-Terminal Truncation Bound to Adp-BEF3
Protein crystallography data
The structure of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3, PDB code: 5vhc
was solved by
M.Chen,
A.Ferre-D'amare,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.50 /
2.49
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.878,
111.516,
62.966,
90.00,
110.67,
90.00
|
R / Rfree (%)
|
19.4 /
23.3
|
Other elements in 5vhc:
The structure of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3
(pdb code 5vhc). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
DHX36 with An N-Terminal Truncation Bound to Adp-BEF3, PDB code: 5vhc:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 5vhc
Go back to
Fluorine Binding Sites List in 5vhc
Fluorine binding site 1 out
of 3 in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1102
b:48.5
occ:1.00
|
F1
|
D:BEF1102
|
0.0
|
48.5
|
1.0
|
BE
|
D:BEF1102
|
1.5
|
45.4
|
1.0
|
MG
|
D:MG1101
|
2.0
|
47.4
|
1.0
|
O3B
|
D:ADP1103
|
2.4
|
41.3
|
1.0
|
F3
|
D:BEF1102
|
2.5
|
40.8
|
1.0
|
F2
|
D:BEF1102
|
2.6
|
50.1
|
1.0
|
OE1
|
D:GLU337
|
3.0
|
45.9
|
1.0
|
OE2
|
D:GLU337
|
3.4
|
61.3
|
1.0
|
PB
|
D:ADP1103
|
3.4
|
40.3
|
1.0
|
O
|
D:HOH1260
|
3.5
|
41.6
|
1.0
|
O1B
|
D:ADP1103
|
3.5
|
41.0
|
1.0
|
CD
|
D:GLU337
|
3.6
|
50.8
|
1.0
|
NH2
|
D:ARG607
|
3.6
|
67.8
|
1.0
|
CA
|
D:SER559
|
3.7
|
48.8
|
1.0
|
N
|
D:SER559
|
3.9
|
48.2
|
1.0
|
OG1
|
D:THR239
|
3.9
|
45.2
|
1.0
|
NH2
|
D:ARG604
|
4.3
|
39.8
|
1.0
|
O2B
|
D:ADP1103
|
4.5
|
38.1
|
1.0
|
O2A
|
D:ADP1103
|
4.5
|
41.5
|
1.0
|
O
|
D:SER559
|
4.5
|
51.4
|
1.0
|
O3A
|
D:ADP1103
|
4.6
|
41.3
|
1.0
|
CB
|
D:SER559
|
4.6
|
45.0
|
1.0
|
C
|
D:SER559
|
4.6
|
48.7
|
1.0
|
NH1
|
D:ARG604
|
4.8
|
46.8
|
1.0
|
OE1
|
D:GLN600
|
4.9
|
41.6
|
1.0
|
NZ
|
D:LYS238
|
4.9
|
41.7
|
1.0
|
CZ
|
D:ARG607
|
4.9
|
61.9
|
1.0
|
CE
|
D:LYS238
|
4.9
|
47.2
|
1.0
|
OG
|
D:SER559
|
5.0
|
47.7
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 5vhc
Go back to
Fluorine Binding Sites List in 5vhc
Fluorine binding site 2 out
of 3 in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1102
b:50.1
occ:1.00
|
F2
|
D:BEF1102
|
0.0
|
50.1
|
1.0
|
BE
|
D:BEF1102
|
1.6
|
45.4
|
1.0
|
F3
|
D:BEF1102
|
2.5
|
40.8
|
1.0
|
O3B
|
D:ADP1103
|
2.5
|
41.3
|
1.0
|
F1
|
D:BEF1102
|
2.6
|
48.5
|
1.0
|
NZ
|
D:LYS238
|
2.9
|
41.7
|
1.0
|
O
|
D:HOH1260
|
2.9
|
41.6
|
1.0
|
PB
|
D:ADP1103
|
3.3
|
40.3
|
1.0
|
CB
|
D:ALA369
|
3.3
|
46.1
|
1.0
|
CE
|
D:LYS238
|
3.3
|
47.2
|
1.0
|
O2B
|
D:ADP1103
|
3.4
|
38.1
|
1.0
|
CA
|
D:THR234
|
3.6
|
40.5
|
1.0
|
MG
|
D:MG1101
|
3.6
|
47.4
|
1.0
|
N
|
D:GLY235
|
3.9
|
37.3
|
1.0
|
CG2
|
D:THR234
|
4.0
|
38.4
|
1.0
|
O1B
|
D:ADP1103
|
4.0
|
41.0
|
1.0
|
O
|
D:GLU233
|
4.1
|
50.3
|
1.0
|
CB
|
D:THR234
|
4.3
|
37.8
|
1.0
|
C
|
D:THR234
|
4.3
|
39.6
|
1.0
|
N
|
D:THR234
|
4.3
|
47.0
|
1.0
|
N
|
D:ALA369
|
4.3
|
42.2
|
1.0
|
CA
|
D:ALA369
|
4.3
|
44.0
|
1.0
|
NH2
|
D:ARG607
|
4.5
|
67.8
|
1.0
|
C
|
D:GLU233
|
4.6
|
49.5
|
1.0
|
O
|
D:GLY232
|
4.7
|
44.2
|
1.0
|
OE2
|
D:GLU337
|
4.7
|
61.3
|
1.0
|
O3A
|
D:ADP1103
|
4.7
|
41.3
|
1.0
|
CD
|
D:LYS238
|
4.8
|
51.6
|
1.0
|
NH2
|
D:ARG604
|
4.8
|
39.8
|
1.0
|
OE1
|
D:GLN600
|
4.9
|
41.6
|
1.0
|
NE2
|
D:GLN600
|
5.0
|
42.8
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 5vhc
Go back to
Fluorine Binding Sites List in 5vhc
Fluorine binding site 3 out
of 3 in the DHX36 with An N-Terminal Truncation Bound to Adp-BEF3
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of DHX36 with An N-Terminal Truncation Bound to Adp-BEF3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1102
b:40.8
occ:1.00
|
F3
|
D:BEF1102
|
0.0
|
40.8
|
1.0
|
BE
|
D:BEF1102
|
1.5
|
45.4
|
1.0
|
NH2
|
D:ARG607
|
2.3
|
67.8
|
1.0
|
O3B
|
D:ADP1103
|
2.3
|
41.3
|
1.0
|
F2
|
D:BEF1102
|
2.5
|
50.1
|
1.0
|
F1
|
D:BEF1102
|
2.5
|
48.5
|
1.0
|
NH2
|
D:ARG604
|
2.8
|
39.8
|
1.0
|
N
|
D:GLY235
|
3.4
|
37.3
|
1.0
|
CZ
|
D:ARG607
|
3.5
|
61.9
|
1.0
|
CA
|
D:THR234
|
3.6
|
40.5
|
1.0
|
CB
|
D:THR234
|
3.6
|
37.8
|
1.0
|
CG2
|
D:THR234
|
3.6
|
38.4
|
1.0
|
CZ
|
D:ARG604
|
3.7
|
43.4
|
1.0
|
PB
|
D:ADP1103
|
3.8
|
40.3
|
1.0
|
NH1
|
D:ARG604
|
3.8
|
46.8
|
1.0
|
C
|
D:THR234
|
3.9
|
39.6
|
1.0
|
NE
|
D:ARG607
|
4.2
|
49.6
|
1.0
|
MG
|
D:MG1101
|
4.3
|
47.4
|
1.0
|
O
|
D:HOH1260
|
4.3
|
41.6
|
1.0
|
NH1
|
D:ARG607
|
4.3
|
69.0
|
1.0
|
CA
|
D:GLY235
|
4.3
|
36.8
|
1.0
|
OE1
|
D:GLN600
|
4.4
|
41.6
|
1.0
|
O2B
|
D:ADP1103
|
4.4
|
38.1
|
1.0
|
O3A
|
D:ADP1103
|
4.5
|
41.3
|
1.0
|
N
|
D:SER559
|
4.7
|
48.2
|
1.0
|
O1B
|
D:ADP1103
|
4.8
|
41.0
|
1.0
|
CA
|
D:SER559
|
4.8
|
48.8
|
1.0
|
N
|
D:THR234
|
4.9
|
47.0
|
1.0
|
NE
|
D:ARG604
|
4.9
|
43.5
|
1.0
|
O
|
D:SER559
|
5.0
|
51.4
|
1.0
|
O
|
D:GLY603
|
5.0
|
54.6
|
1.0
|
|
Reference:
M.C.Chen,
R.Tippana,
N.A.Demeshkina,
P.Murat,
S.Balasubramanian,
S.Myong,
A.R.Ferre-D'amare.
Structural Basis of G-Quadruplex Unfolding By the Deah/Rha Helicase DHX36. Nature V. 558 465 2018.
ISSN: ESSN 1476-4687
PubMed: 29899445
DOI: 10.1038/S41586-018-0209-9
Page generated: Thu Aug 1 16:07:06 2024
|