Fluorine in PDB 4oi0: Structure of A Rna-Processing Protein
Protein crystallography data
The structure of Structure of A Rna-Processing Protein, PDB code: 4oi0
was solved by
A.Dikfidan,
B.Loll,
C.Zeymer,
T.Clausen,
A.Meinhart,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.66 /
2.20
|
Space group
|
P 31
|
Cell size a, b, c (Å), α, β, γ (°)
|
100.710,
100.710,
40.400,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
22.7 /
28
|
Other elements in 4oi0:
The structure of Structure of A Rna-Processing Protein also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of A Rna-Processing Protein
(pdb code 4oi0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Structure of A Rna-Processing Protein, PDB code: 4oi0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 4oi0
Go back to
Fluorine Binding Sites List in 4oi0
Fluorine binding site 1 out
of 4 in the Structure of A Rna-Processing Protein
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure of A Rna-Processing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F503
b:19.9
occ:1.00
|
F1
|
A:ALF503
|
0.0
|
19.9
|
1.0
|
AL
|
A:ALF503
|
1.8
|
21.1
|
1.0
|
F4
|
A:ALF503
|
2.5
|
22.8
|
1.0
|
F3
|
A:ALF503
|
2.5
|
22.4
|
1.0
|
O
|
A:HOH603
|
2.6
|
12.6
|
1.0
|
NH2
|
A:ARG288
|
2.6
|
28.8
|
1.0
|
O3B
|
A:ADP501
|
2.7
|
18.6
|
1.0
|
O5'
|
B:G1
|
2.9
|
24.1
|
1.0
|
C5'
|
B:G1
|
3.3
|
24.6
|
1.0
|
CG
|
A:GLN154
|
3.3
|
20.8
|
1.0
|
MG
|
A:MG502
|
3.5
|
17.9
|
1.0
|
CB
|
A:GLN154
|
3.5
|
19.9
|
1.0
|
NH1
|
A:ARG293
|
3.5
|
24.4
|
1.0
|
F2
|
A:ALF503
|
3.6
|
20.9
|
1.0
|
CZ
|
A:ARG288
|
3.8
|
31.0
|
1.0
|
PB
|
A:ADP501
|
3.9
|
18.1
|
1.0
|
O
|
A:HOH601
|
4.0
|
12.5
|
1.0
|
OD2
|
A:ASP151
|
4.0
|
14.8
|
1.0
|
NH1
|
A:ARG288
|
4.1
|
33.6
|
1.0
|
O2B
|
A:ADP501
|
4.1
|
18.2
|
1.0
|
NH2
|
A:ARG293
|
4.1
|
25.5
|
1.0
|
CZ
|
A:ARG293
|
4.3
|
25.5
|
1.0
|
O1A
|
A:ADP501
|
4.5
|
20.2
|
1.0
|
CD
|
A:GLN154
|
4.5
|
21.6
|
1.0
|
O3A
|
A:ADP501
|
4.6
|
17.5
|
1.0
|
C4'
|
B:G1
|
4.7
|
25.2
|
1.0
|
OE1
|
A:GLN154
|
4.9
|
21.6
|
1.0
|
O
|
A:HOH649
|
4.9
|
31.2
|
1.0
|
OD1
|
A:ASP124
|
4.9
|
19.4
|
1.0
|
NE
|
A:ARG288
|
4.9
|
29.5
|
1.0
|
CA
|
A:GLN154
|
5.0
|
20.3
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 4oi0
Go back to
Fluorine Binding Sites List in 4oi0
Fluorine binding site 2 out
of 4 in the Structure of A Rna-Processing Protein
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure of A Rna-Processing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F503
b:20.9
occ:1.00
|
F2
|
A:ALF503
|
0.0
|
20.9
|
1.0
|
AL
|
A:ALF503
|
1.8
|
21.1
|
1.0
|
F3
|
A:ALF503
|
2.5
|
22.4
|
1.0
|
F4
|
A:ALF503
|
2.5
|
22.8
|
1.0
|
NZ
|
A:LYS127
|
2.6
|
16.9
|
1.0
|
O3B
|
A:ADP501
|
2.7
|
18.6
|
1.0
|
O5'
|
B:G1
|
2.7
|
24.1
|
1.0
|
N
|
A:GLY232
|
3.2
|
17.9
|
1.0
|
CE
|
A:LYS127
|
3.2
|
16.1
|
1.0
|
CA
|
A:THR123
|
3.3
|
18.4
|
1.0
|
CA
|
A:GLY232
|
3.3
|
18.4
|
1.0
|
F1
|
A:ALF503
|
3.6
|
19.9
|
1.0
|
PB
|
A:ADP501
|
3.6
|
18.1
|
1.0
|
O1B
|
A:ADP501
|
3.6
|
17.5
|
1.0
|
C5'
|
B:G1
|
3.7
|
24.6
|
1.0
|
N
|
A:THR123
|
3.8
|
18.6
|
1.0
|
O
|
A:PRO122
|
3.9
|
17.0
|
1.0
|
N
|
A:ASP124
|
3.9
|
18.2
|
1.0
|
CG2
|
A:THR123
|
4.0
|
19.2
|
1.0
|
C
|
A:PRO122
|
4.1
|
17.9
|
1.0
|
C
|
A:CYS231
|
4.1
|
17.5
|
1.0
|
C
|
A:THR123
|
4.1
|
18.8
|
1.0
|
CB
|
A:THR123
|
4.2
|
19.6
|
1.0
|
MG
|
A:MG502
|
4.2
|
17.9
|
1.0
|
O2B
|
A:ADP501
|
4.2
|
18.2
|
1.0
|
O
|
A:HOH602
|
4.4
|
19.1
|
1.0
|
OD2
|
A:ASP151
|
4.6
|
14.8
|
1.0
|
CA
|
A:CYS231
|
4.7
|
18.0
|
1.0
|
CD
|
A:LYS127
|
4.7
|
15.3
|
1.0
|
C
|
A:GLY232
|
4.7
|
19.6
|
1.0
|
O4'
|
B:G1
|
4.8
|
26.8
|
1.0
|
O
|
A:CYS231
|
4.9
|
16.4
|
1.0
|
O
|
A:GLY121
|
4.9
|
17.1
|
1.0
|
C4'
|
B:G1
|
4.9
|
25.2
|
1.0
|
O3A
|
A:ADP501
|
5.0
|
17.5
|
1.0
|
O
|
A:THR230
|
5.0
|
15.8
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 4oi0
Go back to
Fluorine Binding Sites List in 4oi0
Fluorine binding site 3 out
of 4 in the Structure of A Rna-Processing Protein
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure of A Rna-Processing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F503
b:22.4
occ:1.00
|
F3
|
A:ALF503
|
0.0
|
22.4
|
1.0
|
AL
|
A:ALF503
|
1.8
|
21.1
|
1.0
|
F2
|
A:ALF503
|
2.5
|
20.9
|
1.0
|
F1
|
A:ALF503
|
2.5
|
19.9
|
1.0
|
NH2
|
A:ARG293
|
2.6
|
25.5
|
1.0
|
O3B
|
A:ADP501
|
2.8
|
18.6
|
1.0
|
O5'
|
B:G1
|
2.9
|
24.1
|
1.0
|
NH1
|
A:ARG293
|
2.9
|
24.4
|
1.0
|
C5'
|
B:G1
|
3.1
|
24.6
|
1.0
|
CG2
|
A:THR123
|
3.2
|
19.2
|
1.0
|
CZ
|
A:ARG293
|
3.2
|
25.5
|
1.0
|
CB
|
A:THR123
|
3.2
|
19.6
|
1.0
|
CA
|
A:THR123
|
3.2
|
18.4
|
1.0
|
N
|
A:ASP124
|
3.5
|
18.2
|
1.0
|
NH2
|
A:ARG288
|
3.5
|
28.8
|
1.0
|
F4
|
A:ALF503
|
3.6
|
22.8
|
1.0
|
C
|
A:THR123
|
3.9
|
18.8
|
1.0
|
OD1
|
A:ASP124
|
4.2
|
19.4
|
1.0
|
PB
|
A:ADP501
|
4.2
|
18.1
|
1.0
|
N
|
A:THR123
|
4.5
|
18.6
|
1.0
|
CG
|
A:ASP124
|
4.5
|
20.4
|
1.0
|
NE
|
A:ARG293
|
4.5
|
27.1
|
1.0
|
C4'
|
B:G1
|
4.6
|
25.2
|
1.0
|
CA
|
A:ASP124
|
4.6
|
18.2
|
1.0
|
OG1
|
A:THR123
|
4.7
|
19.9
|
1.0
|
CZ
|
A:ARG288
|
4.7
|
31.0
|
1.0
|
OD2
|
A:ASP124
|
4.8
|
20.9
|
1.0
|
O1B
|
A:ADP501
|
4.8
|
17.5
|
1.0
|
O
|
A:HOH603
|
4.8
|
12.6
|
1.0
|
NZ
|
A:LYS127
|
4.9
|
16.9
|
1.0
|
N
|
A:GLY232
|
5.0
|
17.9
|
1.0
|
O4'
|
B:G1
|
5.0
|
26.8
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 4oi0
Go back to
Fluorine Binding Sites List in 4oi0
Fluorine binding site 4 out
of 4 in the Structure of A Rna-Processing Protein
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure of A Rna-Processing Protein within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F503
b:22.8
occ:1.00
|
F4
|
A:ALF503
|
0.0
|
22.8
|
1.0
|
AL
|
A:ALF503
|
1.8
|
21.1
|
1.0
|
MG
|
A:MG502
|
1.8
|
17.9
|
1.0
|
F1
|
A:ALF503
|
2.5
|
19.9
|
1.0
|
F2
|
A:ALF503
|
2.5
|
20.9
|
1.0
|
O3B
|
A:ADP501
|
2.6
|
18.6
|
1.0
|
O
|
A:HOH602
|
2.6
|
19.1
|
1.0
|
O5'
|
B:G1
|
2.7
|
24.1
|
1.0
|
O
|
A:HOH601
|
2.8
|
12.5
|
1.0
|
O2B
|
A:ADP501
|
2.8
|
18.2
|
1.0
|
O
|
A:HOH603
|
2.9
|
12.6
|
1.0
|
OD2
|
A:ASP151
|
3.1
|
14.8
|
1.0
|
PB
|
A:ADP501
|
3.1
|
18.1
|
1.0
|
F3
|
A:ALF503
|
3.6
|
22.4
|
1.0
|
CE
|
A:LYS127
|
3.9
|
16.1
|
1.0
|
O1B
|
A:ADP501
|
3.9
|
17.5
|
1.0
|
NZ
|
A:LYS127
|
3.9
|
16.9
|
1.0
|
C5'
|
B:G1
|
4.0
|
24.6
|
1.0
|
OG1
|
A:THR128
|
4.0
|
13.9
|
1.0
|
O
|
A:THR230
|
4.3
|
15.8
|
1.0
|
CG
|
A:ASP151
|
4.3
|
16.4
|
1.0
|
O3A
|
A:ADP501
|
4.5
|
17.5
|
1.0
|
N
|
A:GLY232
|
4.5
|
17.9
|
1.0
|
CB
|
A:GLN154
|
4.7
|
19.9
|
1.0
|
NH2
|
A:ARG288
|
4.7
|
28.8
|
1.0
|
CA
|
A:CYS231
|
4.7
|
18.0
|
1.0
|
C
|
A:CYS231
|
4.9
|
17.5
|
1.0
|
O1A
|
A:ADP501
|
5.0
|
20.2
|
1.0
|
ND2
|
A:ASN229
|
5.0
|
14.0
|
1.0
|
|
Reference:
A.Dikfidan,
B.Loll,
C.Zeymer,
I.Magler,
T.Clausen,
A.Meinhart.
Rna Specificity and Regulation of Catalysis in the Eukaryotic Polynucleotide Kinase CLP1. Mol.Cell V. 54 975 2014.
ISSN: ISSN 1097-2765
PubMed: 24813946
DOI: 10.1016/J.MOLCEL.2014.04.005
Page generated: Thu Aug 1 04:32:51 2024
|