Fluorine in PDB 2xzl: UPF1-Rna Complex
Enzymatic activity of UPF1-Rna Complex
All present enzymatic activity of UPF1-Rna Complex:
3.6.4.13;
Protein crystallography data
The structure of UPF1-Rna Complex, PDB code: 2xzl
was solved by
S.Chakrabarti,
U.Jayachandran,
F.Bonneau,
F.Fiorini,
C.Basquin,
S.Domcke,
H.Le Hir,
E.Conti,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.882 /
2.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.135,
114.117,
65.730,
90.00,
110.24,
90.00
|
R / Rfree (%)
|
19.74 /
24.31
|
Other elements in 2xzl:
The structure of UPF1-Rna Complex also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the UPF1-Rna Complex
(pdb code 2xzl). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
UPF1-Rna Complex, PDB code: 2xzl:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 2xzl
Go back to
Fluorine Binding Sites List in 2xzl
Fluorine binding site 1 out
of 4 in the UPF1-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of UPF1-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1855
b:7.8
occ:1.00
|
F1
|
A:ALF1855
|
0.0
|
7.8
|
1.0
|
AL
|
A:ALF1855
|
1.8
|
8.6
|
1.0
|
F2
|
A:ALF1855
|
2.5
|
9.6
|
1.0
|
F3
|
A:ALF1855
|
2.5
|
10.3
|
1.0
|
NH1
|
A:ARG639
|
2.7
|
5.8
|
1.0
|
NH2
|
A:ARG801
|
2.8
|
6.3
|
1.0
|
O1B
|
A:ADP1854
|
2.9
|
8.6
|
1.0
|
CA
|
A:PRO432
|
3.0
|
5.5
|
1.0
|
CB
|
A:PRO432
|
3.1
|
4.8
|
1.0
|
N
|
A:GLY433
|
3.1
|
5.5
|
1.0
|
O
|
A:HOH2051
|
3.2
|
4.5
|
1.0
|
NH1
|
A:ARG801
|
3.4
|
6.7
|
1.0
|
C
|
A:PRO432
|
3.5
|
6.2
|
1.0
|
NH2
|
A:ARG639
|
3.5
|
9.1
|
1.0
|
CZ
|
A:ARG801
|
3.5
|
6.9
|
1.0
|
CZ
|
A:ARG639
|
3.6
|
9.8
|
1.0
|
F4
|
A:ALF1855
|
3.6
|
9.5
|
1.0
|
NE2
|
A:GLN601
|
3.9
|
5.5
|
1.0
|
OE1
|
A:GLN601
|
4.0
|
7.6
|
1.0
|
CG
|
A:PRO432
|
4.2
|
4.0
|
1.0
|
CA
|
A:GLY433
|
4.2
|
7.3
|
1.0
|
CD
|
A:GLN601
|
4.3
|
10.0
|
1.0
|
N
|
A:PRO432
|
4.3
|
6.8
|
1.0
|
PB
|
A:ADP1854
|
4.4
|
6.8
|
1.0
|
O
|
A:THR800
|
4.6
|
8.2
|
1.0
|
O
|
A:PRO432
|
4.7
|
5.3
|
1.0
|
OG1
|
A:THR800
|
4.7
|
6.8
|
1.0
|
NZ
|
A:LYS436
|
4.8
|
6.7
|
1.0
|
NE
|
A:ARG801
|
4.8
|
5.4
|
1.0
|
NE
|
A:ARG639
|
4.8
|
6.1
|
1.0
|
O3B
|
A:ADP1854
|
4.9
|
9.9
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 2xzl
Go back to
Fluorine Binding Sites List in 2xzl
Fluorine binding site 2 out
of 4 in the UPF1-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of UPF1-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1855
b:9.6
occ:1.00
|
F2
|
A:ALF1855
|
0.0
|
9.6
|
1.0
|
AL
|
A:ALF1855
|
1.8
|
8.6
|
1.0
|
F1
|
A:ALF1855
|
2.5
|
7.8
|
1.0
|
F4
|
A:ALF1855
|
2.5
|
9.5
|
1.0
|
NH2
|
A:ARG639
|
2.7
|
9.1
|
1.0
|
O1B
|
A:ADP1854
|
2.8
|
8.6
|
1.0
|
NH1
|
A:ARG801
|
2.9
|
6.7
|
1.0
|
O
|
A:HOH2051
|
2.9
|
4.5
|
1.0
|
CA
|
A:GLY767
|
3.1
|
8.3
|
1.0
|
C
|
A:GLY767
|
3.4
|
10.1
|
1.0
|
O
|
A:HOH2090
|
3.4
|
5.5
|
1.0
|
NH1
|
A:ARG639
|
3.5
|
5.8
|
1.0
|
CZ
|
A:ARG639
|
3.5
|
9.8
|
1.0
|
N
|
A:GLY767
|
3.5
|
8.4
|
1.0
|
F3
|
A:ALF1855
|
3.6
|
10.3
|
1.0
|
O
|
A:GLY767
|
3.6
|
9.1
|
1.0
|
MG
|
A:MG1856
|
3.7
|
12.6
|
1.0
|
CZ
|
A:ARG801
|
3.9
|
6.9
|
1.0
|
NH2
|
A:ARG801
|
4.0
|
6.3
|
1.0
|
N
|
A:ARG768
|
4.1
|
9.7
|
1.0
|
PB
|
A:ADP1854
|
4.1
|
6.8
|
1.0
|
O1A
|
A:ADP1854
|
4.3
|
6.3
|
1.0
|
O
|
A:HOH2074
|
4.3
|
18.4
|
1.0
|
O2B
|
A:ADP1854
|
4.4
|
10.2
|
1.0
|
O
|
A:ARG768
|
4.4
|
11.5
|
1.0
|
NE
|
A:ARG639
|
4.7
|
6.1
|
1.0
|
N
|
A:GLY433
|
4.7
|
5.5
|
1.0
|
O3A
|
A:ADP1854
|
4.8
|
14.8
|
1.0
|
O
|
A:HOH2038
|
4.8
|
13.7
|
1.0
|
C
|
A:GLN766
|
4.8
|
10.2
|
1.0
|
C
|
A:ARG768
|
4.9
|
12.4
|
1.0
|
O
|
A:HOH2073
|
5.0
|
20.9
|
1.0
|
CA
|
A:ARG768
|
5.0
|
8.5
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 2xzl
Go back to
Fluorine Binding Sites List in 2xzl
Fluorine binding site 3 out
of 4 in the UPF1-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of UPF1-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1855
b:10.3
occ:1.00
|
F3
|
A:ALF1855
|
0.0
|
10.3
|
1.0
|
AL
|
A:ALF1855
|
1.8
|
8.6
|
1.0
|
F4
|
A:ALF1855
|
2.5
|
9.5
|
1.0
|
F1
|
A:ALF1855
|
2.5
|
7.8
|
1.0
|
NZ
|
A:LYS436
|
2.7
|
6.7
|
1.0
|
O1B
|
A:ADP1854
|
2.8
|
8.6
|
1.0
|
NE2
|
A:GLN601
|
2.8
|
5.5
|
1.0
|
O
|
A:HOH2051
|
2.9
|
4.5
|
1.0
|
CE
|
A:LYS436
|
3.4
|
8.3
|
1.0
|
CA
|
A:PRO432
|
3.5
|
5.5
|
1.0
|
F2
|
A:ALF1855
|
3.6
|
9.6
|
1.0
|
CD
|
A:GLN601
|
3.6
|
10.0
|
1.0
|
OE1
|
A:GLN601
|
3.6
|
7.6
|
1.0
|
O
|
A:HOH2025
|
3.6
|
21.4
|
1.0
|
PB
|
A:ADP1854
|
3.8
|
6.8
|
1.0
|
O3B
|
A:ADP1854
|
3.8
|
9.9
|
1.0
|
N
|
A:GLY433
|
3.9
|
5.5
|
1.0
|
O
|
A:PRO431
|
4.2
|
5.9
|
1.0
|
N
|
A:PRO432
|
4.2
|
6.8
|
1.0
|
C
|
A:PRO432
|
4.3
|
6.2
|
1.0
|
O
|
A:HOH2047
|
4.3
|
20.1
|
1.0
|
CB
|
A:PRO432
|
4.3
|
4.8
|
1.0
|
O2B
|
A:ADP1854
|
4.3
|
10.2
|
1.0
|
C
|
A:PRO431
|
4.5
|
6.6
|
1.0
|
MG
|
A:MG1856
|
4.5
|
12.6
|
1.0
|
O
|
A:HOH2073
|
4.7
|
20.9
|
1.0
|
NH2
|
A:ARG801
|
4.7
|
6.3
|
1.0
|
O
|
A:GLY430
|
4.8
|
12.3
|
1.0
|
CG
|
A:PRO432
|
4.8
|
4.0
|
1.0
|
CD
|
A:LYS436
|
4.9
|
6.7
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 2xzl
Go back to
Fluorine Binding Sites List in 2xzl
Fluorine binding site 4 out
of 4 in the UPF1-Rna Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of UPF1-Rna Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1855
b:9.5
occ:1.00
|
F4
|
A:ALF1855
|
0.0
|
9.5
|
1.0
|
AL
|
A:ALF1855
|
1.8
|
8.6
|
1.0
|
MG
|
A:MG1856
|
2.3
|
12.6
|
1.0
|
O
|
A:HOH2051
|
2.5
|
4.5
|
1.0
|
F3
|
A:ALF1855
|
2.5
|
10.3
|
1.0
|
F2
|
A:ALF1855
|
2.5
|
9.6
|
1.0
|
O1B
|
A:ADP1854
|
2.8
|
8.6
|
1.0
|
O
|
A:HOH2047
|
3.1
|
20.1
|
1.0
|
O
|
A:HOH2025
|
3.3
|
21.4
|
1.0
|
O2B
|
A:ADP1854
|
3.3
|
10.2
|
1.0
|
O
|
A:HOH2073
|
3.3
|
20.9
|
1.0
|
O
|
A:HOH2038
|
3.5
|
13.7
|
1.0
|
F1
|
A:ALF1855
|
3.6
|
7.8
|
1.0
|
PB
|
A:ADP1854
|
3.6
|
6.8
|
1.0
|
CA
|
A:GLY767
|
3.6
|
8.3
|
1.0
|
O
|
A:HOH2090
|
3.8
|
5.5
|
1.0
|
N
|
A:GLY767
|
4.2
|
8.4
|
1.0
|
NZ
|
A:LYS436
|
4.3
|
6.7
|
1.0
|
CE
|
A:LYS436
|
4.3
|
8.3
|
1.0
|
O3B
|
A:ADP1854
|
4.3
|
9.9
|
1.0
|
C
|
A:GLY767
|
4.5
|
10.1
|
1.0
|
OG1
|
A:THR437
|
4.6
|
18.0
|
1.0
|
O
|
A:GLY767
|
4.7
|
9.1
|
1.0
|
OE1
|
A:GLN601
|
4.7
|
7.6
|
1.0
|
NH2
|
A:ARG639
|
4.8
|
9.1
|
1.0
|
O3A
|
A:ADP1854
|
4.9
|
14.8
|
1.0
|
NE2
|
A:GLN601
|
4.9
|
5.5
|
1.0
|
O1A
|
A:ADP1854
|
4.9
|
6.3
|
1.0
|
|
Reference:
S.Chakrabarti,
U.Jayachandran,
F.Bonneau,
F.Fiorini,
C.Basquin,
S.Domcke,
H.Le Hir,
E.Conti.
Molecular Mechanisms For the Rna-Dependent Atpase Activity of UPF1 and Its Regulation By UPF2. Mol.Cell V. 41 693 2011.
ISSN: ISSN 1097-2765
PubMed: 21419344
DOI: 10.1016/J.MOLCEL.2011.02.010
Page generated: Wed Jul 31 16:42:59 2024
|