Fluorine in PDB 1zp0: Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
Enzymatic activity of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
All present enzymatic activity of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone:
1.3.5.1;
Protein crystallography data
The structure of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone, PDB code: 1zp0
was solved by
F.Sun,
X.Huo,
Y.Zhai,
A.Wang,
J.Xu,
D.Su,
M.Bartlam,
Z.Rao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
3.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.330,
83.531,
294.180,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.8 /
29.3
|
Other elements in 1zp0:
The structure of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
(pdb code 1zp0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone, PDB code: 1zp0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 1zp0
Go back to
Fluorine Binding Sites List in 1zp0
Fluorine binding site 1 out
of 6 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
 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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F308
b:90.0
occ:1.00
|
F1
|
C:TTF308
|
0.0
|
90.0
|
1.0
|
C8
|
C:TTF308
|
1.3
|
79.9
|
1.0
|
F2
|
C:TTF308
|
2.1
|
92.5
|
1.0
|
F3
|
C:TTF308
|
2.1
|
84.5
|
1.0
|
C7
|
C:TTF308
|
2.3
|
69.2
|
1.0
|
C6
|
C:TTF308
|
2.8
|
49.8
|
1.0
|
CG
|
B:PRO169
|
3.1
|
56.8
|
1.0
|
O2
|
C:TTF308
|
3.4
|
88.5
|
1.0
|
CB
|
B:PRO169
|
3.6
|
68.3
|
1.0
|
CG
|
C:MET39
|
3.7
|
56.1
|
1.0
|
SD
|
C:MET39
|
4.0
|
60.2
|
1.0
|
C5
|
C:TTF308
|
4.3
|
53.1
|
1.0
|
CD
|
B:PRO169
|
4.5
|
53.2
|
1.0
|
CG1
|
C:ILE43
|
4.6
|
63.9
|
1.0
|
S1
|
C:TTF308
|
4.6
|
59.8
|
1.0
|
C3
|
C:TTF308
|
4.8
|
50.7
|
1.0
|
OG
|
C:SER42
|
4.9
|
92.6
|
1.0
|
CD1
|
C:ILE43
|
4.9
|
68.0
|
1.0
|
O
|
C:MET39
|
4.9
|
69.4
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 1zp0
Go back to
Fluorine Binding Sites List in 1zp0
Fluorine binding site 2 out
of 6 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
 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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F308
b:92.5
occ:1.00
|
F2
|
C:TTF308
|
0.0
|
92.5
|
1.0
|
C8
|
C:TTF308
|
1.3
|
79.9
|
1.0
|
F1
|
C:TTF308
|
2.1
|
90.0
|
1.0
|
F3
|
C:TTF308
|
2.2
|
84.5
|
1.0
|
C7
|
C:TTF308
|
2.3
|
69.2
|
1.0
|
C6
|
C:TTF308
|
2.8
|
49.8
|
1.0
|
O2
|
C:TTF308
|
3.4
|
88.5
|
1.0
|
CB
|
B:PRO169
|
3.5
|
68.3
|
1.0
|
CG
|
B:PRO169
|
3.6
|
56.8
|
1.0
|
CZ3
|
B:TRP172
|
3.9
|
85.9
|
1.0
|
CE3
|
B:TRP172
|
4.2
|
79.3
|
1.0
|
CG2
|
C:ILE30
|
4.3
|
75.1
|
1.0
|
C5
|
C:TTF308
|
4.3
|
53.1
|
1.0
|
CZ2
|
B:TRP173
|
4.5
|
81.6
|
1.0
|
CA
|
B:PRO169
|
4.6
|
60.0
|
1.0
|
NE1
|
B:TRP173
|
4.7
|
81.7
|
1.0
|
CE2
|
B:TRP173
|
4.9
|
79.6
|
1.0
|
O1
|
C:TTF308
|
5.0
|
59.2
|
1.0
|
CH2
|
B:TRP172
|
5.0
|
87.6
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 1zp0
Go back to
Fluorine Binding Sites List in 1zp0
Fluorine binding site 3 out
of 6 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
 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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F308
b:84.5
occ:1.00
|
F3
|
C:TTF308
|
0.0
|
84.5
|
1.0
|
C8
|
C:TTF308
|
1.4
|
79.9
|
1.0
|
F1
|
C:TTF308
|
2.1
|
90.0
|
1.0
|
F2
|
C:TTF308
|
2.2
|
92.5
|
1.0
|
C7
|
C:TTF308
|
2.6
|
69.2
|
1.0
|
O2
|
C:TTF308
|
3.1
|
88.5
|
1.0
|
CZ3
|
C:TRP35
|
3.4
|
0.5
|
1.0
|
CH2
|
C:TRP35
|
3.6
|
0.5
|
1.0
|
CD1
|
C:ILE43
|
3.8
|
68.0
|
1.0
|
C6
|
C:TTF308
|
3.8
|
49.8
|
1.0
|
CG1
|
C:ILE43
|
4.0
|
63.9
|
1.0
|
SD
|
C:MET39
|
4.1
|
60.2
|
1.0
|
CG
|
C:MET39
|
4.4
|
56.1
|
1.0
|
CE3
|
C:TRP35
|
4.6
|
0.7
|
1.0
|
CZ2
|
C:TRP35
|
4.9
|
0.8
|
1.0
|
CG
|
B:PRO169
|
5.0
|
56.8
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 1zp0
Go back to
Fluorine Binding Sites List in 1zp0
Fluorine binding site 4 out
of 6 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
 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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F309
b:0.9
occ:1.00
|
F1
|
D:TTF309
|
0.0
|
0.9
|
1.0
|
C8
|
D:TTF309
|
1.3
|
0.4
|
1.0
|
F2
|
D:TTF309
|
2.1
|
0.7
|
1.0
|
F3
|
D:TTF309
|
2.1
|
0.5
|
1.0
|
C7
|
D:TTF309
|
2.3
|
0.8
|
1.0
|
C6
|
D:TTF309
|
2.7
|
0.3
|
1.0
|
O
|
D:ALA60
|
2.8
|
93.8
|
1.0
|
C
|
D:ALA60
|
3.4
|
89.9
|
1.0
|
O2
|
D:TTF309
|
3.4
|
0.1
|
1.0
|
CA
|
D:TYR61
|
3.6
|
96.5
|
1.0
|
N
|
D:TYR61
|
3.7
|
94.6
|
1.0
|
CG
|
D:PRO64
|
4.1
|
0.4
|
1.0
|
SG
|
D:CYS127
|
4.2
|
0.7
|
1.0
|
C5
|
D:TTF309
|
4.2
|
0.9
|
1.0
|
CB
|
D:ALA60
|
4.3
|
94.4
|
1.0
|
CB
|
D:CYS127
|
4.4
|
99.3
|
1.0
|
CB
|
D:TYR61
|
4.4
|
98.1
|
1.0
|
CA
|
D:ALA60
|
4.4
|
84.6
|
1.0
|
C
|
D:TYR61
|
4.6
|
97.3
|
1.0
|
O
|
D:TYR61
|
4.6
|
1.0
|
1.0
|
CB
|
D:PRO64
|
4.6
|
0.4
|
1.0
|
CA
|
D:CYS127
|
4.6
|
98.3
|
1.0
|
O
|
D:CYS127
|
4.7
|
98.1
|
1.0
|
CD1
|
D:TYR61
|
4.8
|
0.7
|
1.0
|
C
|
D:CYS127
|
5.0
|
97.8
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 1zp0
Go back to
Fluorine Binding Sites List in 1zp0
Fluorine binding site 5 out
of 6 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F309
b:0.7
occ:1.00
|
F2
|
D:TTF309
|
0.0
|
0.7
|
1.0
|
C8
|
D:TTF309
|
1.3
|
0.4
|
1.0
|
F1
|
D:TTF309
|
2.1
|
0.9
|
1.0
|
F3
|
D:TTF309
|
2.2
|
0.5
|
1.0
|
C7
|
D:TTF309
|
2.3
|
0.8
|
1.0
|
C6
|
D:TTF309
|
3.0
|
0.3
|
1.0
|
O2
|
D:TTF309
|
3.3
|
0.1
|
1.0
|
CG1
|
D:VAL130
|
3.6
|
75.4
|
1.0
|
S1
|
D:TTF309
|
3.8
|
0.3
|
1.0
|
CB
|
D:VAL130
|
3.9
|
80.9
|
1.0
|
C5
|
D:TTF309
|
4.2
|
0.9
|
1.0
|
CG2
|
D:VAL130
|
4.4
|
86.4
|
1.0
|
O
|
D:CYS127
|
4.4
|
98.1
|
1.0
|
C3
|
D:TTF309
|
4.4
|
0.8
|
1.0
|
O
|
D:ALA60
|
4.7
|
93.8
|
1.0
|
CA
|
D:CYS127
|
4.8
|
98.3
|
1.0
|
CA
|
D:TYR61
|
4.9
|
96.5
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 1zp0
Go back to
Fluorine Binding Sites List in 1zp0
Fluorine binding site 6 out
of 6 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F309
b:0.5
occ:1.00
|
F3
|
D:TTF309
|
0.0
|
0.5
|
1.0
|
C8
|
D:TTF309
|
1.4
|
0.4
|
1.0
|
F1
|
D:TTF309
|
2.1
|
0.9
|
1.0
|
F2
|
D:TTF309
|
2.2
|
0.7
|
1.0
|
C7
|
D:TTF309
|
2.6
|
0.8
|
1.0
|
O2
|
D:TTF309
|
3.1
|
0.1
|
1.0
|
N
|
D:TYR61
|
3.2
|
94.6
|
1.0
|
CA
|
D:TYR61
|
3.2
|
96.5
|
1.0
|
C
|
D:ALA60
|
3.4
|
89.9
|
1.0
|
CB
|
D:TYR61
|
3.5
|
98.1
|
1.0
|
O
|
D:ALA60
|
3.5
|
93.8
|
1.0
|
O
|
D:LEU57
|
3.8
|
75.2
|
1.0
|
CB
|
D:ALA60
|
3.8
|
94.4
|
1.0
|
C6
|
D:TTF309
|
3.8
|
0.3
|
1.0
|
CA
|
D:ALA60
|
4.2
|
84.6
|
1.0
|
CG
|
D:TYR61
|
4.5
|
0.4
|
1.0
|
C
|
D:TYR61
|
4.7
|
97.3
|
1.0
|
CD1
|
D:TYR61
|
4.7
|
0.7
|
1.0
|
C
|
D:LEU57
|
4.9
|
72.3
|
1.0
|
|
Reference:
F.Sun,
X.Huo,
Y.Zhai,
A.Wang,
J.Xu,
D.Su,
M.Bartlam,
Z.Rao.
Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex II Cell(Cambridge,Mass.) V. 121 1043 2005.
ISSN: ISSN 0092-8674
PubMed: 15989954
DOI: 10.1016/J.CELL.2005.05.025
Page generated: Wed Jul 31 13:40:01 2024
|