Fluorine in PDB 2bu9: Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
Enzymatic activity of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
All present enzymatic activity of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline:
1.21.3.1;
Protein crystallography data
The structure of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline, PDB code: 2bu9
was solved by
A.R.Howard-Jones,
P.J.Rutledge,
I.J.Clifton,
R.M.Adlington,
J.E.Baldwin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
58.03 /
1.3
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.465,
71.012,
100.768,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.9 /
16.8
|
Other elements in 2bu9:
The structure of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
(pdb code 2bu9). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline, PDB code: 2bu9:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 2bu9
Go back to
Fluorine Binding Sites List in 2bu9
Fluorine binding site 1 out
of 6 in the Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1333
b:13.1
occ:1.00
|
F24
|
A:HFV1333
|
0.0
|
13.1
|
1.0
|
C37
|
A:HFV1333
|
1.4
|
10.6
|
1.0
|
F26
|
A:HFV1333
|
2.1
|
12.4
|
1.0
|
F25
|
A:HFV1333
|
2.2
|
12.5
|
1.0
|
C32
|
A:HFV1333
|
2.3
|
10.0
|
1.0
|
F22
|
A:HFV1333
|
2.7
|
11.0
|
1.0
|
OH
|
A:TYR189
|
2.9
|
18.8
|
1.0
|
C33
|
A:HFV1333
|
2.9
|
10.9
|
1.0
|
C30
|
A:HFV1333
|
3.7
|
9.4
|
1.0
|
F23
|
A:HFV1333
|
3.7
|
10.8
|
1.0
|
CG1
|
A:VAL100
|
3.7
|
14.5
|
1.0
|
CZ
|
A:TYR189
|
3.8
|
16.7
|
1.0
|
O
|
A:HOH2326
|
4.0
|
30.3
|
1.0
|
CE1
|
A:TYR189
|
4.0
|
15.3
|
1.0
|
CG2
|
A:VAL100
|
4.1
|
16.6
|
1.0
|
F21
|
A:HFV1333
|
4.1
|
9.6
|
1.0
|
CB
|
A:PHE211
|
4.1
|
13.0
|
1.0
|
C31
|
A:HFV1333
|
4.2
|
10.3
|
1.0
|
O42
|
A:HFV1333
|
4.2
|
11.3
|
1.0
|
CB
|
A:VAL100
|
4.2
|
12.7
|
1.0
|
CD1
|
A:PHE211
|
4.3
|
13.2
|
1.0
|
N29
|
A:HFV1333
|
4.3
|
10.4
|
1.0
|
O
|
A:SER210
|
4.3
|
15.3
|
1.0
|
CG
|
A:PHE211
|
4.3
|
12.8
|
1.0
|
C
|
A:SER210
|
4.9
|
14.1
|
1.0
|
CE2
|
A:TYR189
|
4.9
|
14.3
|
1.0
|
CB
|
A:SER210
|
5.0
|
14.0
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 2bu9
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Fluorine Binding Sites List in 2bu9
Fluorine binding site 2 out
of 6 in the Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1333
b:12.5
occ:1.00
|
F25
|
A:HFV1333
|
0.0
|
12.5
|
1.0
|
C37
|
A:HFV1333
|
1.3
|
10.6
|
1.0
|
F26
|
A:HFV1333
|
2.1
|
12.4
|
1.0
|
F24
|
A:HFV1333
|
2.2
|
13.1
|
1.0
|
C32
|
A:HFV1333
|
2.3
|
10.0
|
1.0
|
C30
|
A:HFV1333
|
2.7
|
9.4
|
1.0
|
C31
|
A:HFV1333
|
2.8
|
10.3
|
1.0
|
OH
|
A:TYR189
|
2.9
|
18.8
|
1.0
|
CB
|
A:PHE211
|
3.0
|
13.0
|
1.0
|
N29
|
A:HFV1333
|
3.1
|
10.4
|
1.0
|
CG
|
A:PHE211
|
3.2
|
12.8
|
1.0
|
O42
|
A:HFV1333
|
3.2
|
11.3
|
1.0
|
O43
|
A:HFV1333
|
3.2
|
13.4
|
1.0
|
CD2
|
A:PHE211
|
3.6
|
12.9
|
1.0
|
C33
|
A:HFV1333
|
3.6
|
10.9
|
1.0
|
CD1
|
A:PHE211
|
3.7
|
13.2
|
1.0
|
CG2
|
A:VAL272
|
3.9
|
15.6
|
1.0
|
F22
|
A:HFV1333
|
4.1
|
11.0
|
1.0
|
F23
|
A:HFV1333
|
4.1
|
10.8
|
1.0
|
CZ
|
A:TYR189
|
4.2
|
16.7
|
1.0
|
C13
|
A:HFV1333
|
4.4
|
10.2
|
1.0
|
CB
|
A:VAL272
|
4.4
|
12.8
|
1.0
|
CE2
|
A:PHE211
|
4.4
|
13.5
|
1.0
|
CA
|
A:PHE211
|
4.4
|
12.6
|
1.0
|
CE1
|
A:PHE211
|
4.5
|
13.3
|
1.0
|
F21
|
A:HFV1333
|
4.7
|
9.6
|
1.0
|
CG1
|
A:VAL272
|
4.7
|
13.7
|
1.0
|
CZ
|
A:PHE211
|
4.8
|
13.2
|
1.0
|
N
|
A:PHE211
|
4.8
|
12.9
|
1.0
|
O
|
A:SER210
|
4.8
|
15.3
|
1.0
|
CE1
|
A:TYR189
|
4.9
|
15.3
|
1.0
|
C
|
A:SER210
|
4.9
|
14.1
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 2bu9
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Fluorine Binding Sites List in 2bu9
Fluorine binding site 3 out
of 6 in the Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1333
b:12.4
occ:1.00
|
F26
|
A:HFV1333
|
0.0
|
12.4
|
1.0
|
C37
|
A:HFV1333
|
1.3
|
10.6
|
1.0
|
F24
|
A:HFV1333
|
2.1
|
13.1
|
1.0
|
F25
|
A:HFV1333
|
2.1
|
12.5
|
1.0
|
C32
|
A:HFV1333
|
2.4
|
10.0
|
1.0
|
F23
|
A:HFV1333
|
2.7
|
10.8
|
1.0
|
C33
|
A:HFV1333
|
2.7
|
10.9
|
1.0
|
CD1
|
A:PHE211
|
3.0
|
13.2
|
1.0
|
F22
|
A:HFV1333
|
3.0
|
11.0
|
1.0
|
N29
|
A:HFV1333
|
3.0
|
10.4
|
1.0
|
C30
|
A:HFV1333
|
3.1
|
9.4
|
1.0
|
CG
|
A:PHE211
|
3.3
|
12.8
|
1.0
|
CE1
|
A:PHE211
|
3.3
|
13.3
|
1.0
|
CG2
|
A:THR331
|
3.5
|
16.9
|
1.0
|
CB
|
A:PHE211
|
3.8
|
13.0
|
1.0
|
CZ
|
A:PHE211
|
3.8
|
13.2
|
1.0
|
CD2
|
A:PHE211
|
3.9
|
12.9
|
1.0
|
C13
|
A:HFV1333
|
3.9
|
10.2
|
1.0
|
F21
|
A:HFV1333
|
4.1
|
9.6
|
1.0
|
C31
|
A:HFV1333
|
4.1
|
10.3
|
1.0
|
CE2
|
A:PHE211
|
4.1
|
13.5
|
1.0
|
CB
|
A:THR331
|
4.3
|
16.2
|
1.0
|
OH
|
A:TYR189
|
4.5
|
18.8
|
1.0
|
C12
|
A:HFV1333
|
4.5
|
7.7
|
1.0
|
O43
|
A:HFV1333
|
4.6
|
13.4
|
1.0
|
O18
|
A:HFV1333
|
4.7
|
11.5
|
1.0
|
O42
|
A:HFV1333
|
4.7
|
11.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 2bu9
Go back to
Fluorine Binding Sites List in 2bu9
Fluorine binding site 4 out
of 6 in the Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1333
b:9.6
occ:1.00
|
F21
|
A:HFV1333
|
0.0
|
9.6
|
1.0
|
C33
|
A:HFV1333
|
1.4
|
10.9
|
1.0
|
F23
|
A:HFV1333
|
2.1
|
10.8
|
1.0
|
F22
|
A:HFV1333
|
2.2
|
11.0
|
1.0
|
C32
|
A:HFV1333
|
2.4
|
10.0
|
1.0
|
C30
|
A:HFV1333
|
2.9
|
9.4
|
1.0
|
CD1
|
A:ILE187
|
3.0
|
14.0
|
1.0
|
O
|
A:HOH2187
|
3.1
|
7.0
|
0.4
|
CG1
|
A:ILE187
|
3.2
|
12.8
|
1.0
|
O
|
A:HOH2185
|
3.4
|
10.9
|
0.2
|
O
|
A:HOH2461
|
3.5
|
18.5
|
1.0
|
CG2
|
A:ILE187
|
3.5
|
13.8
|
1.0
|
O18
|
A:HFV1333
|
3.6
|
11.5
|
1.0
|
C37
|
A:HFV1333
|
3.7
|
10.6
|
1.0
|
N29
|
A:HFV1333
|
3.8
|
10.4
|
1.0
|
CB
|
A:ILE187
|
4.0
|
13.1
|
1.0
|
C13
|
A:HFV1333
|
4.0
|
10.2
|
1.0
|
O
|
A:HOH2460
|
4.0
|
9.2
|
0.4
|
F26
|
A:HFV1333
|
4.1
|
12.4
|
1.0
|
F24
|
A:HFV1333
|
4.1
|
13.1
|
1.0
|
C31
|
A:HFV1333
|
4.1
|
10.3
|
1.0
|
O42
|
A:HFV1333
|
4.3
|
11.3
|
1.0
|
CG2
|
A:VAL100
|
4.4
|
16.6
|
1.0
|
CB
|
A:SER102
|
4.6
|
13.6
|
1.0
|
OG
|
A:SER102
|
4.6
|
15.7
|
1.0
|
F25
|
A:HFV1333
|
4.7
|
12.5
|
1.0
|
CG1
|
A:VAL185
|
4.8
|
12.8
|
1.0
|
CB
|
A:THR331
|
4.8
|
16.2
|
1.0
|
OH
|
A:TYR189
|
4.9
|
18.8
|
1.0
|
OG1
|
A:THR331
|
5.0
|
18.2
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 2bu9
Go back to
Fluorine Binding Sites List in 2bu9
Fluorine binding site 5 out
of 6 in the Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1333
b:10.8
occ:1.00
|
F23
|
A:HFV1333
|
0.0
|
10.8
|
1.0
|
C33
|
A:HFV1333
|
1.3
|
10.9
|
1.0
|
F21
|
A:HFV1333
|
2.1
|
9.6
|
1.0
|
F22
|
A:HFV1333
|
2.1
|
11.0
|
1.0
|
C32
|
A:HFV1333
|
2.4
|
10.0
|
1.0
|
F26
|
A:HFV1333
|
2.7
|
12.4
|
1.0
|
O
|
A:HOH2461
|
2.8
|
18.5
|
1.0
|
C30
|
A:HFV1333
|
2.9
|
9.4
|
1.0
|
N29
|
A:HFV1333
|
2.9
|
10.4
|
1.0
|
C37
|
A:HFV1333
|
3.0
|
10.6
|
1.0
|
O18
|
A:HFV1333
|
3.1
|
11.5
|
1.0
|
C13
|
A:HFV1333
|
3.1
|
10.2
|
1.0
|
CG2
|
A:THR331
|
3.2
|
16.9
|
1.0
|
CB
|
A:THR331
|
3.2
|
16.2
|
1.0
|
O
|
A:HOH2187
|
3.3
|
7.0
|
0.4
|
O
|
A:HOH2185
|
3.4
|
10.9
|
0.2
|
OG1
|
A:THR331
|
3.6
|
18.2
|
1.0
|
F24
|
A:HFV1333
|
3.7
|
13.1
|
1.0
|
O15
|
A:HFV1333
|
4.0
|
8.4
|
1.0
|
F25
|
A:HFV1333
|
4.1
|
12.5
|
1.0
|
C12
|
A:HFV1333
|
4.1
|
7.7
|
1.0
|
C31
|
A:HFV1333
|
4.4
|
10.3
|
1.0
|
O
|
A:HOH2460
|
4.5
|
9.2
|
0.4
|
CA
|
A:THR331
|
4.6
|
15.1
|
1.0
|
C10
|
A:HFV1333
|
4.7
|
8.1
|
1.0
|
CD1
|
A:ILE187
|
4.8
|
14.0
|
1.0
|
N11
|
A:HFV1333
|
4.9
|
8.2
|
1.0
|
O
|
A:THR331
|
4.9
|
17.9
|
1.0
|
O42
|
A:HFV1333
|
5.0
|
11.3
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 2bu9
Go back to
Fluorine Binding Sites List in 2bu9
Fluorine binding site 6 out
of 6 in the Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Isopenicillin N Synthase Complexed with L-Aminoadipoyl-L- Cysteinyl-L-Hexafluorovaline within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1333
b:11.0
occ:1.00
|
F22
|
A:HFV1333
|
0.0
|
11.0
|
1.0
|
C33
|
A:HFV1333
|
1.3
|
10.9
|
1.0
|
F23
|
A:HFV1333
|
2.1
|
10.8
|
1.0
|
F21
|
A:HFV1333
|
2.2
|
9.6
|
1.0
|
C32
|
A:HFV1333
|
2.4
|
10.0
|
1.0
|
F24
|
A:HFV1333
|
2.7
|
13.1
|
1.0
|
C37
|
A:HFV1333
|
2.8
|
10.6
|
1.0
|
F26
|
A:HFV1333
|
3.0
|
12.4
|
1.0
|
O
|
A:HOH2187
|
3.2
|
7.0
|
0.4
|
CG1
|
A:VAL100
|
3.4
|
14.5
|
1.0
|
O
|
A:HOH2460
|
3.4
|
9.2
|
0.4
|
CG2
|
A:VAL100
|
3.4
|
16.6
|
1.0
|
C30
|
A:HFV1333
|
3.7
|
9.4
|
1.0
|
CB
|
A:THR331
|
3.8
|
16.2
|
1.0
|
O
|
A:HOH2185
|
3.9
|
10.9
|
0.2
|
CB
|
A:VAL100
|
4.0
|
12.7
|
1.0
|
F25
|
A:HFV1333
|
4.1
|
12.5
|
1.0
|
CG2
|
A:THR331
|
4.2
|
16.9
|
1.0
|
O
|
A:THR331
|
4.3
|
17.9
|
1.0
|
N29
|
A:HFV1333
|
4.4
|
10.4
|
1.0
|
CG2
|
A:ILE187
|
4.4
|
13.8
|
1.0
|
O
|
A:HOH2461
|
4.4
|
18.5
|
1.0
|
OG1
|
A:THR331
|
4.5
|
18.2
|
1.0
|
OH
|
A:TYR189
|
4.6
|
18.8
|
1.0
|
CA
|
A:THR331
|
4.6
|
15.1
|
1.0
|
C31
|
A:HFV1333
|
4.9
|
10.3
|
1.0
|
C
|
A:THR331
|
5.0
|
16.9
|
1.0
|
C13
|
A:HFV1333
|
5.0
|
10.2
|
1.0
|
O18
|
A:HFV1333
|
5.0
|
11.5
|
1.0
|
|
Reference:
A.R.Howard-Jones,
P.J.Rutledge,
I.J.Clifton,
R.M.Adlington,
J.E.Baldwin.
Unique Binding of A Non-Natural L,L,L-Substrate By Isopenicillin N Synthase Biochem.Biophys.Res.Commun. V. 336 702 2005.
ISSN: ISSN 0006-291X
PubMed: 16143309
DOI: 10.1016/J.BBRC.2005.08.155
Page generated: Wed Jul 31 13:53:19 2024
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