Potassium in PDB 7nf0: T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn
Enzymatic activity of T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn
All present enzymatic activity of T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn:
4.1.1.102;
Protein crystallography data
The structure of T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn, PDB code: 7nf0
was solved by
A.Saaret,
D.Leys,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
63.50 /
1.35
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.593,
74.593,
345.772,
90,
90,
120
|
R / Rfree (%)
|
16.6 /
18.4
|
Other elements in 7nf0:
The structure of T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn
(pdb code 7nf0). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn, PDB code: 7nf0:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 7nf0
Go back to
Potassium Binding Sites List in 7nf0
Potassium binding site 1 out
of 4 in the T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K703
b:11.7
occ:1.00
|
O
|
A:LEU471
|
2.6
|
11.3
|
1.0
|
O
|
A:ARG431
|
2.6
|
11.6
|
1.0
|
O
|
A:ASP469
|
2.7
|
11.2
|
1.0
|
OD2
|
A:ASP437
|
2.8
|
12.6
|
1.0
|
O
|
A:HOH1121
|
2.8
|
13.4
|
1.0
|
O
|
A:HOH849
|
3.2
|
13.6
|
1.0
|
OD2
|
A:ASP469
|
3.3
|
15.5
|
1.0
|
CG
|
A:ASP437
|
3.4
|
12.6
|
1.0
|
CG
|
A:ASP469
|
3.7
|
13.5
|
1.0
|
C
|
A:LEU471
|
3.7
|
10.7
|
1.0
|
C
|
A:ASP469
|
3.8
|
11.1
|
1.0
|
C
|
A:ARG431
|
3.8
|
10.9
|
1.0
|
CB
|
A:ASP437
|
3.9
|
11.5
|
1.0
|
OD1
|
A:ASP469
|
4.0
|
14.0
|
1.0
|
OD1
|
B:ASN457
|
4.0
|
15.9
|
1.0
|
N
|
A:LEU471
|
4.1
|
11.0
|
1.0
|
OD1
|
A:ASP437
|
4.1
|
13.6
|
1.0
|
CA
|
A:CYS432
|
4.2
|
10.7
|
1.0
|
O
|
A:HOH913
|
4.3
|
13.2
|
1.0
|
CB
|
A:ASP469
|
4.3
|
11.5
|
1.0
|
CA
|
A:LEU472
|
4.4
|
12.0
|
1.0
|
N
|
A:LEU472
|
4.4
|
11.5
|
1.0
|
CA
|
A:ALA470
|
4.4
|
10.2
|
1.0
|
N
|
A:CYS432
|
4.5
|
10.7
|
1.0
|
N
|
A:ALA470
|
4.5
|
10.6
|
1.0
|
CA
|
A:LEU471
|
4.5
|
11.9
|
1.0
|
C
|
A:ALA470
|
4.6
|
10.9
|
1.0
|
CA
|
A:ASP469
|
4.7
|
11.3
|
1.0
|
N
|
A:ARG433
|
4.7
|
11.0
|
1.0
|
CA
|
A:ARG431
|
4.9
|
9.6
|
1.0
|
C
|
A:LEU472
|
4.9
|
12.0
|
1.0
|
|
Potassium binding site 2 out
of 4 in 7nf0
Go back to
Potassium Binding Sites List in 7nf0
Potassium binding site 2 out
of 4 in the T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K704
b:10.5
occ:1.00
|
OE2
|
A:GLU243
|
2.8
|
9.9
|
1.0
|
O
|
A:MET235
|
2.8
|
11.1
|
1.0
|
O9
|
A:BYN702
|
2.8
|
9.6
|
1.0
|
O
|
A:ALA232
|
2.9
|
10.1
|
1.0
|
O7
|
A:BYN702
|
3.0
|
9.4
|
1.0
|
O
|
A:TRP179
|
3.0
|
9.3
|
1.0
|
O
|
A:SER233
|
3.1
|
10.5
|
1.0
|
O
|
A:HOH851
|
3.4
|
10.1
|
1.0
|
P1
|
A:BYN702
|
3.4
|
9.3
|
1.0
|
C
|
A:SER233
|
3.5
|
9.4
|
1.0
|
CD
|
A:GLU243
|
3.6
|
9.5
|
1.0
|
MN
|
A:MN705
|
3.7
|
8.8
|
0.7
|
CA
|
A:SER233
|
3.7
|
9.7
|
1.0
|
O10
|
A:BYN702
|
3.7
|
10.3
|
1.0
|
CG
|
A:GLU243
|
3.8
|
10.7
|
1.0
|
C
|
A:MET235
|
3.9
|
10.4
|
1.0
|
C
|
A:ALA232
|
3.9
|
9.9
|
1.0
|
N
|
A:MET235
|
4.1
|
10.4
|
1.0
|
O6
|
A:BYN702
|
4.2
|
11.7
|
1.0
|
C22
|
A:BYN702
|
4.2
|
10.0
|
1.0
|
C21
|
A:BYN702
|
4.2
|
9.6
|
1.0
|
C
|
A:TRP179
|
4.2
|
8.8
|
1.0
|
CB
|
A:SER180
|
4.3
|
10.2
|
1.0
|
N
|
A:SER233
|
4.3
|
10.1
|
1.0
|
CA
|
A:SER180
|
4.4
|
8.9
|
1.0
|
N
|
A:SER234
|
4.4
|
9.7
|
1.0
|
CA
|
A:MET235
|
4.6
|
10.9
|
1.0
|
OE1
|
A:GLU243
|
4.7
|
10.4
|
1.0
|
C
|
A:SER234
|
4.8
|
10.3
|
1.0
|
OD1
|
A:ASN178
|
4.8
|
11.7
|
1.0
|
N
|
A:SER180
|
4.8
|
9.1
|
1.0
|
O8
|
A:BYN702
|
4.9
|
9.7
|
1.0
|
N
|
A:PRO236
|
4.9
|
10.1
|
1.0
|
N
|
A:ILE237
|
4.9
|
10.4
|
1.0
|
CG1
|
A:ILE237
|
4.9
|
12.1
|
1.0
|
|
Potassium binding site 3 out
of 4 in 7nf0
Go back to
Potassium Binding Sites List in 7nf0
Potassium binding site 3 out
of 4 in the T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K703
b:12.4
occ:1.00
|
O
|
B:ARG431
|
2.6
|
11.2
|
1.0
|
O
|
B:LEU471
|
2.7
|
13.2
|
1.0
|
O
|
B:ASP469
|
2.7
|
12.3
|
1.0
|
OD2
|
B:ASP437
|
2.7
|
12.5
|
1.0
|
O
|
B:HOH1077
|
2.8
|
12.7
|
1.0
|
O
|
B:HOH857
|
3.3
|
13.5
|
1.0
|
OD2
|
B:ASP469
|
3.3
|
14.9
|
1.0
|
CG
|
B:ASP437
|
3.4
|
12.3
|
1.0
|
CG
|
B:ASP469
|
3.6
|
14.1
|
1.0
|
C
|
B:LEU471
|
3.7
|
12.1
|
1.0
|
C
|
B:ASP469
|
3.8
|
12.3
|
1.0
|
C
|
B:ARG431
|
3.8
|
10.2
|
1.0
|
CB
|
B:ASP437
|
3.9
|
11.4
|
1.0
|
OD1
|
B:ASP469
|
4.0
|
14.2
|
1.0
|
OD1
|
A:ASN457
|
4.0
|
16.3
|
1.0
|
OD1
|
B:ASP437
|
4.1
|
14.3
|
1.0
|
N
|
B:LEU471
|
4.1
|
11.8
|
1.0
|
CA
|
B:CYS432
|
4.2
|
11.0
|
1.0
|
O
|
B:HOH879
|
4.2
|
12.6
|
1.0
|
CB
|
B:ASP469
|
4.3
|
13.0
|
1.0
|
N
|
B:LEU472
|
4.4
|
11.6
|
1.0
|
CA
|
B:LEU472
|
4.4
|
12.0
|
1.0
|
N
|
B:CYS432
|
4.4
|
10.7
|
1.0
|
CA
|
B:ALA470
|
4.5
|
11.0
|
1.0
|
N
|
B:ALA470
|
4.5
|
11.8
|
1.0
|
CA
|
B:LEU471
|
4.5
|
12.0
|
1.0
|
C
|
B:ALA470
|
4.6
|
10.8
|
1.0
|
N
|
B:ARG433
|
4.7
|
9.8
|
1.0
|
CA
|
B:ASP469
|
4.7
|
11.9
|
1.0
|
CA
|
B:ARG431
|
4.9
|
9.9
|
1.0
|
C
|
B:LEU472
|
4.9
|
12.9
|
1.0
|
|
Potassium binding site 4 out
of 4 in 7nf0
Go back to
Potassium Binding Sites List in 7nf0
Potassium binding site 4 out
of 4 in the T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of T. Atroviride Fdc Variant Tafdcv in Complex with Hydroxylated Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K704
b:14.8
occ:1.00
|
OE2
|
B:GLU243
|
2.8
|
15.3
|
1.0
|
O
|
B:MET235
|
2.8
|
14.4
|
1.0
|
O8
|
B:BYN702
|
2.9
|
12.3
|
1.0
|
O
|
B:ALA232
|
2.9
|
15.9
|
1.0
|
O7
|
B:BYN702
|
3.0
|
12.9
|
1.0
|
O
|
B:TRP179
|
3.0
|
12.8
|
1.0
|
O
|
B:SER233
|
3.1
|
14.3
|
1.0
|
O
|
B:HOH818
|
3.4
|
13.8
|
1.0
|
P1
|
B:BYN702
|
3.5
|
12.9
|
1.0
|
C
|
B:SER233
|
3.5
|
13.3
|
1.0
|
CD
|
B:GLU243
|
3.6
|
15.4
|
1.0
|
MN
|
B:MN705
|
3.7
|
12.7
|
0.7
|
O9
|
B:BYN702
|
3.7
|
13.7
|
1.0
|
CA
|
B:SER233
|
3.7
|
13.7
|
1.0
|
CG
|
B:GLU243
|
3.8
|
14.4
|
1.0
|
C
|
B:MET235
|
3.9
|
16.2
|
1.0
|
C
|
B:ALA232
|
4.0
|
14.8
|
1.0
|
N
|
B:MET235
|
4.1
|
16.2
|
1.0
|
C
|
B:TRP179
|
4.1
|
12.2
|
1.0
|
O6
|
B:BYN702
|
4.2
|
15.1
|
1.0
|
C22
|
B:BYN702
|
4.2
|
14.3
|
1.0
|
C21
|
B:BYN702
|
4.3
|
13.7
|
1.0
|
CB
|
B:SER180
|
4.3
|
12.8
|
1.0
|
N
|
B:SER233
|
4.3
|
14.4
|
1.0
|
CA
|
B:SER180
|
4.4
|
12.2
|
1.0
|
N
|
B:SER234
|
4.4
|
14.2
|
1.0
|
CA
|
B:MET235
|
4.6
|
15.7
|
1.0
|
OE1
|
B:GLU243
|
4.6
|
14.2
|
1.0
|
OD1
|
B:ASN178
|
4.8
|
17.1
|
1.0
|
N
|
B:SER180
|
4.8
|
12.9
|
1.0
|
C
|
B:SER234
|
4.8
|
16.9
|
1.0
|
O10
|
B:BYN702
|
4.8
|
12.8
|
1.0
|
N
|
B:PRO236
|
4.9
|
16.6
|
1.0
|
N
|
B:ILE237
|
5.0
|
15.3
|
1.0
|
CG1
|
B:ILE237
|
5.0
|
17.1
|
1.0
|
|
Reference:
A.Saaret,
B.Villiers,
F.Stricher,
M.Anissimova,
M.Cadillon,
R.Spiess,
S.Hay,
D.Leys.
Directed Evolution of Prenylated Fmn-Dependent Fdc Supports Efficient in Vivo Isobutene Production Nat Commun 2021.
ISSN: ESSN 2041-1723
Page generated: Mon Aug 12 19:29:51 2024
|