Potassium in PDB 7ney: Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn
Enzymatic activity of Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn
All present enzymatic activity of Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn:
4.1.1.102;
Protein crystallography data
The structure of Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn, PDB code: 7ney
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)
|
63.19 /
1.74
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.212,
74.212,
346.561,
90,
90,
120
|
R / Rfree (%)
|
18.2 /
21.5
|
Other elements in 7ney:
The structure of Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn
(pdb code 7ney). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the
Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn, PDB code: 7ney:
Jump to Potassium binding site number:
1;
2;
3;
4;
Potassium binding site 1 out
of 4 in 7ney
Go back to
Potassium Binding Sites List in 7ney
Potassium binding site 1 out
of 4 in the Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K602
b:34.3
occ:1.00
|
OE2
|
A:GLU243
|
2.8
|
19.3
|
1.0
|
O2P
|
A:4LU601
|
2.9
|
18.5
|
1.0
|
O
|
A:MET235
|
3.0
|
18.2
|
1.0
|
O
|
A:ALA232
|
3.0
|
18.7
|
1.0
|
O5'
|
A:4LU601
|
3.0
|
18.8
|
1.0
|
O
|
A:TRP179
|
3.1
|
16.6
|
1.0
|
O
|
A:SER233
|
3.2
|
18.2
|
1.0
|
P
|
A:4LU601
|
3.4
|
19.0
|
1.0
|
O
|
A:HOH720
|
3.4
|
18.0
|
1.0
|
C
|
A:SER233
|
3.6
|
18.2
|
1.0
|
O3P
|
A:4LU601
|
3.6
|
20.7
|
1.0
|
CD
|
A:GLU243
|
3.6
|
20.4
|
1.0
|
MN
|
A:MN604
|
3.7
|
21.4
|
1.0
|
CA
|
A:SER233
|
3.8
|
16.4
|
1.0
|
CG
|
A:GLU243
|
3.8
|
21.2
|
1.0
|
C
|
A:MET235
|
4.0
|
18.6
|
1.0
|
C
|
A:ALA232
|
4.0
|
16.6
|
1.0
|
N
|
A:MET235
|
4.1
|
17.1
|
1.0
|
O4'
|
A:4LU601
|
4.1
|
22.4
|
1.0
|
C4'
|
A:4LU601
|
4.2
|
20.0
|
1.0
|
C5'
|
A:4LU601
|
4.2
|
18.2
|
1.0
|
C
|
A:TRP179
|
4.3
|
16.0
|
1.0
|
CB
|
A:SER180
|
4.4
|
17.7
|
1.0
|
N
|
A:SER233
|
4.4
|
17.0
|
1.0
|
N
|
A:SER234
|
4.4
|
17.0
|
1.0
|
CA
|
A:SER180
|
4.5
|
15.3
|
1.0
|
CA
|
A:MET235
|
4.7
|
18.4
|
1.0
|
OE1
|
A:GLU243
|
4.7
|
18.3
|
1.0
|
C
|
A:SER234
|
4.8
|
18.5
|
1.0
|
OD1
|
A:ASN178
|
4.8
|
19.8
|
1.0
|
O1P
|
A:4LU601
|
4.9
|
20.1
|
1.0
|
N
|
A:ILE237
|
4.9
|
20.0
|
1.0
|
N
|
A:SER180
|
4.9
|
16.4
|
1.0
|
N
|
A:PRO236
|
5.0
|
18.3
|
1.0
|
CG1
|
A:ILE237
|
5.0
|
24.4
|
1.0
|
|
Potassium binding site 2 out
of 4 in 7ney
Go back to
Potassium Binding Sites List in 7ney
Potassium binding site 2 out
of 4 in the Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K603
b:30.3
occ:1.00
|
O
|
A:ARG431
|
2.6
|
20.7
|
1.0
|
O
|
A:LEU471
|
2.6
|
23.8
|
1.0
|
OD2
|
A:ASP437
|
2.8
|
23.2
|
1.0
|
O
|
A:ASP469
|
2.8
|
20.2
|
1.0
|
O
|
A:HOH903
|
2.8
|
27.4
|
1.0
|
OD2
|
A:ASP469
|
3.3
|
30.1
|
1.0
|
O
|
A:HOH741
|
3.4
|
28.9
|
1.0
|
CG
|
A:ASP437
|
3.4
|
24.3
|
1.0
|
C
|
A:LEU471
|
3.7
|
23.6
|
1.0
|
CG
|
A:ASP469
|
3.7
|
30.0
|
1.0
|
C
|
A:ASP469
|
3.8
|
21.6
|
1.0
|
C
|
A:ARG431
|
3.8
|
16.8
|
1.0
|
OD1
|
A:ASP469
|
4.0
|
27.7
|
1.0
|
CB
|
A:ASP437
|
4.0
|
23.2
|
1.0
|
OD1
|
B:ASN457
|
4.0
|
38.3
|
1.0
|
OD1
|
A:ASP437
|
4.1
|
26.3
|
1.0
|
N
|
A:LEU471
|
4.1
|
22.8
|
1.0
|
CA
|
A:CYS432
|
4.2
|
18.2
|
1.0
|
O
|
A:HOH758
|
4.3
|
25.1
|
1.0
|
CA
|
A:LEU472
|
4.4
|
24.6
|
1.0
|
N
|
A:LEU472
|
4.4
|
23.7
|
1.0
|
CB
|
A:ASP469
|
4.5
|
22.7
|
1.0
|
N
|
A:CYS432
|
4.5
|
18.7
|
1.0
|
CA
|
A:ALA470
|
4.5
|
20.4
|
1.0
|
N
|
A:ALA470
|
4.5
|
19.4
|
1.0
|
C
|
A:ALA470
|
4.6
|
19.7
|
1.0
|
CA
|
A:LEU471
|
4.6
|
23.3
|
1.0
|
CA
|
A:ASP469
|
4.8
|
22.2
|
1.0
|
N
|
A:ARG433
|
4.8
|
18.2
|
1.0
|
C
|
A:LEU472
|
4.9
|
26.2
|
1.0
|
CA
|
A:ARG431
|
4.9
|
16.8
|
1.0
|
N
|
A:THR473
|
5.0
|
26.5
|
1.0
|
|
Potassium binding site 3 out
of 4 in 7ney
Go back to
Potassium Binding Sites List in 7ney
Potassium binding site 3 out
of 4 in the Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K602
b:28.1
occ:1.00
|
O
|
B:LEU471
|
2.6
|
21.9
|
1.0
|
O
|
B:ARG431
|
2.6
|
18.2
|
1.0
|
O
|
B:HOH829
|
2.8
|
25.3
|
1.0
|
O
|
B:ASP469
|
2.8
|
20.9
|
1.0
|
OD2
|
B:ASP437
|
2.8
|
21.8
|
1.0
|
O
|
B:HOH758
|
3.3
|
23.0
|
1.0
|
CG
|
B:ASP437
|
3.4
|
23.8
|
1.0
|
OD2
|
B:ASP469
|
3.5
|
27.0
|
1.0
|
C
|
B:LEU471
|
3.7
|
18.6
|
1.0
|
CG
|
B:ASP469
|
3.8
|
24.3
|
1.0
|
C
|
B:ARG431
|
3.8
|
18.3
|
1.0
|
C
|
B:ASP469
|
3.8
|
20.2
|
1.0
|
CB
|
B:ASP437
|
4.0
|
21.7
|
1.0
|
N
|
B:LEU471
|
4.0
|
19.9
|
1.0
|
OD1
|
B:ASP437
|
4.1
|
26.3
|
1.0
|
OD1
|
B:ASP469
|
4.1
|
23.3
|
1.0
|
O
|
B:HOH746
|
4.2
|
22.2
|
1.0
|
CA
|
B:CYS432
|
4.2
|
18.2
|
1.0
|
OD1
|
A:ASN457
|
4.3
|
31.7
|
1.0
|
CA
|
B:LEU472
|
4.4
|
21.5
|
1.0
|
N
|
B:LEU472
|
4.4
|
18.9
|
1.0
|
CB
|
B:ASP469
|
4.4
|
21.1
|
1.0
|
N
|
B:CYS432
|
4.5
|
18.2
|
1.0
|
CA
|
B:ALA470
|
4.5
|
19.6
|
1.0
|
C
|
B:ALA470
|
4.5
|
17.6
|
1.0
|
CA
|
B:LEU471
|
4.5
|
21.1
|
1.0
|
N
|
B:ALA470
|
4.5
|
19.8
|
1.0
|
N
|
B:ARG433
|
4.8
|
17.9
|
1.0
|
CA
|
B:ASP469
|
4.8
|
20.0
|
1.0
|
CA
|
B:ARG431
|
4.9
|
17.5
|
1.0
|
C
|
B:LEU472
|
4.9
|
22.4
|
1.0
|
O
|
B:HOH779
|
5.0
|
32.5
|
1.0
|
|
Potassium binding site 4 out
of 4 in 7ney
Go back to
Potassium Binding Sites List in 7ney
Potassium binding site 4 out
of 4 in the Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Structure of T. Atroviride Fdc Wild-Type (Tafdc) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K603
b:37.1
occ:1.00
|
O
|
B:MET235
|
2.8
|
21.6
|
1.0
|
OE2
|
B:GLU243
|
2.8
|
21.9
|
1.0
|
O
|
B:ALA232
|
2.9
|
24.1
|
1.0
|
O5'
|
B:4LU601
|
3.0
|
21.0
|
1.0
|
O
|
B:SER233
|
3.1
|
21.8
|
1.0
|
O2P
|
B:4LU601
|
3.1
|
23.1
|
1.0
|
O
|
B:TRP179
|
3.2
|
20.0
|
1.0
|
O
|
B:HOH720
|
3.4
|
19.6
|
1.0
|
C
|
B:SER233
|
3.5
|
24.5
|
1.0
|
P
|
B:4LU601
|
3.6
|
20.1
|
1.0
|
CD
|
B:GLU243
|
3.6
|
24.4
|
1.0
|
O3P
|
B:4LU601
|
3.6
|
21.6
|
1.0
|
CG
|
B:GLU243
|
3.8
|
25.6
|
1.0
|
CA
|
B:SER233
|
3.8
|
22.2
|
1.0
|
MN
|
B:MN604
|
3.8
|
23.2
|
1.0
|
C
|
B:MET235
|
3.9
|
22.8
|
1.0
|
C
|
B:ALA232
|
3.9
|
22.2
|
1.0
|
N
|
B:MET235
|
4.1
|
19.3
|
1.0
|
O4'
|
B:4LU601
|
4.1
|
25.9
|
1.0
|
C4'
|
B:4LU601
|
4.2
|
22.5
|
1.0
|
C5'
|
B:4LU601
|
4.2
|
22.5
|
1.0
|
N
|
B:SER234
|
4.3
|
22.0
|
1.0
|
N
|
B:SER233
|
4.3
|
22.1
|
1.0
|
C
|
B:TRP179
|
4.4
|
18.7
|
1.0
|
CB
|
B:SER180
|
4.5
|
22.2
|
1.0
|
CA
|
B:MET235
|
4.5
|
20.7
|
1.0
|
CA
|
B:SER180
|
4.6
|
20.4
|
1.0
|
OE1
|
B:GLU243
|
4.7
|
20.6
|
1.0
|
C
|
B:SER234
|
4.8
|
22.3
|
1.0
|
CG1
|
B:ILE237
|
4.8
|
25.2
|
1.0
|
N
|
B:PRO236
|
4.8
|
23.5
|
1.0
|
N
|
B:ILE237
|
4.9
|
24.6
|
1.0
|
CA
|
B:SER234
|
5.0
|
21.6
|
1.0
|
OD1
|
B:ASN178
|
5.0
|
24.0
|
1.0
|
N
|
B:SER180
|
5.0
|
20.4
|
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 19:29:44 2024
|