Potassium in PDB 7nf4: Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn
Enzymatic activity of Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn
All present enzymatic activity of Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn:
4.1.1.102;
Protein crystallography data
The structure of Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn, PDB code: 7nf4
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)
|
85.07 /
1.69
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.45,
97.01,
177.03,
90,
90,
90
|
R / Rfree (%)
|
19.1 /
22
|
Other elements in 7nf4:
The structure of Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn
(pdb code 7nf4). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the
Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn, PDB code: 7nf4:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
Potassium binding site 1 out
of 5 in 7nf4
Go back to
Potassium Binding Sites List in 7nf4
Potassium binding site 1 out
of 5 in the Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) 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 A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K602
b:15.1
occ:1.00
|
O
|
A:MET225
|
2.8
|
16.6
|
1.0
|
O
|
A:ALA222
|
2.8
|
15.0
|
1.0
|
OE2
|
A:GLU233
|
2.8
|
13.0
|
1.0
|
O10
|
A:BYN603
|
2.9
|
14.2
|
1.0
|
O7
|
A:BYN603
|
3.0
|
14.6
|
1.0
|
O
|
A:SER223
|
3.1
|
15.9
|
1.0
|
O
|
A:TRP169
|
3.1
|
13.4
|
1.0
|
O
|
A:HOH725
|
3.3
|
12.9
|
1.0
|
P1
|
A:BYN603
|
3.4
|
14.5
|
1.0
|
C
|
A:SER223
|
3.5
|
16.7
|
1.0
|
CD
|
A:GLU233
|
3.6
|
15.4
|
1.0
|
MN
|
A:MN601
|
3.7
|
16.5
|
1.0
|
O8
|
A:BYN603
|
3.7
|
13.8
|
1.0
|
CA
|
A:SER223
|
3.8
|
15.8
|
1.0
|
CG
|
A:GLU233
|
3.8
|
15.6
|
1.0
|
C
|
A:MET225
|
3.9
|
17.4
|
1.0
|
C
|
A:ALA222
|
3.9
|
15.0
|
1.0
|
N
|
A:MET225
|
4.0
|
16.8
|
1.0
|
C22
|
A:BYN603
|
4.2
|
13.6
|
1.0
|
O6
|
A:BYN603
|
4.2
|
18.4
|
1.0
|
C21
|
A:BYN603
|
4.3
|
15.0
|
1.0
|
N
|
A:SER223
|
4.3
|
14.7
|
1.0
|
N
|
A:SER224
|
4.3
|
16.7
|
0.5
|
C
|
A:TRP169
|
4.3
|
13.5
|
1.0
|
N
|
A:SER224
|
4.3
|
15.9
|
0.5
|
CB
|
A:SER170
|
4.3
|
14.4
|
1.0
|
CA
|
A:MET225
|
4.5
|
19.0
|
1.0
|
CA
|
A:SER170
|
4.5
|
14.2
|
1.0
|
OE1
|
A:GLU233
|
4.7
|
15.3
|
1.0
|
C
|
A:SER224
|
4.7
|
18.1
|
0.5
|
C
|
A:SER224
|
4.8
|
17.0
|
0.5
|
ND2
|
A:ASN168
|
4.8
|
13.0
|
1.0
|
N
|
A:PRO226
|
4.9
|
16.4
|
1.0
|
O9
|
A:BYN603
|
4.9
|
16.1
|
1.0
|
N
|
A:SER170
|
4.9
|
14.2
|
1.0
|
N
|
A:ILE227
|
4.9
|
16.2
|
1.0
|
CG1
|
A:ILE227
|
4.9
|
19.4
|
1.0
|
CA
|
A:SER224
|
5.0
|
17.2
|
0.5
|
CA
|
A:SER224
|
5.0
|
15.8
|
0.5
|
|
Potassium binding site 2 out
of 5 in 7nf4
Go back to
Potassium Binding Sites List in 7nf4
Potassium binding site 2 out
of 5 in the Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) 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 A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K604
b:18.8
occ:1.00
|
O
|
A:LEU461
|
2.6
|
20.1
|
1.0
|
O
|
A:ARG421
|
2.7
|
17.3
|
1.0
|
O
|
A:ASP459
|
2.7
|
17.5
|
1.0
|
O
|
A:HOH783
|
2.8
|
24.6
|
1.0
|
OD2
|
A:ASP427
|
2.8
|
17.9
|
1.0
|
O
|
A:HOH880
|
2.9
|
22.6
|
1.0
|
CG
|
A:ASP427
|
3.4
|
20.0
|
1.0
|
O
|
A:HOH736
|
3.4
|
23.3
|
1.0
|
C
|
A:LEU461
|
3.7
|
16.6
|
1.0
|
C
|
A:ASP459
|
3.8
|
17.6
|
1.0
|
C
|
A:ARG421
|
3.8
|
16.3
|
1.0
|
CB
|
A:ASP427
|
3.8
|
18.2
|
1.0
|
N
|
A:LEU461
|
4.0
|
17.3
|
1.0
|
ND2
|
B:ASN447
|
4.1
|
26.3
|
1.0
|
OD1
|
A:ASP427
|
4.2
|
19.1
|
1.0
|
CA
|
A:CYS422
|
4.3
|
15.7
|
1.0
|
CA
|
A:ALA460
|
4.3
|
16.7
|
1.0
|
C
|
A:ALA460
|
4.3
|
16.9
|
1.0
|
O
|
A:HOH718
|
4.3
|
20.3
|
1.0
|
CG
|
A:ASP459
|
4.4
|
24.7
|
1.0
|
CB
|
A:ASP459
|
4.4
|
20.2
|
1.0
|
N
|
A:ALA460
|
4.5
|
17.3
|
1.0
|
N
|
A:CYS422
|
4.5
|
15.8
|
1.0
|
CA
|
A:LEU461
|
4.5
|
18.7
|
1.0
|
N
|
A:MET462
|
4.6
|
17.6
|
1.0
|
OD1
|
A:ASP459
|
4.6
|
24.5
|
1.0
|
CA
|
A:MET462
|
4.7
|
18.1
|
1.0
|
OD2
|
A:ASP459
|
4.7
|
23.8
|
1.0
|
CA
|
A:ASP459
|
4.8
|
18.1
|
1.0
|
N
|
A:ARG423
|
4.8
|
15.3
|
1.0
|
CA
|
A:ARG421
|
4.9
|
16.0
|
1.0
|
|
Potassium binding site 3 out
of 5 in 7nf4
Go back to
Potassium Binding Sites List in 7nf4
Potassium binding site 3 out
of 5 in the Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) 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 A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K602
b:17.8
occ:1.00
|
OE2
|
B:GLU233
|
2.8
|
17.8
|
1.0
|
O
|
B:ALA222
|
2.8
|
17.3
|
1.0
|
O10
|
B:BYN604
|
2.8
|
17.0
|
1.0
|
O
|
B:MET225
|
2.8
|
19.9
|
1.0
|
O
|
B:SER223
|
3.0
|
19.0
|
1.0
|
O7
|
B:BYN604
|
3.0
|
18.2
|
1.0
|
O
|
B:TRP169
|
3.1
|
19.3
|
1.0
|
O
|
B:HOH753
|
3.3
|
16.4
|
1.0
|
P1
|
B:BYN604
|
3.4
|
18.0
|
1.0
|
C
|
B:SER223
|
3.5
|
20.3
|
1.0
|
CD
|
B:GLU233
|
3.6
|
21.2
|
1.0
|
MN
|
B:MN601
|
3.7
|
19.0
|
1.0
|
O8
|
B:BYN604
|
3.7
|
17.0
|
1.0
|
CA
|
B:SER223
|
3.8
|
18.8
|
1.0
|
CG
|
B:GLU233
|
3.9
|
20.8
|
1.0
|
C
|
B:ALA222
|
3.9
|
18.4
|
1.0
|
C
|
B:MET225
|
3.9
|
19.1
|
1.0
|
N
|
B:MET225
|
4.1
|
19.1
|
1.0
|
O6
|
B:BYN604
|
4.2
|
19.6
|
1.0
|
C
|
B:TRP169
|
4.2
|
17.4
|
1.0
|
C22
|
B:BYN604
|
4.3
|
18.7
|
1.0
|
C21
|
B:BYN604
|
4.3
|
19.1
|
1.0
|
N
|
B:SER223
|
4.3
|
17.8
|
1.0
|
N
|
B:SER224
|
4.4
|
20.3
|
0.5
|
N
|
B:SER224
|
4.4
|
19.0
|
0.5
|
CB
|
B:SER170
|
4.4
|
17.6
|
1.0
|
CA
|
B:SER170
|
4.5
|
17.1
|
1.0
|
CA
|
B:MET225
|
4.6
|
19.5
|
1.0
|
OE1
|
B:GLU233
|
4.7
|
17.4
|
1.0
|
C
|
B:SER224
|
4.8
|
20.2
|
0.5
|
C
|
B:SER224
|
4.8
|
21.4
|
0.5
|
CG1
|
B:ILE227
|
4.8
|
21.0
|
1.0
|
O9
|
B:BYN604
|
4.8
|
16.8
|
1.0
|
N
|
B:SER170
|
4.8
|
17.4
|
1.0
|
ND2
|
B:ASN168
|
4.9
|
18.9
|
1.0
|
N
|
B:ILE227
|
4.9
|
18.8
|
1.0
|
N
|
B:PRO226
|
4.9
|
18.1
|
1.0
|
CA
|
B:SER224
|
5.0
|
21.0
|
0.5
|
|
Potassium binding site 4 out
of 5 in 7nf4
Go back to
Potassium Binding Sites List in 7nf4
Potassium binding site 4 out
of 5 in the Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) 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 A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K603
b:17.4
occ:1.00
|
O
|
B:LEU461
|
2.6
|
19.9
|
1.0
|
O
|
B:ARG421
|
2.7
|
17.1
|
1.0
|
O
|
B:ASP459
|
2.7
|
15.7
|
1.0
|
O
|
B:HOH810
|
2.7
|
27.3
|
1.0
|
O
|
B:HOH844
|
2.8
|
21.1
|
1.0
|
OD2
|
B:ASP427
|
2.8
|
18.9
|
1.0
|
O
|
B:HOH768
|
3.4
|
26.3
|
1.0
|
CG
|
B:ASP427
|
3.4
|
20.3
|
1.0
|
C
|
B:LEU461
|
3.7
|
19.9
|
1.0
|
C
|
B:ASP459
|
3.8
|
16.6
|
1.0
|
C
|
B:ARG421
|
3.9
|
16.3
|
1.0
|
CB
|
B:ASP427
|
3.9
|
18.2
|
1.0
|
N
|
B:LEU461
|
4.0
|
19.9
|
1.0
|
OD1
|
B:ASP427
|
4.2
|
21.1
|
1.0
|
ND2
|
A:ASN447
|
4.2
|
26.5
|
1.0
|
CA
|
B:CYS422
|
4.3
|
16.1
|
1.0
|
CA
|
B:ALA460
|
4.3
|
17.0
|
1.0
|
C
|
B:ALA460
|
4.4
|
18.3
|
1.0
|
O
|
B:HOH730
|
4.4
|
20.1
|
1.0
|
CG
|
B:ASP459
|
4.4
|
23.6
|
1.0
|
CB
|
B:ASP459
|
4.5
|
18.6
|
1.0
|
N
|
B:ALA460
|
4.5
|
17.4
|
1.0
|
N
|
B:CYS422
|
4.5
|
15.8
|
1.0
|
CA
|
B:LEU461
|
4.5
|
20.3
|
1.0
|
N
|
B:MET462
|
4.6
|
18.9
|
1.0
|
OD2
|
B:ASP459
|
4.7
|
26.8
|
1.0
|
CA
|
B:MET462
|
4.7
|
19.8
|
1.0
|
OD1
|
B:ASP459
|
4.7
|
20.5
|
1.0
|
CA
|
B:ASP459
|
4.8
|
17.8
|
1.0
|
N
|
B:ARG423
|
4.9
|
15.5
|
1.0
|
CA
|
B:ARG421
|
5.0
|
15.9
|
1.0
|
|
Potassium binding site 5 out
of 5 in 7nf4
Go back to
Potassium Binding Sites List in 7nf4
Potassium binding site 5 out
of 5 in the Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Structure of A. Niger Fdc T395M R435P P438W Variant (Anfdcii) in Complex with Prfmn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:K605
b:32.2
occ:1.00
|
OG1
|
B:THR374
|
3.2
|
22.7
|
1.0
|
CA
|
B:PHE379
|
3.8
|
19.9
|
1.0
|
N
|
B:PHE379
|
3.8
|
20.1
|
1.0
|
C
|
B:GLY378
|
3.9
|
20.9
|
1.0
|
CB
|
B:THR374
|
3.9
|
20.1
|
1.0
|
O
|
B:GLY378
|
3.9
|
20.2
|
1.0
|
CD
|
B:ARG382
|
3.9
|
33.7
|
1.0
|
CG2
|
B:THR374
|
4.1
|
20.5
|
1.0
|
CE
|
B:MET372
|
4.2
|
31.8
|
1.0
|
CD1
|
B:PHE379
|
4.2
|
22.6
|
1.0
|
CB
|
B:PHE379
|
4.3
|
20.2
|
1.0
|
NH1
|
B:ARG382
|
4.3
|
44.7
|
1.0
|
CB
|
B:ARG382
|
4.4
|
26.3
|
1.0
|
CA
|
B:GLY378
|
4.6
|
19.4
|
1.0
|
CG
|
B:PHE379
|
4.8
|
19.6
|
1.0
|
CG
|
B:ARG382
|
4.8
|
29.3
|
1.0
|
O
|
B:HOH803
|
4.9
|
20.3
|
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 19:32:13 2024
|