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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:

Manganese (Mn) 2 atoms

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

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