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:

Manganese (Mn) 2 atoms

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: Sat Aug 21 14:37:03 2021

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