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Potassium in PDB 7nf1: Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct

Enzymatic activity of Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct

All present enzymatic activity of Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct:
4.1.1.102;

Protein crystallography data

The structure of Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct, PDB code: 7nf1 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) 64.65 / 1.77
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.647, 74.647, 345.752, 90, 90, 120
R / Rfree (%) 17.5 / 20.6

Other elements in 7nf1:

The structure of Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct 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 Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct (pdb code 7nf1). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct, PDB code: 7nf1:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 7nf1

Go back to Potassium Binding Sites List in 7nf1
Potassium binding site 1 out of 7 in the Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct


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 Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:18.7
occ:1.00
 O A:ARG431 2.6 16.8 1.0
O A:LEU471 2.7 18.2 1.0
O A:ASP469 2.7 18.7 1.0
OD2 A:ASP437 2.7 20.6 1.0
O A:HOH945 2.8 18.3 1.0
O A:HOH752 3.3 21.9 1.0
OD2 A:ASP469 3.3 22.0 1.0
CG A:ASP437 3.4 20.9 1.0
C A:LEU471 3.6 18.7 1.0
CG A:ASP469 3.7 22.0 1.0
C A:ASP469 3.8 17.9 1.0
C A:ARG431 3.8 14.4 1.0
CB A:ASP437 3.9 19.1 1.0
OD1 B:ASN457 4.0 23.4 1.0
OD1 A:ASP437 4.0 20.3 1.0
OD1 A:ASP469 4.0 20.4 1.0
N A:LEU471 4.1 17.8 1.0
CA A:CYS432 4.3 15.6 1.0
O B:HOH831 4.4 19.9 1.0
CB A:ASP469 4.4 17.9 1.0
N A:LEU472 4.4 16.9 1.0
CA A:LEU472 4.5 17.6 1.0
CA A:ALA470 4.5 15.8 1.0
CA A:LEU471 4.5 20.0 1.0
N A:CYS432 4.5 15.2 1.0
N A:ALA470 4.5 15.7 1.0
C A:ALA470 4.6 17.2 1.0
CA A:ASP469 4.7 18.2 1.0
N A:ARG433 4.7 14.9 1.0
CA A:ARG431 4.9 14.3 1.0
C A:LEU472 5.0 16.7 1.0

Potassium binding site 2 out of 7 in 7nf1

Go back to Potassium Binding Sites List in 7nf1
Potassium binding site 2 out of 7 in the Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct


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 Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:15.8
occ:1.00
 O A:MET235 2.8 18.5 1.0
OE2 A:GLU243 2.8 15.9 1.0
O9 A:JRK601 2.9 15.8 1.0
O A:ALA232 2.9 15.4 1.0
O6 A:JRK601 3.0 17.4 1.0
O A:SER233 3.0 16.2 1.0
O A:TRP179 3.1 13.7 1.0
P1 A:JRK601 3.5 16.1 1.0
O A:HOH763 3.5 12.7 1.0
C A:SER233 3.5 18.0 1.0
CD A:GLU243 3.6 17.4 1.0
MN A:MN605 3.7 21.1 1.0
CA A:SER233 3.7 15.5 1.0
O7 A:JRK601 3.7 16.7 1.0
CG A:GLU243 3.8 17.2 1.0
C A:MET235 3.9 16.6 1.0
C A:ALA232 3.9 16.0 1.0
N A:MET235 4.0 15.7 1.0
O5 A:JRK601 4.1 20.3 1.0
C17 A:JRK601 4.2 17.5 1.0
C16 A:JRK601 4.2 17.2 1.0
C A:TRP179 4.3 14.1 1.0
N A:SER233 4.3 16.0 1.0
N A:SER234 4.4 15.1 1.0
CB A:SER180 4.4 16.9 1.0
CA A:SER180 4.4 14.1 1.0
CA A:MET235 4.6 17.2 1.0
OE1 A:GLU243 4.6 16.7 1.0
C A:SER234 4.7 16.2 1.0
N A:SER180 4.8 14.0 1.0
N A:PRO236 4.8 16.8 1.0
OD1 A:ASN178 4.8 17.4 1.0
O8 A:JRK601 4.9 18.2 1.0
CG1 A:ILE237 4.9 18.5 1.0
N A:ILE237 5.0 15.6 1.0
CA A:SER234 5.0 15.4 1.0

Potassium binding site 3 out of 7 in 7nf1

Go back to Potassium Binding Sites List in 7nf1
Potassium binding site 3 out of 7 in the Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct


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 Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:40.8
occ:1.00
 O A:HOH968 2.5 33.2 1.0
NH1 A:ARG75 3.4 23.1 1.0
NH2 A:ARG28 3.6 25.5 1.0
NH2 A:ARG75 3.7 20.3 1.0
NH1 A:ARG28 3.9 25.5 1.0
CZ A:ARG75 4.0 21.8 1.0
CZ A:ARG28 4.2 27.4 1.0
CD A:ARG21 4.2 24.1 1.0
CG1 A:VAL24 4.2 18.6 1.0
CD2 A:LEU62 4.5 20.8 1.0
CD1 A:ILE320 4.5 18.6 1.0

Potassium binding site 4 out of 7 in 7nf1

Go back to Potassium Binding Sites List in 7nf1
Potassium binding site 4 out of 7 in the Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct


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 Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:39.9
occ:1.00
 NH1 B:ARG75 3.6 28.8 1.0
NH2 B:ARG75 3.7 27.3 1.0
NH2 B:ARG28 3.7 32.9 1.0
CZ B:ARG75 4.1 24.8 1.0
NH1 B:ARG28 4.2 33.0 1.0
CD B:ARG21 4.2 26.2 1.0
CG1 B:VAL24 4.3 24.7 1.0
CZ B:ARG28 4.4 32.6 1.0
O B:HOH925 4.6 33.5 1.0
CD2 B:LEU62 4.6 24.9 1.0
CD1 B:ILE320 4.7 22.6 1.0

Potassium binding site 5 out of 7 in 7nf1

Go back to Potassium Binding Sites List in 7nf1
Potassium binding site 5 out of 7 in the Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K603

b:54.8
occ:1.00
 N B:ASP173 3.6 28.8 1.0
CB B:ASP173 3.9 32.3 1.0
CG B:ASP173 3.9 35.9 1.0
CD B:PRO172 4.0 22.4 1.0
OE1 B:GLN208 4.0 33.9 1.0
OD2 B:ASP173 4.1 38.0 1.0
CB B:PRO172 4.1 24.1 1.0
CG B:PRO172 4.1 23.9 1.0
N B:PRO172 4.2 22.8 1.0
OD1 B:ASP173 4.3 35.0 1.0
CA B:ASP173 4.4 29.7 1.0
C B:PRO172 4.4 28.2 1.0
CA B:PRO172 4.4 25.0 1.0
CB B:SER171 4.4 20.0 1.0
CD B:GLN208 4.5 29.8 1.0
OG B:SER171 4.9 24.4 1.0
C B:SER171 4.9 20.4 1.0

Potassium binding site 6 out of 7 in 7nf1

Go back to Potassium Binding Sites List in 7nf1
Potassium binding site 6 out of 7 in the Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K604

b:19.1
occ:1.00
 O B:LEU471 2.6 18.8 1.0
O B:ARG431 2.6 16.6 1.0
O B:ASP469 2.7 19.7 1.0
OD2 B:ASP437 2.8 18.2 1.0
O B:HOH908 2.8 19.8 1.0
O B:HOH755 3.2 20.1 1.0
OD2 B:ASP469 3.3 23.3 1.0
CG B:ASP437 3.4 19.0 1.0
C B:LEU471 3.6 17.6 1.0
CG B:ASP469 3.7 20.1 1.0
C B:ASP469 3.8 17.2 1.0
C B:ARG431 3.8 14.9 1.0
CB B:ASP437 3.9 18.4 1.0
OD1 B:ASP469 4.0 19.2 1.0
N B:LEU471 4.1 17.7 1.0
OD1 A:ASN457 4.1 24.6 1.0
OD1 B:ASP437 4.1 21.3 1.0
CA B:CYS432 4.3 15.2 1.0
O A:HOH829 4.3 17.0 1.0
N B:LEU472 4.4 16.7 1.0
CB B:ASP469 4.4 18.0 1.0
CA B:ALA470 4.4 17.9 1.0
CA B:LEU472 4.5 17.6 1.0
N B:ALA470 4.5 18.0 1.0
N B:CYS432 4.5 14.4 1.0
CA B:LEU471 4.5 19.1 1.0
C B:ALA470 4.5 16.4 1.0
CA B:ASP469 4.7 17.9 1.0
N B:ARG433 4.7 14.5 1.0
CA B:ARG431 4.9 14.3 1.0
C B:LEU472 4.9 19.1 1.0
O B:HOH749 5.0 30.7 1.0

Potassium binding site 7 out of 7 in 7nf1

Go back to Potassium Binding Sites List in 7nf1
Potassium binding site 7 out of 7 in the Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Structure of T. Atroviride Variant Tafdcv in Complex with Prfmn- Butynoic Acid Adduct within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K605

b:20.8
occ:1.00
 OE2 B:GLU243 2.8 21.4 1.0
O B:MET235 2.8 20.4 1.0
O8 B:JRK601 2.9 20.4 1.0
O B:SER233 3.0 20.1 1.0
O6 B:JRK601 3.0 19.0 1.0
O B:ALA232 3.0 21.8 1.0
O B:TRP179 3.0 18.2 1.0
O B:HOH733 3.4 17.2 1.0
C B:SER233 3.4 20.0 1.0
P1 B:JRK601 3.5 19.6 1.0
CD B:GLU243 3.6 21.5 1.0
O9 B:JRK601 3.7 21.3 1.0
CA B:SER233 3.7 18.6 1.0
MN B:MN606 3.7 24.2 1.0
CG B:GLU243 3.8 21.5 1.0
C B:MET235 3.8 22.6 1.0
C B:ALA232 4.0 21.8 1.0
N B:MET235 4.1 22.0 1.0
O5 B:JRK601 4.1 19.2 1.0
C17 B:JRK601 4.2 18.2 1.0
C16 B:JRK601 4.2 17.4 1.0
C B:TRP179 4.2 19.4 1.0
N B:SER234 4.3 20.1 1.0
N B:SER233 4.3 20.3 1.0
CB B:SER180 4.4 18.1 1.0
CA B:SER180 4.4 19.0 1.0
CA B:MET235 4.5 22.2 1.0
OE1 B:GLU243 4.6 22.1 1.0
C B:SER234 4.8 21.4 1.0
N B:SER180 4.8 18.2 1.0
N B:PRO236 4.8 21.5 1.0
OD1 B:ASN178 4.9 22.2 1.0
N B:ILE237 4.9 22.6 1.0
O7 B:JRK601 4.9 17.6 1.0
CA B:SER234 5.0 21.1 1.0
CA B:PRO236 5.0 22.2 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 19:31:38 2024

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