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Potassium in PDB 6r3o: Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid

Enzymatic activity of Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid

All present enzymatic activity of Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid:
4.1.1.102;

Protein crystallography data

The structure of Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid, PDB code: 6r3o was solved by S.S.Bailey, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.92 / 1.13
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 95.830, 64.100, 87.610, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 17

Other elements in 6r3o:

The structure of Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid (pdb code 6r3o). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid, PDB code: 6r3o:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6r3o

Go back to Potassium Binding Sites List in 6r3o
Potassium binding site 1 out of 2 in the Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K603

b:9.0
occ:1.00
 OE2 A:GLU233 2.8 8.6 1.0
O A:MET225 2.8 8.9 1.0
O A:ALA222 2.8 8.6 1.0
O2P A:4LU601 2.8 7.9 1.0
O5' A:4LU601 3.0 8.4 1.0
O A:TRP169 3.1 8.4 1.0
O A:SER223 3.1 9.6 1.0
O A:HOH769 3.3 8.9 1.0
P A:4LU601 3.4 8.3 1.0
C A:SER223 3.5 8.9 1.0
O3P A:4LU601 3.6 8.8 1.0
CD A:GLU233 3.6 8.3 1.0
MN A:MN602 3.7 8.5 1.0
CA A:SER223 3.7 8.6 1.0
CG A:GLU233 3.8 9.2 1.0
C A:ALA222 3.9 8.5 1.0
C A:MET225 3.9 8.7 1.0
N A:MET225 4.1 8.3 1.0
C5' A:4LU601 4.2 8.6 1.0
C A:TRP169 4.2 8.0 1.0
N A:SER223 4.3 8.2 1.0
C4' A:4LU601 4.3 8.3 1.0
O4' A:4LU601 4.3 9.4 1.0
CB A:SER170 4.3 8.5 1.0
N A:SER224 4.4 8.0 0.5
N A:SER224 4.4 8.4 0.5
CA A:SER170 4.4 8.4 1.0
CA A:MET225 4.6 8.7 1.0
OE1 A:GLU233 4.7 9.0 1.0
C A:SER224 4.8 9.0 0.5
C A:SER224 4.8 9.2 0.5
ND2 A:ASN168 4.8 9.0 1.0
O1P A:4LU601 4.9 9.0 1.0
N A:SER170 4.9 7.8 1.0
N A:ILE227 4.9 8.6 1.0
CG1 A:ILE227 4.9 10.8 1.0
CA A:SER224 4.9 8.2 0.5
N A:PRO226 4.9 8.4 1.0
CB A:SER223 5.0 8.7 1.0

Potassium binding site 2 out of 2 in 6r3o

Go back to Potassium Binding Sites List in 6r3o
Potassium binding site 2 out of 2 in the Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Aspergillus Niger Ferric Acid Decarboxylase (Fdc) L439G Variant in Complex with Prfmn (Purified in the Radical Form) and Phenylpropiolic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:9.9
occ:1.00
 O A:ARG421 2.6 9.7 1.0
O A:LEU461 2.6 11.4 1.0
O A:ASP459 2.7 9.6 1.0
O A:HOH949 2.8 16.3 1.0
O A:HOH1236 2.8 12.5 1.0
OD2 A:ASP427 2.8 10.2 1.0
CG A:ASP427 3.4 11.0 1.0
O A:HOH1065 3.5 17.9 1.0
C A:ASP459 3.7 8.8 1.0
C A:LEU461 3.8 10.2 1.0
C A:ARG421 3.8 8.5 1.0
CB A:ASP427 3.9 9.7 1.0
CA A:CYS422 4.1 8.6 1.0
OD1 A:ASP427 4.1 11.6 1.0
N A:LEU461 4.2 9.5 1.0
O A:HOH804 4.3 11.0 1.0
CA A:ALA460 4.3 8.9 1.0
C A:ALA460 4.4 9.0 1.0
N A:ALA460 4.4 8.5 1.0
N A:CYS422 4.4 8.5 1.0
CG A:ASP459 4.5 11.8 1.0
CB A:ASP459 4.5 10.0 1.0
CA A:LEU461 4.6 9.2 1.0
N A:MET462 4.6 10.0 1.0
CA A:MET462 4.7 10.4 1.0
N A:ARG423 4.7 8.6 1.0
OD1 A:ASP459 4.7 12.2 1.0
CA A:ASP459 4.8 9.3 1.0
OD2 A:ASP459 4.8 15.6 1.0
CA A:ARG421 4.9 8.6 1.0
CB A:CYS422 5.0 8.9 1.0

Reference:

S.S.Bailey, K.A.P.Payne, A.Saaret, S.A.Marshall, I.Gostimskaya, I.Kosov, K.Fisher, S.Hay, D.Leys. Atomic Description of An Enzyme Reaction Dependent on Reversible 1,3-Dipolar Cycloaddition To Be Published.
Page generated: Mon Dec 14 01:17:46 2020

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