Potassium in PDB 6eve: Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form

All present enzymatic activity of Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form:
4.1.1.102;

The structure of Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form, PDB code: 6eve was solved by S.S.Bailey, L.David, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.89 / 2.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	117.480, 98.640, 118.170, 90.00, 97.24, 90.00
R / Rfree (%)	18.3 / 22.6

The structure of Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form also contains other interesting chemical elements:

Manganese

(Mn)

5 atoms

The binding sites of Potassium atom in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form (pdb code 6eve). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form, PDB code: 6eve:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form within 5.0Å range: probe atom residue distance (Å) B Occ A:K603 b:18.6 occ:1.00 OE2 A:GLU236 2.7 20.6 1.0 O A:MET228 2.9 19.0 1.0 O A:SER226 3.0 17.4 1.0 O5' A:4LU601 3.1 17.1 1.0 O A:TRP171 3.1 16.2 1.0 O2P A:4LU601 3.1 18.6 1.0 O A:VAL225 3.2 15.2 1.0 P A:4LU601 3.5 18.6 1.0 CD A:GLU236 3.6 22.0 1.0 C A:SER226 3.6 16.8 1.0 O A:HOH780 3.6 18.1 1.0 O1P A:4LU601 3.8 17.8 1.0 MN A:MN602 3.8 24.1 1.0 CG A:GLU236 3.8 22.8 1.0 CA A:SER226 3.9 16.0 1.0 C A:MET228 4.0 17.6 1.0 N A:MET228 4.1 15.5 1.0 C5' A:4LU601 4.2 16.6 1.0 C A:VAL225 4.2 17.2 1.0 O4' A:4LU601 4.3 17.4 1.0 C4' A:4LU601 4.3 16.6 1.0 C A:TRP171 4.3 17.6 1.0 CB A:SER172 4.3 17.9 1.0 CA A:SER172 4.4 17.1 1.0 N A:SER227 4.5 16.3 0.5 N A:SER227 4.5 15.5 0.5 N A:SER226 4.5 15.5 1.0 CA A:MET228 4.6 16.8 1.0 OE1 A:GLU236 4.6 19.5 1.0 C A:SER227 4.8 17.2 0.5 OD1 A:ASN170 4.8 19.0 1.0 C A:SER227 4.8 16.4 0.5 N A:SER172 4.8 16.3 1.0 O3P A:4LU601 4.9 18.5 1.0

Potassium binding site 2 out of 3 in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form within 5.0Å range: probe atom residue distance (Å) B Occ B:K603 b:21.1 occ:1.00 OE2 B:GLU236 2.8 21.8 1.0 O B:MET228 2.9 22.5 1.0 O B:SER226 2.9 22.1 1.0 O5' B:4LU601 2.9 19.6 1.0 O2P B:4LU601 3.1 18.2 1.0 O B:TRP171 3.1 19.2 1.0 O B:VAL225 3.1 17.6 1.0 C B:SER226 3.5 20.4 1.0 P B:4LU601 3.5 18.7 1.0 O B:HOH717 3.6 18.6 1.0 CD B:GLU236 3.6 23.1 1.0 O1P B:4LU601 3.7 18.2 1.0 CA B:SER226 3.9 18.5 1.0 MN B:MN602 3.9 27.5 1.0 CG B:GLU236 3.9 24.3 1.0 C B:MET228 4.0 20.7 1.0 N B:MET228 4.1 20.0 1.0 C5' B:4LU601 4.1 18.3 1.0 C B:VAL225 4.2 18.3 1.0 C4' B:4LU601 4.2 18.0 1.0 O4' B:4LU601 4.2 17.9 1.0 C B:TRP171 4.2 19.7 1.0 CB B:SER172 4.3 22.1 1.0 N B:SER227 4.4 20.8 0.5 N B:SER227 4.4 20.5 0.5 CA B:SER172 4.4 21.3 1.0 N B:SER226 4.5 17.6 1.0 CA B:MET228 4.6 20.9 1.0 OE1 B:GLU236 4.7 19.4 1.0 C B:SER227 4.7 21.2 0.5 C B:SER227 4.7 21.4 0.5 CA B:SER227 4.8 21.4 0.5 N B:SER172 4.8 19.6 1.0 CA B:SER227 4.9 21.0 0.5 OD1 B:ASN170 4.9 21.5 1.0 O3P B:4LU601 5.0 18.4 1.0

Potassium binding site 3 out of 3 in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form within 5.0Å range: probe atom residue distance (Å) B Occ C:K603 b:19.4 occ:1.00 OE2 C:GLU236 2.8 19.0 1.0 O C:MET228 2.9 19.9 1.0 O C:TRP171 3.0 14.9 1.0 O C:SER226 3.0 19.6 1.0 O5' C:4LU601 3.0 18.7 1.0 O2P C:4LU601 3.0 15.8 1.0 O C:VAL225 3.2 18.0 1.0 P C:4LU601 3.5 17.9 1.0 C C:SER226 3.5 19.3 1.0 O C:HOH722 3.6 17.4 1.0 CD C:GLU236 3.7 20.1 1.0 O1P C:4LU601 3.8 16.3 1.0 CA C:SER226 3.8 18.6 1.0 CG C:GLU236 3.9 21.5 1.0 MN C:MN602 3.9 24.4 1.0 C C:MET228 3.9 22.4 1.0 N C:MET228 4.0 18.3 1.0 C C:TRP171 4.1 18.0 1.0 O4' C:4LU601 4.1 20.4 1.0 C4' C:4LU601 4.2 18.4 1.0 C5' C:4LU601 4.2 18.1 1.0 C C:VAL225 4.2 18.5 1.0 CA C:SER172 4.3 18.4 1.0 CB C:SER172 4.3 18.9 1.0 N C:SER227 4.5 19.1 0.5 N C:SER227 4.5 19.2 0.5 N C:SER226 4.5 18.8 1.0 CA C:MET228 4.6 20.8 1.0 C C:SER227 4.7 19.2 0.5 N C:SER172 4.7 17.4 1.0 C C:SER227 4.7 19.4 0.5 OE1 C:GLU236 4.7 20.3 1.0 O3P C:4LU601 4.9 16.3 1.0 OD1 C:ASN170 4.9 17.7 1.0 N C:PRO229 4.9 21.8 1.0 CA C:SER227 5.0 19.6 0.5 CA C:SER227 5.0 19.8 0.5

S.S.Bailey, K.A.P.Payne, K.Fisher, S.A.Marshall, M.J.Cliff, R.Spiess, D.A.Parker, S.E.J.Rigby, D.Leys. The Role of Conserved Residues in Fdc Decarboxylase in Prenylated Flavin Mononucleotide Oxidative Maturation, Cofactor Isomerization, and Catalysis. J. Biol. Chem. V. 293 2272 2018.
ISSN: ESSN 1083-351X
PubMed: 29259125
DOI: 10.1074/JBC.RA117.000881