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Potassium in PDB 4za5: Structure of A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms.

Enzymatic activity of Structure of A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms.

All present enzymatic activity of Structure of A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms.:
4.1.1.61;

Protein crystallography data

The structure of Structure of A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms., PDB code: 4za5 was solved by K.A.P.Payne, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.01 / 1.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.020, 63.790, 87.720, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 15.6

Other elements in 4za5:

The structure of Structure of A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms. 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 FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms. (pdb code 4za5). 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 A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms., PDB code: 4za5:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in 4za5

Go back to Potassium Binding Sites List in 4za5
Potassium binding site 1 out of 3 in the Structure of A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms.


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 FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:6.4
occ:0.60
 K A:K604 0.0 6.4 0.6
K A:K604 0.7 10.9 0.4
O A:SER223 2.5 10.5 0.5
O6 A:FZZ602 2.6 7.3 0.5
O A:MET225 2.8 6.5 0.5
OE2 A:GLU233 2.8 8.2 1.0
O8 A:FZZ602 2.9 7.8 0.5
O2P A:4LU601 2.9 6.6 0.5
O A:ALA222 2.9 9.8 1.0
O5' A:4LU601 3.0 6.3 0.5
O A:TRP169 3.0 7.2 1.0
O A:SER223 3.0 8.9 0.5
O A:MET225 3.1 10.0 0.5
O A:HOH709 3.3 8.1 1.0
C A:SER223 3.3 8.5 0.5
P1 A:FZZ602 3.3 7.4 0.5
P A:4LU601 3.4 6.3 0.5
C22 A:FZZ602 3.4 8.3 0.5
C A:SER223 3.4 8.8 0.5
CD A:GLU233 3.6 8.1 1.0
CA A:SER223 3.6 8.4 0.5
MN A:MN603 3.7 6.9 0.6
CA A:SER223 3.7 8.5 0.5
O3P A:4LU601 3.7 7.9 0.5
MN A:MN603 3.7 8.8 0.4
CG A:GLU233 3.7 8.2 1.0
O7 A:FZZ602 3.9 9.4 0.5
C A:ALA222 3.9 8.3 1.0
C A:MET225 4.0 8.5 0.5
C A:MET225 4.0 8.8 0.5
N A:MET225 4.1 9.7 0.5
N A:MET225 4.1 9.6 0.5
C A:TRP169 4.2 7.4 1.0
N A:SER223 4.3 8.4 0.5
N A:SER223 4.3 8.3 0.5
C5' A:4LU601 4.3 7.4 0.5
N A:SER224 4.3 7.9 0.5
CB A:SER170 4.3 6.9 0.5
O4 A:FZZ602 4.4 7.3 0.5
N A:SER224 4.4 8.3 0.5
C4' A:4LU601 4.4 7.1 0.5
CA A:SER170 4.4 7.1 0.5
O4' A:4LU601 4.5 8.2 0.5
CA A:SER170 4.5 7.0 0.5
CA A:MET225 4.6 9.3 0.5
CA A:MET225 4.6 9.5 0.5
OE1 A:GLU233 4.7 8.2 1.0
CB A:SER170 4.7 8.8 0.5
O9 A:FZZ602 4.7 8.0 0.5
C A:SER224 4.7 9.3 0.5
C21 A:FZZ602 4.8 8.4 0.5
C A:SER224 4.8 9.3 0.5
ND2 A:ASN168 4.8 8.1 1.0
N A:SER170 4.8 7.1 0.5
N A:PRO226 4.9 8.2 0.5
O1P A:4LU601 4.9 8.8 0.5
N A:SER170 4.9 7.2 0.5
CB A:SER223 4.9 7.4 0.5
N A:ILE227 4.9 8.6 1.0
CG1 A:ILE227 4.9 10.2 1.0
CA A:SER224 4.9 8.0 0.5
CA A:SER224 5.0 8.1 0.5
CB A:SER223 5.0 7.6 0.5
C20 A:FZZ602 5.0 8.8 0.5

Potassium binding site 2 out of 3 in 4za5

Go back to Potassium Binding Sites List in 4za5
Potassium binding site 2 out of 3 in the Structure of A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms.


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 FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K604

b:10.9
occ:0.40
 K A:K604 0.0 10.9 0.4
K A:K604 0.7 6.4 0.6
O A:MET225 2.4 6.5 0.5
OE2 A:GLU233 2.6 8.2 1.0
O A:ALA222 2.6 9.8 1.0
O A:MET225 2.7 10.0 0.5
O A:SER223 2.9 10.5 0.5
O A:HOH709 3.0 8.1 1.0
O6 A:FZZ602 3.0 7.3 0.5
O8 A:FZZ602 3.2 7.8 0.5
O2P A:4LU601 3.2 6.6 0.5
CD A:GLU233 3.4 8.1 1.0
O A:TRP169 3.5 7.2 1.0
CG A:GLU233 3.5 8.2 1.0
O5' A:4LU601 3.5 6.3 0.5
O A:SER223 3.5 8.9 0.5
MN A:MN603 3.6 8.8 0.4
C A:SER223 3.6 8.5 0.5
MN A:MN603 3.6 6.9 0.6
P1 A:FZZ602 3.7 7.4 0.5
C A:MET225 3.7 8.5 0.5
C A:MET225 3.7 8.8 0.5
C22 A:FZZ602 3.8 8.3 0.5
C A:ALA222 3.8 8.3 1.0
C A:SER223 3.8 8.8 0.5
P A:4LU601 3.8 6.3 0.5
O3P A:4LU601 3.8 7.9 0.5
CA A:SER223 3.9 8.4 0.5
O7 A:FZZ602 3.9 9.4 0.5
CA A:SER223 3.9 8.5 0.5
N A:MET225 4.0 9.7 0.5
N A:MET225 4.1 9.6 0.5
CG1 A:ILE227 4.3 10.2 1.0
N A:SER223 4.3 8.4 0.5
N A:SER223 4.3 8.3 0.5
CA A:MET225 4.4 9.3 0.5
CA A:MET225 4.4 9.5 0.5
N A:ILE227 4.4 8.6 1.0
N A:SER224 4.5 7.9 0.5
OE1 A:GLU233 4.6 8.2 1.0
N A:PRO226 4.6 8.2 0.5
N A:SER224 4.6 8.3 0.5
O4' A:4LU601 4.7 8.2 0.5
C A:TRP169 4.7 7.4 1.0
N A:PRO226 4.7 7.8 0.5
CB A:MET225 4.7 10.5 0.5
CA A:PRO226 4.8 8.0 0.5
C4' A:4LU601 4.8 7.1 0.5
C A:SER224 4.8 9.3 0.5
CA A:PRO226 4.8 8.1 0.5
C5' A:4LU601 4.8 7.4 0.5
CG2 A:ILE227 4.9 10.4 1.0
C A:SER224 4.9 9.3 0.5
CB A:MET225 4.9 10.6 0.5
CD1 A:ILE227 4.9 10.5 1.0
O4 A:FZZ602 4.9 7.3 0.5
CB A:ILE227 5.0 9.3 1.0
CA A:ALA222 5.0 8.6 1.0

Potassium binding site 3 out of 3 in 4za5

Go back to Potassium Binding Sites List in 4za5
Potassium binding site 3 out of 3 in the Structure of A. Niger FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms.


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 FDC1 with the Prenylated-Flavin Cofactor in the Iminium and Ketimine Forms. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K605

b:8.8
occ:1.00
 O A:ARG421 2.6 8.9 1.0
O A:LEU461 2.7 10.4 1.0
O A:ASP459 2.7 8.6 1.0
OD2 A:ASP427 2.8 9.2 1.0
CG A:ASP427 3.4 9.3 1.0
C A:ASP459 3.7 7.9 1.0
C A:LEU461 3.8 9.2 1.0
C A:ARG421 3.8 7.7 1.0
CB A:ASP427 3.9 8.7 1.0
OD1 A:ASP427 4.1 10.6 1.0
CA A:CYS422 4.1 8.0 1.0
N A:LEU461 4.2 8.8 1.0
CA A:ALA460 4.3 8.2 1.0
C A:ALA460 4.4 8.2 1.0
N A:ALA460 4.4 7.7 1.0
N A:CYS422 4.4 8.0 1.0
CG A:ASP459 4.5 11.0 1.0
CB A:ASP459 4.5 9.7 1.0
CA A:LEU461 4.6 8.7 1.0
N A:MET462 4.6 9.7 1.0
CA A:MET462 4.7 9.3 1.0
N A:ARG423 4.8 7.2 1.0
OD1 A:ASP459 4.8 11.9 1.0
CA A:ASP459 4.8 8.1 1.0
OD2 A:ASP459 4.8 15.5 1.0
CA A:ARG421 4.9 8.0 1.0
CB A:CYS422 5.0 8.3 1.0

Reference:

K.A.Payne, M.D.White, K.Fisher, B.Khara, S.S.Bailey, D.Parker, N.J.Rattray, D.K.Trivedi, R.Goodacre, R.Beveridge, P.Barran, S.E.Rigby, N.S.Scrutton, S.Hay, D.Leys. New Cofactor Supports Alpha , Beta-Unsaturated Acid Decarboxylation Via 1,3-Dipolar Cycloaddition. Nature V. 522 502 2015.
ISSN: ESSN 1476-4687
PubMed: 26083754
DOI: 10.1038/NATURE14560
Page generated: Sun Dec 13 23:53:02 2020

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