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Potassium in PDB 4zac: Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form.

Protein crystallography data

The structure of Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form., PDB code: 4zac was solved by M.D.White, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.19 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 114.410, 96.180, 116.640, 90.00, 96.58, 90.00
R / Rfree (%) 16.3 / 19.2

Other elements in 4zac:

The structure of Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Sodium (Na) 3 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. (pdb code 4zac). 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 S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form., PDB code: 4zac:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 4zac

Go back to Potassium Binding Sites List in 4zac
Potassium binding site 1 out of 4 in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor 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 S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K602

b:16.0
occ:1.00
 OE2 A:GLU236 2.8 13.1 1.0
O A:MET228 2.8 15.4 1.0
O A:SER226 2.9 14.5 1.0
O5' A:4LU604 3.0 13.9 1.0
O1P A:4LU604 3.0 14.5 1.0
O A:TRP171 3.0 14.0 1.0
O A:VAL225 3.0 15.0 1.0
C A:SER226 3.5 14.6 1.0
P A:4LU604 3.5 15.2 1.0
CD A:GLU236 3.6 16.1 1.0
O A:HOH774 3.6 15.6 1.0
CG A:GLU236 3.6 17.0 1.0
O3P A:4LU604 3.8 15.8 1.0
CA A:SER226 3.8 14.4 1.0
MN A:MN603 3.9 16.6 0.8
C A:MET228 3.9 14.7 1.0
N A:MET228 3.9 13.3 1.0
C4' A:4LU604 4.1 13.1 1.0
C A:VAL225 4.1 13.3 1.0
O4' A:4LU604 4.1 16.9 1.0
C5' A:4LU604 4.2 13.6 1.0
C A:TRP171 4.2 14.5 1.0
CB A:SER172 4.2 15.8 1.0
CA A:SER172 4.4 14.8 1.0
N A:SER227 4.4 15.8 0.5
N A:SER227 4.4 14.2 0.5
N A:SER226 4.4 14.3 1.0
CA A:MET228 4.5 13.0 1.0
OE1 A:GLU236 4.6 17.4 1.0
C A:SER227 4.7 13.8 0.5
C A:SER227 4.7 15.4 0.5
OD1 A:ASN170 4.8 19.1 1.0
N A:SER172 4.8 14.5 1.0
CA A:SER227 4.9 13.6 0.5
N A:PRO229 4.9 15.8 1.0
O2P A:4LU604 4.9 16.7 1.0
CA A:SER227 4.9 16.2 0.5
CB A:MET228 5.0 16.6 1.0

Potassium binding site 2 out of 4 in 4zac

Go back to Potassium Binding Sites List in 4zac
Potassium binding site 2 out of 4 in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor 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 S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K602

b:16.3
occ:1.00
 OE2 B:GLU236 2.8 16.6 1.0
O B:MET228 2.8 18.0 1.0
O1P B:4LU604 2.9 15.7 1.0
O B:SER226 2.9 16.5 1.0
O5' B:4LU604 3.0 13.6 1.0
O B:TRP171 3.0 13.5 1.0
O B:VAL225 3.0 16.3 1.0
P B:4LU604 3.4 15.5 1.0
C B:SER226 3.5 16.5 1.0
CD B:GLU236 3.6 17.1 1.0
O B:HOH747 3.6 16.1 1.0
CG B:GLU236 3.7 19.0 1.0
O3P B:4LU604 3.7 16.1 1.0
CA B:SER226 3.8 14.5 1.0
MN B:MN603 3.9 17.8 0.8
N B:MET228 3.9 14.4 1.0
C B:MET228 3.9 13.9 1.0
C4' B:4LU604 4.1 15.7 1.0
C B:VAL225 4.1 15.2 1.0
C5' B:4LU604 4.1 17.3 1.0
O4' B:4LU604 4.1 18.0 1.0
C B:TRP171 4.1 12.3 1.0
CB B:SER172 4.2 15.7 1.0
CA B:SER172 4.3 14.0 1.0
N B:SER227 4.4 17.0 0.5
N B:SER227 4.4 15.0 0.5
N B:SER226 4.4 15.7 1.0
CA B:MET228 4.5 15.9 1.0
C B:SER227 4.6 16.3 0.5
OE1 B:GLU236 4.6 16.0 1.0
C B:SER227 4.6 14.1 0.5
N B:SER172 4.7 13.8 1.0
OD1 B:ASN170 4.8 19.4 1.0
CA B:SER227 4.9 11.7 0.5
O2P B:4LU604 4.9 16.2 1.0
CA B:SER227 4.9 16.1 0.5
N B:PRO229 4.9 15.6 1.0

Potassium binding site 3 out of 4 in 4zac

Go back to Potassium Binding Sites List in 4zac
Potassium binding site 3 out of 4 in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor 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 S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K602

b:22.0
occ:1.00
 O C:MET228 2.7 20.8 1.0
OE2 C:GLU236 2.8 21.1 1.0
O3P C:4LU603 2.9 20.8 1.0
O C:SER226 3.0 19.6 1.0
O5' C:4LU603 3.0 18.8 1.0
O C:VAL225 3.0 19.8 1.0
O C:TRP171 3.0 19.3 1.0
P C:4LU603 3.4 19.7 1.0
C C:SER226 3.5 22.8 1.0
CD C:GLU236 3.5 28.7 1.0
O C:HOH715 3.5 18.6 1.0
CG C:GLU236 3.7 25.5 1.0
O2P C:4LU603 3.8 19.3 1.0
CA C:SER226 3.8 19.8 1.0
C C:MET228 3.8 20.2 1.0
MN C:MN601 3.8 21.6 0.8
N C:MET228 3.9 19.2 1.0
O4' C:4LU603 4.1 19.9 1.0
C C:VAL225 4.1 18.0 1.0
C5' C:4LU603 4.2 21.1 1.0
CB C:SER172 4.2 18.9 1.0
C C:TRP171 4.2 17.6 1.0
C4' C:4LU603 4.2 20.8 1.0
CA C:SER172 4.4 18.8 1.0
CA C:MET228 4.4 19.9 1.0
N C:SER227 4.4 21.1 0.5
N C:SER227 4.4 22.3 0.5
N C:SER226 4.4 20.5 1.0
C C:SER227 4.6 20.3 0.5
C C:SER227 4.6 21.7 0.5
OE1 C:GLU236 4.7 23.2 1.0
N C:SER172 4.8 18.9 1.0
OD1 C:ASN170 4.8 23.2 1.0
N C:PRO229 4.8 20.4 1.0
O1P C:4LU603 4.9 19.9 1.0
CA C:SER227 4.9 21.0 0.5
CA C:SER227 4.9 23.2 0.5
CG1 C:ILE230 5.0 22.2 1.0

Potassium binding site 4 out of 4 in 4zac

Go back to Potassium Binding Sites List in 4zac
Potassium binding site 4 out of 4 in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form.


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K602

b:18.3
occ:1.00
 OE2 D:GLU236 2.8 19.3 1.0
O D:MET228 2.8 18.7 1.0
O5' D:4LU603 2.9 16.3 1.0
O1P D:4LU603 2.9 15.7 1.0
O D:SER226 2.9 17.7 1.0
O D:TRP171 3.0 18.5 1.0
O D:VAL225 3.1 18.4 1.0
P D:4LU603 3.4 16.7 1.0
C D:SER226 3.5 17.2 1.0
CD D:GLU236 3.5 17.6 1.0
O D:HOH753 3.6 17.1 1.0
O3P D:4LU603 3.7 16.5 1.0
CG D:GLU236 3.7 18.2 1.0
CA D:SER226 3.7 16.5 1.0
MN D:MN601 3.9 20.4 0.8
C D:MET228 3.9 17.8 1.0
N D:MET228 3.9 15.5 1.0
CB D:SER172 4.1 13.7 1.0
C4' D:4LU603 4.1 16.0 1.0
C D:VAL225 4.1 16.5 1.0
O4' D:4LU603 4.1 18.6 1.0
C5' D:4LU603 4.1 17.5 1.0
C D:TRP171 4.2 16.7 1.0
CA D:SER172 4.2 15.6 1.0
N D:SER227 4.4 18.2 0.5
N D:SER227 4.4 16.5 0.5
N D:SER226 4.4 16.2 1.0
CA D:MET228 4.5 16.7 1.0
OE1 D:GLU236 4.6 18.5 1.0
C D:SER227 4.6 18.6 0.5
C D:SER227 4.7 16.8 0.5
OD1 D:ASN170 4.7 23.4 1.0
N D:SER172 4.8 16.2 1.0
N D:PRO229 4.9 16.9 1.0
O2P D:4LU603 4.9 18.0 1.0
CA D:SER227 4.9 14.2 0.5
CA D:SER227 5.0 17.6 0.5

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: Mon Aug 12 12:46:53 2024

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