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Manganese in PDB 6evf: Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form

Enzymatic activity of Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form

All present enzymatic activity of Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form:
4.1.1.102;

Protein crystallography data

The structure of Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form, PDB code: 6evf was solved by S.S.Bailey, L.David, K.A.P.Payne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.35 / 2.06
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 114.100, 96.820, 116.780, 90.00, 96.61, 90.00
R / Rfree (%) 16.7 / 21.3

Other elements in 6evf:

The structure of Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form also contains other interesting chemical elements:

Potassium (K) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form (pdb code 6evf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form, PDB code: 6evf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6evf

Go back to Manganese Binding Sites List in 6evf
Manganese binding site 1 out of 4 in the Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:32.6
occ:1.00
 ND2 A:ASN170 2.1 16.2 1.0
O2P A:4LU601 2.3 21.3 1.0
OE2 A:GLU236 2.3 18.9 1.0
O A:HOH769 2.4 18.4 1.0
O A:HOH723 2.4 17.7 1.0
ND1 A:HIS193 2.5 18.2 1.0
CG A:ASN170 3.2 18.4 1.0
CD A:GLU236 3.3 21.1 1.0
P A:4LU601 3.4 17.6 1.0
CE1 A:HIS193 3.4 20.4 1.0
CG A:HIS193 3.5 18.5 1.0
OD1 A:ASN170 3.5 19.7 1.0
OE1 A:GLU236 3.5 20.2 1.0
O1P A:4LU601 3.6 18.4 1.0
CB A:HIS193 3.8 19.2 1.0
K A:K603 3.8 20.9 1.0
O3P A:4LU601 4.3 21.4 1.0
CG1 A:ILE230 4.3 22.2 1.0
CZ2 A:TRP168 4.3 22.1 1.0
O A:ILE230 4.3 21.6 1.0
O5' A:4LU601 4.5 17.2 1.0
CB A:ASN170 4.5 19.1 1.0
NE2 A:HIS193 4.5 19.6 1.0
O A:VAL234 4.6 19.9 1.0
CG A:GLU236 4.6 22.2 1.0
O A:PRO231 4.6 19.9 1.0
CD2 A:HIS193 4.6 18.4 1.0
NE1 A:TRP168 4.7 22.1 1.0
O A:TRP171 4.9 19.0 1.0
CE2 A:TRP168 4.9 21.0 1.0

Manganese binding site 2 out of 4 in 6evf

Go back to Manganese Binding Sites List in 6evf
Manganese binding site 2 out of 4 in the Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn602

b:36.4
occ:1.00
 ND2 B:ASN170 2.2 18.3 1.0
O2P B:4LU601 2.3 24.6 1.0
OE2 B:GLU236 2.3 19.9 1.0
O B:HOH724 2.3 19.5 1.0
O B:HOH791 2.4 20.2 1.0
ND1 B:HIS193 2.4 17.4 1.0
CG B:ASN170 3.2 20.4 1.0
CD B:GLU236 3.3 22.7 1.0
CE1 B:HIS193 3.3 18.5 1.0
P B:4LU601 3.4 21.5 1.0
CG B:HIS193 3.5 19.1 1.0
OD1 B:ASN170 3.5 23.0 1.0
O1P B:4LU601 3.6 23.0 1.0
OE1 B:GLU236 3.6 22.9 1.0
CB B:HIS193 3.8 20.3 1.0
K B:K603 3.9 21.8 1.0
O3P B:4LU601 4.2 22.7 1.0
O B:ILE230 4.2 21.6 1.0
CZ2 B:TRP168 4.2 23.9 1.0
CG1 B:ILE230 4.3 25.3 1.0
NE2 B:HIS193 4.5 18.8 1.0
O5' B:4LU601 4.5 22.9 1.0
CB B:ASN170 4.5 22.1 1.0
NE1 B:TRP168 4.5 24.8 1.0
CD2 B:HIS193 4.6 19.3 1.0
O B:PRO231 4.6 24.1 1.0
O B:VAL234 4.6 28.4 1.0
CG B:GLU236 4.7 22.6 1.0
CE2 B:TRP168 4.8 25.1 1.0
O B:TRP171 4.8 20.7 1.0

Manganese binding site 3 out of 4 in 6evf

Go back to Manganese Binding Sites List in 6evf
Manganese binding site 3 out of 4 in the Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:32.7
occ:1.00
 O2P C:4LU601 2.2 19.5 1.0
OE2 C:GLU236 2.2 19.4 1.0
ND2 C:ASN170 2.2 15.0 1.0
O C:HOH894 2.3 55.8 1.0
O C:HOH725 2.3 17.4 1.0
ND1 C:HIS193 2.4 20.5 1.0
CE1 C:HIS193 3.2 22.7 1.0
CG C:ASN170 3.2 17.1 1.0
CD C:GLU236 3.2 21.8 1.0
P C:4LU601 3.3 18.8 1.0
CG C:HIS193 3.5 21.8 1.0
OD1 C:ASN170 3.5 20.5 1.0
O1P C:4LU601 3.5 22.7 1.0
OE1 C:GLU236 3.6 20.6 1.0
K C:K603 3.8 21.9 1.0
CB C:HIS193 3.8 21.5 1.0
O3P C:4LU601 4.2 18.9 1.0
O C:ILE230 4.2 20.9 1.0
CG1 C:ILE230 4.3 23.3 1.0
CZ2 C:TRP168 4.4 24.4 1.0
NE2 C:HIS193 4.4 24.3 1.0
O5' C:4LU601 4.5 19.5 1.0
CG C:GLU236 4.5 23.0 1.0
CD2 C:HIS193 4.5 23.1 1.0
CB C:ASN170 4.6 16.1 1.0
NE1 C:TRP168 4.7 23.7 1.0
O C:VAL234 4.7 26.4 1.0
O C:TRP171 4.8 16.7 1.0
O C:PRO231 4.8 25.8 1.0
CE2 C:TRP168 4.9 23.2 1.0
O C:MET228 5.0 20.4 1.0

Manganese binding site 4 out of 4 in 6evf

Go back to Manganese Binding Sites List in 6evf
Manganese binding site 4 out of 4 in the Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of E285D S. Cerevisiae FDC1 with Prfmn in the Hydroxylated Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn602

b:36.6
occ:1.00
 O2P D:4LU601 2.1 22.9 1.0
ND2 D:ASN170 2.3 18.2 1.0
O D:HOH782 2.3 23.6 1.0
OE2 D:GLU236 2.4 26.5 1.0
O D:HOH714 2.4 19.6 1.0
ND1 D:HIS193 2.4 20.2 1.0
CE1 D:HIS193 3.3 22.3 1.0
CD D:GLU236 3.3 29.0 1.0
CG D:ASN170 3.3 21.1 1.0
P D:4LU601 3.3 23.4 1.0
CG D:HIS193 3.4 21.1 1.0
OE1 D:GLU236 3.5 24.1 1.0
O1P D:4LU601 3.5 23.7 1.0
OD1 D:ASN170 3.6 23.2 1.0
CB D:HIS193 3.7 20.8 1.0
K D:K603 3.9 24.4 1.0
O D:ILE230 4.1 24.8 1.0
CG1 D:ILE230 4.3 25.2 1.0
O3P D:4LU601 4.3 20.9 1.0
CZ2 D:TRP168 4.3 27.8 1.0
NE2 D:HIS193 4.4 23.8 1.0
O5' D:4LU601 4.5 21.3 1.0
CD2 D:HIS193 4.5 23.4 1.0
O D:PRO231 4.6 26.4 1.0
CB D:ASN170 4.6 23.8 1.0
O D:VAL234 4.6 27.9 1.0
NE1 D:TRP168 4.6 28.2 1.0
CG D:GLU236 4.6 29.7 1.0
O D:TRP171 4.8 20.8 1.0
CE2 D:TRP168 4.9 28.1 1.0

Reference:

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
Page generated: Sun Oct 6 04:21:32 2024

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