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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6eve:

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

Potassium (K) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 5 binding sites of Manganese where determined in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form, PDB code: 6eve:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 6eve

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Manganese binding site 1 out of 5 in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium 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 R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn602

b:24.1
occ:1.00
 O2P A:4LU601 2.1 18.6 1.0
ND2 A:ASN170 2.2 13.8 1.0
O A:HOH780 2.3 18.1 1.0
O A:HOH859 2.4 14.0 1.0
OE2 A:GLU236 2.4 20.6 1.0
ND1 A:HIS193 2.5 19.3 1.0
CG A:ASN170 3.2 17.2 1.0
P A:4LU601 3.4 18.6 1.0
CD A:GLU236 3.4 22.0 1.0
CE1 A:HIS193 3.4 19.9 1.0
OD1 A:ASN170 3.5 19.0 1.0
CG A:HIS193 3.5 20.1 1.0
OE1 A:GLU236 3.6 19.5 1.0
O1P A:4LU601 3.6 17.8 1.0
CB A:HIS193 3.8 20.0 1.0
K A:K603 3.8 18.6 1.0
O3P A:4LU601 4.3 18.5 1.0
O A:ILE230 4.4 18.3 1.0
CG1 A:ILE230 4.4 18.8 1.0
CZ2 A:TRP168 4.5 21.4 1.0
O5' A:4LU601 4.5 17.1 1.0
CB A:ASN170 4.6 17.1 1.0
NE2 A:HIS193 4.6 20.4 1.0
CD2 A:HIS193 4.7 22.0 1.0
O A:VAL234 4.7 23.2 1.0
CG A:GLU236 4.8 22.8 1.0
O A:TRP171 4.8 16.2 1.0
NE1 A:TRP168 4.8 22.6 1.0
O A:PRO231 4.8 21.9 1.0

Manganese binding site 2 out of 5 in 6eve

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Manganese binding site 2 out of 5 in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium 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 R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn602

b:27.5
occ:1.00
 ND2 B:ASN170 2.2 17.1 1.0
O2P B:4LU601 2.3 18.2 1.0
OE2 B:GLU236 2.4 21.8 1.0
ND1 B:HIS193 2.4 16.9 1.0
O B:HOH846 2.4 15.1 1.0
O B:HOH717 2.4 18.6 1.0
CE1 B:HIS193 3.2 18.5 1.0
CG B:ASN170 3.3 19.9 1.0
CD B:GLU236 3.3 23.1 1.0
CG B:HIS193 3.4 18.0 1.0
P B:4LU601 3.4 18.7 1.0
OE1 B:GLU236 3.6 19.4 1.0
O1P B:4LU601 3.6 18.2 1.0
OD1 B:ASN170 3.7 21.5 1.0
CB B:HIS193 3.8 17.8 1.0
K B:K603 3.9 21.1 1.0
CZ2 B:TRP168 4.3 23.8 1.0
O B:ILE230 4.3 21.1 1.0
CG1 B:ILE230 4.3 23.7 1.0
O3P B:4LU601 4.4 18.4 1.0
NE2 B:HIS193 4.4 17.9 1.0
O5' B:4LU601 4.5 19.6 1.0
CD2 B:HIS193 4.5 19.4 1.0
CB B:ASN170 4.6 20.7 1.0
O B:VAL234 4.6 25.6 1.0
NE1 B:TRP168 4.7 26.1 1.0
CG B:GLU236 4.7 24.3 1.0
O B:PRO231 4.9 24.5 1.0
CE2 B:TRP168 4.9 25.8 1.0
O B:TRP171 4.9 19.2 1.0

Manganese binding site 3 out of 5 in 6eve

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Manganese binding site 3 out of 5 in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium 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 R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn602

b:24.4
occ:1.00
 O C:HOH906 2.2 16.1 1.0
O2P C:4LU601 2.3 15.8 1.0
ND2 C:ASN170 2.3 14.5 1.0
O C:HOH722 2.4 17.4 1.0
OE2 C:GLU236 2.4 19.0 1.0
ND1 C:HIS193 2.5 20.2 1.0
CG C:ASN170 3.3 16.4 1.0
CD C:GLU236 3.3 20.1 1.0
CE1 C:HIS193 3.3 20.0 1.0
P C:4LU601 3.5 17.9 1.0
OD1 C:ASN170 3.5 17.7 1.0
CG C:HIS193 3.6 20.9 1.0
OE1 C:GLU236 3.6 20.3 1.0
O1P C:4LU601 3.7 16.3 1.0
K C:K603 3.9 19.4 1.0
CB C:HIS193 3.9 20.2 1.0
O3P C:4LU601 4.3 16.3 1.0
CG1 C:ILE230 4.4 20.6 1.0
O C:ILE230 4.4 17.3 1.0
CZ2 C:TRP168 4.4 21.2 1.0
NE2 C:HIS193 4.5 20.8 1.0
O5' C:4LU601 4.6 18.7 1.0
CB C:ASN170 4.6 16.3 1.0
CD2 C:HIS193 4.7 20.2 1.0
O C:VAL234 4.7 25.3 1.0
CG C:GLU236 4.7 21.5 1.0
NE1 C:TRP168 4.7 21.9 1.0
O C:PRO231 4.8 21.1 1.0
O C:TRP171 4.8 14.9 1.0
CE2 C:TRP168 5.0 21.8 1.0

Manganese binding site 4 out of 5 in 6eve

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Manganese binding site 4 out of 5 in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium 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 R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn602

b:24.6
occ:1.00
 O D:HOH894 2.0 21.5 1.0
ND2 D:ASN170 2.2 14.0 1.0
OE2 D:GLU236 2.3 23.1 1.0
O D:HOH737 2.3 18.5 1.0
O2P D:4LU601 2.4 16.8 1.0
ND1 D:HIS193 2.4 21.1 1.0
CG D:ASN170 3.2 18.4 1.0
CE1 D:HIS193 3.3 22.4 1.0
CD D:GLU236 3.3 25.6 1.0
O1P D:4LU601 3.4 19.3 1.0
CG D:HIS193 3.4 21.3 1.0
P D:4LU601 3.4 18.9 1.0
OD1 D:ASN170 3.5 22.9 1.0
OE1 D:GLU236 3.7 26.9 1.0
CB D:HIS193 3.8 20.6 1.0
MN D:MN603 3.9 32.5 1.0
O3P D:4LU601 4.3 18.1 1.0
CZ2 D:TRP168 4.4 27.9 1.0
NE2 D:HIS193 4.4 23.4 1.0
O D:ILE230 4.4 26.1 1.0
CG1 D:ILE230 4.5 22.6 1.0
CD2 D:HIS193 4.5 23.1 1.0
CB D:ASN170 4.6 19.1 1.0
O5' D:4LU601 4.6 18.6 1.0
CG D:GLU236 4.6 26.9 1.0
O D:VAL234 4.7 24.3 1.0
O D:PRO231 4.8 25.3 1.0
O D:TRP171 4.8 16.9 1.0
NE1 D:TRP168 4.8 24.9 1.0

Manganese binding site 5 out of 5 in 6eve

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Manganese binding site 5 out of 5 in the Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of R175A S. Cerevisiae FDC1 with Prfmn in the Iminium Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn603

b:32.5
occ:1.00
 O D:MET228 2.9 23.2 1.0
O D:SER226 3.0 20.4 1.0
O2P D:4LU601 3.0 16.8 1.0
OE2 D:GLU236 3.0 23.1 1.0
O D:VAL225 3.0 20.0 1.0
O5' D:4LU601 3.0 18.6 1.0
O D:TRP171 3.1 16.9 1.0
C D:SER226 3.4 20.4 1.0
P D:4LU601 3.5 18.9 1.0
CD D:GLU236 3.7 25.6 1.0
CA D:SER226 3.7 20.2 1.0
O D:HOH737 3.8 18.5 1.0
CG D:GLU236 3.8 26.9 1.0
O1P D:4LU601 3.8 19.3 1.0
MN D:MN602 3.9 24.6 1.0
C D:MET228 4.0 23.9 1.0
N D:MET228 4.0 23.2 1.0
C D:VAL225 4.1 21.5 1.0
C5' D:4LU601 4.2 20.1 1.0
O4' D:4LU601 4.2 19.3 1.0
C D:TRP171 4.3 20.5 1.0
CB D:SER172 4.3 19.9 1.0
C4' D:4LU601 4.3 21.2 1.0
N D:SER227 4.3 21.8 0.5
N D:SER227 4.3 21.5 0.5
N D:SER226 4.4 20.9 1.0
CA D:SER172 4.4 21.0 1.0
CA D:MET228 4.6 23.8 1.0
C D:SER227 4.7 21.9 0.5
C D:SER227 4.7 21.7 0.5
OE1 D:GLU236 4.7 26.9 1.0
CA D:SER227 4.8 21.9 0.5
N D:SER172 4.8 20.7 1.0
CA D:SER227 4.9 22.3 0.5
O3P D:4LU601 4.9 18.1 1.0
OD1 D:ASN170 4.9 22.9 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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