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Manganese 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:

Potassium (K) 4 atoms
Sodium (Na) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of S. Cerevisiae FDC1 with the Prenylated-Flavin Cofactor in the Iminium Form., PDB code: 4zac:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4zac

Go back to Manganese Binding Sites List in 4zac
Manganese 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 Manganese with other atoms in the Mn 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:Mn603

b:16.6
occ:0.75
OE2 A:GLU236 2.2 13.1 1.0
O1P A:4LU604 2.2 14.5 1.0
ND2 A:ASN170 2.2 13.1 1.0
O A:HOH867 2.3 17.9 1.0
O A:HOH774 2.3 15.6 1.0
ND1 A:HIS193 2.5 16.2 1.0
CD A:GLU236 3.2 16.1 1.0
CG A:ASN170 3.2 14.4 1.0
CE1 A:HIS193 3.4 16.9 1.0
P A:4LU604 3.5 15.2 1.0
CG A:HIS193 3.5 15.4 1.0
OD1 A:ASN170 3.5 19.1 1.0
OE1 A:GLU236 3.6 17.4 1.0
O3P A:4LU604 3.7 15.8 1.0
CB A:HIS193 3.8 15.0 1.0
K A:K602 3.9 16.0 1.0
CZ2 A:TRP168 4.2 17.0 1.0
CG1 A:ILE230 4.3 16.7 1.0
O A:ILE230 4.4 17.9 1.0
O2P A:4LU604 4.4 16.7 1.0
CB A:ASN170 4.5 14.1 1.0
CG A:GLU236 4.5 17.0 1.0
NE2 A:HIS193 4.5 18.0 1.0
NE1 A:TRP168 4.6 18.4 1.0
O A:VAL234 4.6 19.5 1.0
O5' A:4LU604 4.6 13.9 1.0
CD2 A:HIS193 4.6 17.6 1.0
O A:PRO231 4.7 19.2 1.0
CE2 A:TRP168 4.8 19.7 1.0
O A:TRP171 4.9 14.0 1.0

Manganese binding site 2 out of 4 in 4zac

Go back to Manganese Binding Sites List in 4zac
Manganese 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 Manganese with other atoms in the Mn 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:Mn603

b:17.8
occ:0.75
O1P B:4LU604 2.2 15.7 1.0
OE2 B:GLU236 2.2 16.6 1.0
O B:HOH788 2.2 18.4 1.0
ND2 B:ASN170 2.2 12.3 1.0
O B:HOH747 2.3 16.1 1.0
ND1 B:HIS193 2.4 15.4 1.0
CD B:GLU236 3.2 17.1 1.0
CG B:ASN170 3.2 14.4 1.0
CE1 B:HIS193 3.3 19.0 1.0
P B:4LU604 3.4 15.5 1.0
CG B:HIS193 3.5 14.1 1.0
OE1 B:GLU236 3.5 16.0 1.0
OD1 B:ASN170 3.5 19.4 1.0
O3P B:4LU604 3.7 16.1 1.0
CB B:HIS193 3.8 13.9 1.0
K B:K602 3.9 16.3 1.0
CG1 B:ILE230 4.3 18.9 1.0
CZ2 B:TRP168 4.3 20.0 1.0
O2P B:4LU604 4.3 16.2 1.0
O B:ILE230 4.4 17.7 1.0
O B:VAL234 4.5 19.7 1.0
NE2 B:HIS193 4.5 19.2 1.0
NE1 B:TRP168 4.5 20.0 1.0
CB B:ASN170 4.5 14.9 1.0
CG B:GLU236 4.5 19.0 1.0
O5' B:4LU604 4.6 13.6 1.0
CD2 B:HIS193 4.6 17.6 1.0
O B:PRO231 4.7 20.3 1.0
O B:TRP171 4.8 13.5 1.0
CE2 B:TRP168 4.9 18.9 1.0
CD1 B:ILE230 5.0 21.0 1.0
O B:MET228 5.0 18.0 1.0

Manganese binding site 3 out of 4 in 4zac

Go back to Manganese Binding Sites List in 4zac
Manganese 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 Manganese with other atoms in the Mn 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:Mn601

b:21.6
occ:0.75
O3P C:4LU603 2.1 20.8 1.0
O C:HOH867 2.1 22.9 1.0
OE2 C:GLU236 2.2 21.1 1.0
O C:HOH715 2.2 18.6 1.0
ND2 C:ASN170 2.3 15.0 1.0
ND1 C:HIS193 2.4 19.3 1.0
CD C:GLU236 3.2 28.7 1.0
CG C:ASN170 3.2 17.3 1.0
CE1 C:HIS193 3.3 24.1 1.0
P C:4LU603 3.4 19.7 1.0
CG C:HIS193 3.5 20.7 1.0
OE1 C:GLU236 3.5 23.2 1.0
O2P C:4LU603 3.5 19.3 1.0
OD1 C:ASN170 3.6 23.2 1.0
CB C:HIS193 3.8 19.3 1.0
K C:K602 3.8 22.0 1.0
CZ2 C:TRP168 4.3 23.9 1.0
CG1 C:ILE230 4.3 22.2 1.0
O1P C:4LU603 4.3 19.9 1.0
O C:ILE230 4.3 24.0 1.0
NE2 C:HIS193 4.5 24.6 1.0
O5' C:4LU603 4.5 18.8 1.0
CB C:ASN170 4.6 19.1 1.0
O C:VAL234 4.6 24.1 1.0
CG C:GLU236 4.6 25.5 1.0
NE1 C:TRP168 4.6 22.1 1.0
CD2 C:HIS193 4.6 19.9 1.0
O C:PRO231 4.7 26.0 1.0
O C:TRP171 4.7 19.3 1.0
CE2 C:TRP168 4.9 23.4 1.0
O C:MET228 5.0 20.8 1.0

Manganese binding site 4 out of 4 in 4zac

Go back to Manganese Binding Sites List in 4zac
Manganese 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 Manganese with other atoms in the Mn 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:Mn601

b:20.4
occ:0.75
OE2 D:GLU236 2.2 19.3 1.0
ND2 D:ASN170 2.2 13.1 1.0
O1P D:4LU603 2.2 15.7 1.0
O D:HOH770 2.3 18.9 1.0
O D:HOH753 2.3 17.1 1.0
ND1 D:HIS193 2.4 17.3 1.0
CD D:GLU236 3.2 17.6 1.0
CG D:ASN170 3.2 18.2 1.0
CE1 D:HIS193 3.3 17.7 1.0
P D:4LU603 3.4 16.7 1.0
CG D:HIS193 3.5 16.0 1.0
OE1 D:GLU236 3.5 18.5 1.0
OD1 D:ASN170 3.6 23.4 1.0
O3P D:4LU603 3.7 16.5 1.0
CB D:HIS193 3.8 16.8 1.0
K D:K602 3.9 18.3 1.0
CZ2 D:TRP168 4.3 19.4 1.0
CG1 D:ILE230 4.3 18.1 1.0
O D:ILE230 4.3 18.3 1.0
O2P D:4LU603 4.3 18.0 1.0
CB D:ASN170 4.5 16.0 1.0
NE2 D:HIS193 4.5 18.6 1.0
NE1 D:TRP168 4.5 21.5 1.0
O5' D:4LU603 4.5 16.3 1.0
CG D:GLU236 4.5 18.2 1.0
O D:VAL234 4.5 22.7 1.0
CD2 D:HIS193 4.6 18.4 1.0
O D:PRO231 4.7 21.1 1.0
CE2 D:TRP168 4.8 22.7 1.0
O D:TRP171 4.8 18.5 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: Tue Dec 15 04:34:36 2020

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