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Manganese in PDB 1of6: Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese

Enzymatic activity of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese

All present enzymatic activity of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese:
4.1.2.15;

Protein crystallography data

The structure of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese, PDB code: 1of6 was solved by V.Koenig, A.Pfeil, G.Heinrich, G.Braus, T.R.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.129, 94.696, 104.843, 64.71, 85.51, 75.61
R / Rfree (%) 19.5 / 23.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese (pdb code 1of6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese, PDB code: 1of6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1of6

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Manganese binding site 1 out of 8 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1369

b:34.0
occ:1.00
 OE2 A:GLU316 1.9 31.0 1.0
OD2 A:ASP342 1.9 40.9 1.0
NE2 A:HIS282 2.2 32.3 1.0
SG A:CYS76 2.6 35.9 1.0
CD A:GLU316 2.8 38.7 1.0
CG A:ASP342 3.0 41.9 1.0
CE1 A:HIS282 3.0 36.2 1.0
OE1 A:GLU316 3.0 37.3 1.0
CD2 A:HIS282 3.4 35.0 1.0
CB A:ASP342 3.5 40.2 1.0
CB A:CYS76 3.7 33.2 1.0
OD1 A:ASP342 4.0 35.8 1.0
NH2 A:ARG107 4.1 37.7 1.0
CA A:CYS76 4.1 34.0 1.0
O A:HOH2033 4.1 37.6 1.0
ND1 A:HIS282 4.2 36.4 1.0
CG A:GLU316 4.2 40.4 1.0
O A:HOH2094 4.3 34.9 1.0
CG A:HIS282 4.4 34.1 1.0
O A:HOH2030 4.4 39.0 1.0
CG A:LYS112 4.5 58.6 1.0
O A:CYS76 4.7 32.6 1.0
CA A:ASP342 4.8 39.9 1.0
C A:CYS76 4.8 34.7 1.0
CZ A:ARG107 4.8 41.1 1.0
N A:ASP342 4.8 40.1 1.0

Manganese binding site 2 out of 8 in 1of6

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Manganese binding site 2 out of 8 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1369

b:31.9
occ:1.00
 OE2 B:GLU316 1.9 36.7 1.0
O B:HOH2091 2.0 32.7 1.0
OD2 B:ASP342 2.0 36.9 1.0
NE2 B:HIS282 2.4 38.6 1.0
SG B:CYS76 2.5 37.4 1.0
CD B:GLU316 2.7 39.7 1.0
OE1 B:GLU316 2.8 45.2 1.0
CG B:ASP342 2.9 42.7 1.0
CE1 B:HIS282 3.3 37.9 1.0
CB B:ASP342 3.4 41.7 1.0
CD2 B:HIS282 3.4 40.6 1.0
CB B:CYS76 3.6 36.1 1.0
O B:HOH2009 4.0 38.2 1.0
O B:HOH2087 4.1 42.7 1.0
OD1 B:ASP342 4.1 40.5 1.0
CA B:CYS76 4.1 36.7 1.0
CG B:GLU316 4.2 37.2 1.0
O B:HOH2071 4.3 39.6 1.0
NH2 B:ARG107 4.3 36.8 1.0
ND1 B:HIS282 4.4 38.0 1.0
CG B:HIS282 4.5 39.9 1.0
O B:CYS76 4.6 37.0 1.0
O B:HOH2021 4.6 40.8 1.0
CA B:ASP342 4.7 41.7 1.0
C B:CYS76 4.8 37.6 1.0
N B:ASP342 4.9 41.2 1.0
CZ B:ARG107 5.0 36.5 1.0

Manganese binding site 3 out of 8 in 1of6

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Manganese binding site 3 out of 8 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1370

b:38.3
occ:1.00
 OE2 C:GLU316 2.0 45.5 1.0
OD2 C:ASP342 2.1 43.6 1.0
NE2 C:HIS282 2.3 44.9 1.0
SG C:CYS76 2.5 39.9 1.0
CD C:GLU316 2.8 46.3 1.0
OE1 C:GLU316 2.9 46.7 1.0
CE1 C:HIS282 3.1 46.0 1.0
CG C:ASP342 3.1 48.5 1.0
CD2 C:HIS282 3.4 43.8 1.0
CB C:ASP342 3.6 46.4 1.0
CB C:CYS76 3.7 40.8 1.0
CA C:CYS76 4.2 41.2 1.0
OD1 C:ASP342 4.2 45.2 1.0
ND1 C:HIS282 4.2 41.3 1.0
CG C:GLU316 4.2 43.7 1.0
O C:HOH2024 4.3 45.1 1.0
NH2 C:ARG107 4.3 43.9 1.0
CG C:HIS282 4.4 42.9 1.0
O C:CYS76 4.7 41.0 1.0
CA C:ASP342 4.8 46.3 1.0
C C:CYS76 4.8 42.1 1.0
N C:ASP342 4.8 46.6 1.0
CD C:LYS112 4.8 63.7 1.0
O C:HOH2052 5.0 42.5 1.0
CZ C:ARG107 5.0 43.5 1.0

Manganese binding site 4 out of 8 in 1of6

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Manganese binding site 4 out of 8 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1369

b:30.3
occ:1.00
 OE2 D:GLU316 1.9 32.1 1.0
OD2 D:ASP342 2.0 29.6 1.0
NE2 D:HIS282 2.3 39.8 1.0
SG D:CYS76 2.6 31.5 1.0
CD D:GLU316 2.8 36.5 1.0
OE1 D:GLU316 3.0 35.1 1.0
CG D:ASP342 3.0 33.8 1.0
CE1 D:HIS282 3.2 40.9 1.0
CD2 D:HIS282 3.2 38.3 1.0
CB D:ASP342 3.4 34.9 1.0
CB D:CYS76 3.7 31.3 1.0
OD1 D:ASP342 4.1 33.9 1.0
O D:HOH2015 4.2 32.1 1.0
CA D:CYS76 4.2 33.4 1.0
CG D:GLU316 4.2 32.1 1.0
NH2 D:ARG107 4.3 32.9 1.0
ND1 D:HIS282 4.3 35.8 1.0
CG D:HIS282 4.4 37.6 1.0
O D:CYS76 4.7 35.4 1.0
O D:HOH2029 4.7 38.1 1.0
CA D:ASP342 4.7 35.2 1.0
N D:ASP342 4.8 36.3 1.0
C D:CYS76 4.8 36.4 1.0
CG D:LYS112 4.9 51.7 1.0

Manganese binding site 5 out of 8 in 1of6

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Manganese binding site 5 out of 8 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1369

b:45.6
occ:1.00
 NE2 E:HIS282 2.0 39.9 1.0
SG E:CYS76 2.1 51.1 1.0
OE2 E:GLU316 2.3 52.0 1.0
OD2 E:ASP342 2.5 60.0 1.0
CE1 E:HIS282 2.9 43.6 1.0
CD E:GLU316 3.0 46.6 1.0
CD2 E:HIS282 3.1 44.6 1.0
OE1 E:GLU316 3.1 46.0 1.0
CG E:ASP342 3.2 58.7 1.0
CB E:ASP342 3.5 57.8 1.0
CB E:CYS76 3.6 49.2 1.0
ND1 E:HIS282 4.1 42.1 1.0
CA E:CYS76 4.2 48.7 1.0
CG E:HIS282 4.2 42.1 1.0
OD1 E:ASP342 4.2 59.1 1.0
NH2 E:ARG107 4.3 45.8 1.0
CG E:GLU316 4.4 48.0 1.0
CG E:LYS112 4.5 66.8 1.0
O E:CYS76 4.7 49.1 1.0
CA E:ASP342 4.8 57.1 1.0
C E:CYS76 4.9 49.7 1.0
CZ E:ARG107 5.0 46.0 1.0
N E:ASP342 5.0 57.2 1.0

Manganese binding site 6 out of 8 in 1of6

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Manganese binding site 6 out of 8 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1369

b:33.9
occ:1.00
 O F:HOH2088 1.8 35.3 1.0
OD2 F:ASP342 1.9 34.6 1.0
OE2 F:GLU316 2.0 37.5 1.0
NE2 F:HIS282 2.2 40.8 1.0
SG F:CYS76 2.5 34.8 1.0
CD F:GLU316 2.7 40.0 1.0
OE1 F:GLU316 2.8 44.3 1.0
CG F:ASP342 2.9 42.2 1.0
CE1 F:HIS282 3.1 41.5 1.0
CD2 F:HIS282 3.1 40.0 1.0
CB F:ASP342 3.5 40.7 1.0
CB F:CYS76 3.5 35.8 1.0
O F:HOH2012 3.9 30.9 1.0
OD1 F:ASP342 4.0 39.9 1.0
CA F:CYS76 4.1 36.6 1.0
CG F:GLU316 4.2 39.2 1.0
ND1 F:HIS282 4.2 43.5 1.0
CG F:HIS282 4.3 42.1 1.0
NH2 F:ARG107 4.3 40.7 1.0
O F:HOH2072 4.3 43.9 1.0
CA F:ASP342 4.7 40.7 1.0
O F:CYS76 4.7 38.7 1.0
C F:CYS76 4.8 38.6 1.0
N F:ASP342 4.8 41.5 1.0
O F:HOH2050 4.9 35.5 1.0

Manganese binding site 7 out of 8 in 1of6

Go back to Manganese Binding Sites List in 1of6
Manganese binding site 7 out of 8 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1368

b:45.0
occ:1.00
 NE2 G:HIS282 2.0 40.8 1.0
OE2 G:GLU316 2.1 49.6 1.0
SG G:CYS76 2.2 44.6 1.0
OD2 G:ASP342 2.4 57.0 1.0
CD G:GLU316 2.8 53.3 1.0
CE1 G:HIS282 2.8 44.2 1.0
OE1 G:GLU316 2.9 52.4 1.0
CG G:ASP342 3.1 57.8 1.0
CD2 G:HIS282 3.1 46.9 1.0
CB G:ASP342 3.3 55.4 1.0
CB G:CYS76 3.6 49.7 1.0
ND1 G:HIS282 4.0 45.8 1.0
CA G:CYS76 4.1 48.5 1.0
OD1 G:ASP342 4.2 62.3 1.0
CG G:HIS282 4.2 43.5 1.0
NZ G:LYS112 4.2 49.3 1.0
CG G:GLU316 4.2 50.7 1.0
CD G:LYS112 4.3 56.3 1.0
NH2 G:ARG107 4.3 45.7 1.0
O G:HOH2021 4.5 49.5 1.0
CA G:ASP342 4.7 54.8 1.0
O G:CYS76 4.7 49.1 1.0
C G:CYS76 4.8 49.1 1.0
CE G:LYS112 4.9 55.4 1.0
N G:ASP342 4.9 55.4 1.0

Manganese binding site 8 out of 8 in 1of6

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Manganese binding site 8 out of 8 in the Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Tyrosine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn1368

b:37.8
occ:1.00
 OE2 H:GLU316 2.0 35.3 1.0
OD2 H:ASP342 2.1 36.8 1.0
NE2 H:HIS282 2.4 45.6 1.0
SG H:CYS76 2.5 36.2 1.0
CD H:GLU316 2.8 40.0 1.0
OE1 H:GLU316 2.9 44.9 1.0
CG H:ASP342 3.1 38.6 1.0
CE1 H:HIS282 3.3 42.5 1.0
CD2 H:HIS282 3.4 43.8 1.0
CB H:ASP342 3.5 42.7 1.0
CB H:CYS76 3.6 37.0 1.0
CA H:CYS76 4.1 38.6 1.0
NH2 H:ARG107 4.2 37.1 1.0
O H:HOH2014 4.2 36.4 1.0
OD1 H:ASP342 4.2 39.7 1.0
CG H:GLU316 4.3 34.8 1.0
ND1 H:HIS282 4.4 43.8 1.0
CG H:HIS282 4.5 44.4 1.0
O H:HOH2040 4.6 51.4 1.0
CA H:ASP342 4.7 42.6 1.0
N H:ASP342 4.8 43.4 1.0
O H:CYS76 4.8 40.8 1.0
C H:CYS76 4.8 41.0 1.0
CG H:LYS112 4.9 58.9 1.0
CZ H:ARG107 5.0 39.8 1.0

Reference:

V.Koenig, A.Pfeil, G.Heinrich, G.Braus, T.R.Schneider. Crystal Structure of the Double Complex of the Tyrosine Sensitive Dahp Synthase From Yeast To Be Published.
Page generated: Sat Oct 5 11:56:11 2024

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