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

Enzymatic activity of Crystal Structure of the Tyrosine-Regulated 3-Deoxy-D-Arabino- Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Complexed with Phenylalanine 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 Phenylalanine 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 Phenylalanine and Manganese, PDB code: 1ofr 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) 37.20 / 2.70
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 82.287, 94.034, 105.121, 65.14, 85.68, 75.73
R / Rfree (%) 23.2 / 27.4

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 Phenylalanine and Manganese (pdb code 1ofr). 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 Phenylalanine and Manganese, PDB code: 1ofr:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1ofr

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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 Phenylalanine 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 Phenylalanine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn400

b:54.7
occ:1.00
 OE2 A:GLU316 2.3 45.1 1.0
OD2 A:ASP342 2.3 59.3 1.0
NE2 A:HIS282 2.6 53.1 1.0
CE1 A:HIS282 3.0 51.3 1.0
SG A:CYS76 3.0 40.8 1.0
CD A:GLU316 3.0 46.7 1.0
OE1 A:GLU316 3.4 50.6 1.0
CG A:ASP342 3.4 52.8 1.0
CD2 A:HIS282 3.8 50.5 1.0
CB A:ASP342 3.9 49.8 1.0
ND1 A:HIS282 4.2 52.0 1.0
CG A:GLU316 4.3 42.6 1.0
CB A:CYS76 4.3 38.1 1.0
NH2 A:ARG107 4.3 37.0 1.0
OD1 A:ASP342 4.4 54.6 1.0
NH1 A:ARG107 4.6 33.9 1.0
CG A:HIS282 4.6 50.2 1.0
O A:CYS76 4.6 42.2 1.0
CA A:CYS76 4.7 38.7 1.0
O A:HOH2004 4.9 42.0 1.0
CZ A:ARG107 4.9 37.1 1.0

Manganese binding site 2 out of 8 in 1ofr

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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 Phenylalanine 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 Phenylalanine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn400

b:51.0
occ:1.00
 OE2 H:GLU316 2.5 51.4 1.0
SG H:CYS76 2.5 35.9 1.0
NE2 H:HIS282 2.6 67.1 1.0
OD2 H:ASP342 2.6 57.2 1.0
OE1 H:GLU316 3.0 57.4 1.0
CD H:GLU316 3.1 53.8 1.0
CG H:ASP342 3.3 57.1 1.0
CD2 H:HIS282 3.4 66.2 1.0
CB H:ASP342 3.5 56.8 1.0
CE1 H:HIS282 3.6 67.5 1.0
CB H:CYS76 3.7 37.6 1.0
CG H:LYS112 3.7 80.2 1.0
CA H:CYS76 4.2 38.4 1.0
NH2 H:ARG107 4.3 47.8 1.0
OD1 H:ASP342 4.4 57.5 1.0
O H:CYS76 4.4 39.3 1.0
CG H:HIS282 4.6 66.1 1.0
CG H:GLU316 4.6 53.3 1.0
ND1 H:HIS282 4.7 66.8 1.0
CD H:LYS112 4.7 77.8 1.0
CB H:LYS112 4.7 81.5 1.0
C H:CYS76 4.8 40.4 1.0
CA H:ASP342 4.8 57.5 1.0
N H:ASP342 4.9 59.0 1.0

Manganese binding site 3 out of 8 in 1ofr

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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 Phenylalanine 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 Phenylalanine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn400

b:65.6
occ:1.00
 OD2 C:ASP342 2.1 70.0 1.0
OE2 C:GLU316 2.3 42.9 1.0
NE2 C:HIS282 2.6 50.6 1.0
CG C:ASP342 2.9 65.2 1.0
CD C:GLU316 3.0 45.6 1.0
SG C:CYS76 3.2 41.3 1.0
CE1 C:HIS282 3.3 50.8 1.0
OE1 C:GLU316 3.3 48.2 1.0
CB C:ASP342 3.5 63.8 1.0
CD2 C:HIS282 3.6 49.7 1.0
OD1 C:ASP342 3.8 65.2 1.0
NH2 C:ARG107 4.1 43.8 1.0
CD C:LYS112 4.2 83.2 1.0
CG C:GLU316 4.3 41.8 1.0
ND1 C:HIS282 4.3 51.2 1.0
CB C:CYS76 4.4 40.3 1.0
CG C:HIS282 4.5 49.3 1.0
CE C:LYS112 4.6 84.5 1.0
O C:CYS76 4.8 40.1 1.0
CA C:CYS76 4.8 39.5 1.0
NZ C:LYS112 4.8 83.9 1.0
CA C:ASP342 4.9 63.0 1.0

Manganese binding site 4 out of 8 in 1ofr

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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 Phenylalanine 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 Phenylalanine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn400

b:36.9
occ:1.00
 OD2 D:ASP342 2.3 47.8 1.0
OE2 D:GLU316 2.5 39.3 1.0
SG D:CYS76 2.6 36.8 1.0
NE2 D:HIS282 3.0 50.2 1.0
CG D:ASP342 3.3 45.8 1.0
CD D:GLU316 3.4 36.3 1.0
OE1 D:GLU316 3.5 39.0 1.0
CB D:ASP342 3.6 44.0 1.0
CD2 D:HIS282 3.6 48.2 1.0
CE1 D:HIS282 3.9 53.3 1.0
CB D:CYS76 3.9 38.0 1.0
NZ D:LYS112 4.0 75.7 1.0
NH2 D:ARG107 4.3 34.5 1.0
CG D:LYS112 4.4 76.5 1.0
OD1 D:ASP342 4.4 43.4 1.0
CA D:CYS76 4.5 35.9 1.0
O D:CYS76 4.5 38.0 1.0
CG D:HIS282 4.8 48.7 1.0
CG D:GLU316 4.8 33.8 1.0
ND1 D:HIS282 4.8 51.7 1.0
CE D:LYS112 4.9 75.0 1.0
C D:CYS76 4.9 38.5 1.0
CA D:ASP342 4.9 41.6 1.0

Manganese binding site 5 out of 8 in 1ofr

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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 Phenylalanine 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 Phenylalanine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn400

b:74.0
occ:1.00
 OD2 E:ASP342 2.3 72.7 1.0
OE2 E:GLU316 2.4 62.3 1.0
NE2 E:HIS282 2.8 56.1 1.0
SG E:CYS76 2.8 49.6 1.0
CG E:ASP342 3.3 73.4 1.0
CD E:GLU316 3.3 60.6 1.0
CD2 E:HIS282 3.5 54.6 1.0
OE1 E:GLU316 3.6 61.0 1.0
CB E:ASP342 3.6 72.5 1.0
CE1 E:HIS282 3.8 57.8 1.0
NH2 E:ARG107 4.0 54.0 1.0
CB E:CYS76 4.0 41.4 1.0
OD1 E:ASP342 4.4 72.4 1.0
CG E:LYS112 4.5 80.2 1.0
CA E:CYS76 4.6 41.9 1.0
O E:CYS76 4.6 46.9 1.0
CG E:GLU316 4.7 57.1 1.0
CG E:HIS282 4.8 54.1 1.0
ND1 E:HIS282 4.9 56.7 1.0
CZ E:ARG107 5.0 55.8 1.0

Manganese binding site 6 out of 8 in 1ofr

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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 Phenylalanine 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 Phenylalanine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn400

b:42.5
occ:1.00
 OE2 F:GLU316 2.2 31.4 1.0
OD2 F:ASP342 2.5 42.7 1.0
SG F:CYS76 2.8 32.5 1.0
NE2 F:HIS282 2.8 40.1 1.0
CD F:GLU316 3.1 36.0 1.0
OE1 F:GLU316 3.3 39.6 1.0
CG F:ASP342 3.4 38.2 1.0
CE1 F:HIS282 3.5 39.1 1.0
CB F:ASP342 3.7 34.6 1.0
CD2 F:HIS282 3.8 41.5 1.0
CB F:CYS76 4.0 36.6 1.0
NH2 F:ARG107 4.5 37.9 1.0
OD1 F:ASP342 4.5 41.3 1.0
CG F:GLU316 4.5 33.2 1.0
CA F:CYS76 4.6 35.2 1.0
ND1 F:HIS282 4.7 45.0 1.0
CD F:LYS112 4.7 69.1 1.0
CE F:LYS112 4.7 66.4 1.0
O F:CYS76 4.7 38.2 1.0
CG F:HIS282 4.8 44.0 1.0

Manganese binding site 7 out of 8 in 1ofr

Go back to Manganese Binding Sites List in 1ofr
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 Phenylalanine 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 Phenylalanine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn400

b:70.8
occ:1.00
 NE2 G:HIS282 2.1 57.1 1.0
OE2 G:GLU316 2.4 67.6 1.0
OD2 G:ASP342 2.5 80.5 1.0
CE1 G:HIS282 2.7 56.6 1.0
SG G:CYS76 2.7 48.9 1.0
CD G:GLU316 3.1 64.5 1.0
OE1 G:GLU316 3.2 66.8 1.0
CD2 G:HIS282 3.4 56.8 1.0
CG G:ASP342 3.6 79.4 1.0
CB G:CYS76 3.9 46.5 1.0
ND1 G:HIS282 4.0 55.6 1.0
NH2 G:ARG107 4.1 54.9 1.0
CB G:ASP342 4.1 77.6 1.0
CG G:HIS282 4.3 55.5 1.0
CA G:CYS76 4.4 44.4 1.0
NZ G:LYS112 4.4 60.6 1.0
CG G:GLU316 4.6 61.3 1.0
O G:CYS76 4.6 48.1 1.0
OD1 G:ASP342 4.6 79.7 1.0
CD G:LYS112 4.8 64.3 1.0
C G:CYS76 4.9 45.0 1.0
CE G:LYS112 4.9 63.8 1.0

Manganese binding site 8 out of 8 in 1ofr

Go back to Manganese Binding Sites List in 1ofr
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 Phenylalanine 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 Phenylalanine and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn400

b:52.9
occ:1.00
 OD2 B:ASP342 2.4 68.2 1.0
OE2 B:GLU316 2.5 37.9 1.0
NE2 B:HIS282 2.8 49.2 1.0
SG B:CYS76 2.9 39.9 1.0
CG B:ASP342 3.2 64.7 1.0
CD B:GLU316 3.2 40.7 1.0
OE1 B:GLU316 3.2 43.7 1.0
CB B:ASP342 3.4 62.0 1.0
CE1 B:HIS282 3.5 48.6 1.0
CD2 B:HIS282 3.5 48.2 1.0
CB B:CYS76 4.2 36.5 1.0
OD1 B:ASP342 4.2 63.9 1.0
ND1 B:HIS282 4.5 49.1 1.0
NH2 B:ARG107 4.5 30.5 1.0
CG B:HIS282 4.5 47.1 1.0
CG B:GLU316 4.6 38.8 1.0
CD B:PRO113 4.6 74.0 1.0
CA B:CYS76 4.8 35.6 1.0
CB B:LYS112 4.8 63.7 1.0
O B:CYS76 4.9 40.9 1.0
CA B:ASP342 4.9 61.0 1.0

Reference:

V.Koenig, A.Pfeil, G.Heinrich, G.Braus, T.R.Schneider. Substrate and Metal Complexes of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase From Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism. J.Mol.Biol. V. 337 675 2004.
ISSN: ISSN 0022-2836
PubMed: 15019786
DOI: 10.1016/J.JMB.2004.01.055
Page generated: Sat Oct 5 11:56:11 2024

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