Manganese in PDB 2f1d: X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
Enzymatic activity of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
All present enzymatic activity of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase:
4.2.1.19;
Protein crystallography data
The structure of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase, PDB code: 2f1d
was solved by
D.W.Rice,
S.E.Glynn,
P.J.Baker,
S.E.Sedelnikova,
C.L.Davies,
T.C.Eadsforth,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
3.00
|
Space group
|
H 3 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
157.949,
157.949,
479.965,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
24 /
28.6
|
Manganese Binding Sites:
Manganese binding site 1 out
of 32 in 2f1d
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Manganese Binding Sites List in 2f1d
Manganese binding site 1 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn300
b:17.4
occ:1.00
|
OE1
|
B:GLU77
|
2.3
|
17.4
|
1.0
|
NE2
|
B:HIS145
|
2.3
|
17.4
|
1.0
|
NE2
|
A:HIS170
|
2.4
|
17.4
|
1.0
|
NE2
|
B:HIS73
|
2.5
|
17.4
|
1.0
|
CE1
|
A:HIS170
|
3.2
|
17.4
|
1.0
|
CD2
|
B:HIS145
|
3.3
|
17.4
|
1.0
|
CE1
|
B:HIS145
|
3.4
|
17.4
|
1.0
|
CD
|
B:GLU77
|
3.4
|
17.4
|
1.0
|
CD2
|
B:HIS73
|
3.4
|
17.4
|
1.0
|
CD2
|
A:HIS170
|
3.5
|
17.4
|
1.0
|
CE1
|
B:HIS73
|
3.5
|
17.4
|
1.0
|
OE2
|
B:GLU77
|
3.8
|
17.4
|
1.0
|
OD2
|
A:ASP108
|
4.0
|
17.4
|
1.0
|
ND1
|
A:HIS170
|
4.4
|
17.4
|
1.0
|
CG
|
B:HIS145
|
4.4
|
17.4
|
1.0
|
ND1
|
B:HIS145
|
4.5
|
17.4
|
1.0
|
CG
|
A:HIS170
|
4.5
|
17.4
|
1.0
|
ND1
|
B:HIS73
|
4.6
|
17.4
|
1.0
|
CG
|
B:HIS73
|
4.6
|
17.4
|
1.0
|
CG
|
B:GLU77
|
4.6
|
17.4
|
1.0
|
CB
|
B:GLU77
|
4.7
|
17.4
|
1.0
|
CG
|
A:ASP108
|
5.0
|
17.4
|
1.0
|
|
Manganese binding site 2 out
of 32 in 2f1d
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Manganese Binding Sites List in 2f1d
Manganese binding site 2 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn301
b:17.4
occ:1.00
|
NE2
|
B:HIS74
|
2.3
|
17.4
|
1.0
|
NE2
|
A:HIS47
|
2.3
|
17.4
|
1.0
|
OE1
|
A:GLU173
|
2.4
|
17.4
|
1.0
|
NE2
|
A:HIS169
|
2.5
|
17.4
|
1.0
|
OE2
|
A:GLU173
|
3.1
|
17.4
|
1.0
|
CD
|
A:GLU173
|
3.1
|
17.4
|
1.0
|
CE1
|
B:HIS74
|
3.1
|
17.4
|
1.0
|
CE1
|
A:HIS47
|
3.2
|
17.4
|
1.0
|
CD2
|
B:HIS74
|
3.3
|
17.4
|
1.0
|
CE1
|
A:HIS169
|
3.3
|
17.4
|
1.0
|
CD2
|
A:HIS47
|
3.4
|
17.4
|
1.0
|
CD2
|
A:HIS169
|
3.5
|
17.4
|
1.0
|
ND1
|
B:HIS74
|
4.3
|
17.4
|
1.0
|
ND1
|
A:HIS47
|
4.3
|
17.4
|
1.0
|
CG
|
B:HIS74
|
4.4
|
17.4
|
1.0
|
CG
|
A:HIS47
|
4.5
|
17.4
|
1.0
|
ND1
|
A:HIS169
|
4.5
|
17.4
|
1.0
|
CG
|
A:GLU173
|
4.6
|
17.4
|
1.0
|
CG
|
A:HIS169
|
4.6
|
17.4
|
1.0
|
OE2
|
B:GLU21
|
4.8
|
17.4
|
1.0
|
|
Manganese binding site 3 out
of 32 in 2f1d
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Manganese Binding Sites List in 2f1d
Manganese binding site 3 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn300
b:17.4
occ:1.00
|
NE2
|
B:HIS170
|
2.4
|
17.4
|
1.0
|
NE2
|
G:HIS145
|
2.4
|
17.4
|
1.0
|
OE1
|
G:GLU77
|
2.5
|
17.4
|
1.0
|
NE2
|
G:HIS73
|
2.6
|
17.4
|
1.0
|
CE1
|
G:HIS145
|
3.1
|
17.4
|
1.0
|
CD
|
G:GLU77
|
3.2
|
17.4
|
1.0
|
CD2
|
B:HIS170
|
3.3
|
17.4
|
1.0
|
OE2
|
G:GLU77
|
3.3
|
17.4
|
1.0
|
CE1
|
B:HIS170
|
3.3
|
17.4
|
1.0
|
CD2
|
G:HIS145
|
3.5
|
17.4
|
1.0
|
CD2
|
G:HIS73
|
3.6
|
17.4
|
1.0
|
CE1
|
G:HIS73
|
3.6
|
17.4
|
1.0
|
OD2
|
B:ASP108
|
3.9
|
17.4
|
1.0
|
ND1
|
G:HIS145
|
4.3
|
17.4
|
1.0
|
ND1
|
B:HIS170
|
4.5
|
17.4
|
1.0
|
CG
|
B:HIS170
|
4.5
|
17.4
|
1.0
|
CG
|
G:HIS145
|
4.6
|
17.4
|
1.0
|
CG
|
G:GLU77
|
4.6
|
17.4
|
1.0
|
ND1
|
G:HIS73
|
4.7
|
17.4
|
1.0
|
CG
|
G:HIS73
|
4.7
|
17.4
|
1.0
|
CG
|
B:ASP108
|
4.9
|
17.4
|
1.0
|
CD1
|
B:LEU107
|
5.0
|
17.4
|
1.0
|
|
Manganese binding site 4 out
of 32 in 2f1d
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Manganese Binding Sites List in 2f1d
Manganese binding site 4 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn301
b:17.4
occ:1.00
|
OE1
|
B:GLU173
|
2.1
|
17.4
|
1.0
|
NE2
|
B:HIS169
|
2.4
|
17.4
|
1.0
|
NE2
|
G:HIS74
|
2.4
|
17.4
|
1.0
|
NE2
|
B:HIS47
|
2.4
|
17.4
|
1.0
|
CD
|
B:GLU173
|
3.1
|
17.4
|
1.0
|
CE1
|
B:HIS169
|
3.2
|
17.4
|
1.0
|
CE1
|
G:HIS74
|
3.3
|
17.4
|
1.0
|
OE2
|
B:GLU173
|
3.3
|
17.4
|
1.0
|
CD2
|
B:HIS47
|
3.4
|
17.4
|
1.0
|
CD2
|
B:HIS169
|
3.4
|
17.4
|
1.0
|
CD2
|
G:HIS74
|
3.4
|
17.4
|
1.0
|
CE1
|
B:HIS47
|
3.4
|
17.4
|
1.0
|
ND1
|
B:HIS169
|
4.3
|
17.4
|
1.0
|
CG
|
B:GLU173
|
4.4
|
17.4
|
1.0
|
ND1
|
G:HIS74
|
4.4
|
17.4
|
1.0
|
CG
|
B:HIS169
|
4.4
|
17.4
|
1.0
|
OE2
|
G:GLU21
|
4.5
|
17.4
|
1.0
|
ND1
|
B:HIS47
|
4.5
|
17.4
|
1.0
|
CG
|
B:HIS47
|
4.5
|
17.4
|
1.0
|
CG
|
G:HIS74
|
4.5
|
17.4
|
1.0
|
CB
|
B:GLU173
|
4.9
|
17.4
|
1.0
|
|
Manganese binding site 5 out
of 32 in 2f1d
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Manganese Binding Sites List in 2f1d
Manganese binding site 5 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn300
b:17.4
occ:1.00
|
NE2
|
C:HIS170
|
2.5
|
17.4
|
1.0
|
CD2
|
C:HIS170
|
3.4
|
17.4
|
1.0
|
CE1
|
C:HIS170
|
3.5
|
17.4
|
1.0
|
OD2
|
C:ASP108
|
4.0
|
17.4
|
1.0
|
CG
|
C:HIS170
|
4.6
|
17.4
|
1.0
|
ND1
|
C:HIS170
|
4.6
|
17.4
|
1.0
|
CG
|
C:ASP108
|
5.0
|
17.4
|
1.0
|
|
Manganese binding site 6 out
of 32 in 2f1d
Go back to
Manganese Binding Sites List in 2f1d
Manganese binding site 6 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mn301
b:17.4
occ:1.00
|
OE1
|
C:GLU173
|
2.1
|
17.4
|
1.0
|
NE2
|
C:HIS47
|
2.4
|
17.4
|
1.0
|
NE2
|
C:HIS169
|
2.5
|
17.4
|
1.0
|
CD
|
C:GLU173
|
2.8
|
17.4
|
1.0
|
OE2
|
C:GLU173
|
2.8
|
17.4
|
1.0
|
CD2
|
C:HIS47
|
3.3
|
17.4
|
1.0
|
CE1
|
C:HIS47
|
3.3
|
17.4
|
1.0
|
CE1
|
C:HIS169
|
3.3
|
17.4
|
1.0
|
CD2
|
C:HIS169
|
3.4
|
17.4
|
1.0
|
CG
|
C:GLU173
|
4.3
|
17.4
|
1.0
|
ND1
|
C:HIS47
|
4.4
|
17.4
|
1.0
|
CG
|
C:HIS47
|
4.5
|
17.4
|
1.0
|
ND1
|
C:HIS169
|
4.5
|
17.4
|
1.0
|
CG
|
C:HIS169
|
4.5
|
17.4
|
1.0
|
CB
|
C:GLU173
|
5.0
|
17.4
|
1.0
|
|
Manganese binding site 7 out
of 32 in 2f1d
Go back to
Manganese Binding Sites List in 2f1d
Manganese binding site 7 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn300
b:17.4
occ:1.00
|
NE2
|
D:HIS170
|
2.4
|
17.4
|
1.0
|
NE2
|
A:HIS73
|
2.5
|
17.4
|
1.0
|
NE2
|
A:HIS145
|
2.5
|
17.4
|
1.0
|
OE1
|
A:GLU77
|
2.7
|
17.4
|
1.0
|
CD
|
A:GLU77
|
3.2
|
17.4
|
1.0
|
OE2
|
A:GLU77
|
3.3
|
17.4
|
1.0
|
CE1
|
A:HIS73
|
3.4
|
17.4
|
1.0
|
CE1
|
D:HIS170
|
3.4
|
17.4
|
1.0
|
CD2
|
D:HIS170
|
3.4
|
17.4
|
1.0
|
CD2
|
A:HIS145
|
3.5
|
17.4
|
1.0
|
CD2
|
A:HIS73
|
3.5
|
17.4
|
1.0
|
CE1
|
A:HIS145
|
3.5
|
17.4
|
1.0
|
OD2
|
D:ASP108
|
3.6
|
17.4
|
1.0
|
CG
|
A:GLU77
|
4.4
|
17.4
|
1.0
|
ND1
|
A:HIS73
|
4.5
|
17.4
|
1.0
|
ND1
|
D:HIS170
|
4.5
|
17.4
|
1.0
|
CG
|
D:HIS170
|
4.6
|
17.4
|
1.0
|
CG
|
A:HIS73
|
4.6
|
17.4
|
1.0
|
ND1
|
A:HIS145
|
4.6
|
17.4
|
1.0
|
CG
|
A:HIS145
|
4.6
|
17.4
|
1.0
|
CG
|
D:ASP108
|
4.8
|
17.4
|
1.0
|
CB
|
A:GLU77
|
4.8
|
17.4
|
1.0
|
|
Manganese binding site 8 out
of 32 in 2f1d
Go back to
Manganese Binding Sites List in 2f1d
Manganese binding site 8 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mn301
b:17.4
occ:1.00
|
NE2
|
A:HIS74
|
2.2
|
17.4
|
1.0
|
OE1
|
D:GLU173
|
2.3
|
17.4
|
1.0
|
NE2
|
D:HIS169
|
2.3
|
17.4
|
1.0
|
NE2
|
D:HIS47
|
2.4
|
17.4
|
1.0
|
CE1
|
A:HIS74
|
3.1
|
17.4
|
1.0
|
CD
|
D:GLU173
|
3.1
|
17.4
|
1.0
|
CE1
|
D:HIS169
|
3.2
|
17.4
|
1.0
|
CE1
|
D:HIS47
|
3.2
|
17.4
|
1.0
|
CD2
|
A:HIS74
|
3.2
|
17.4
|
1.0
|
OE2
|
D:GLU173
|
3.3
|
17.4
|
1.0
|
CD2
|
D:HIS169
|
3.4
|
17.4
|
1.0
|
CD2
|
D:HIS47
|
3.5
|
17.4
|
1.0
|
ND1
|
A:HIS74
|
4.3
|
17.4
|
1.0
|
ND1
|
D:HIS169
|
4.3
|
17.4
|
1.0
|
CG
|
A:HIS74
|
4.3
|
17.4
|
1.0
|
ND1
|
D:HIS47
|
4.4
|
17.4
|
1.0
|
CG
|
D:HIS169
|
4.4
|
17.4
|
1.0
|
CG
|
D:GLU173
|
4.5
|
17.4
|
1.0
|
CG
|
D:HIS47
|
4.5
|
17.4
|
1.0
|
|
Manganese binding site 9 out
of 32 in 2f1d
Go back to
Manganese Binding Sites List in 2f1d
Manganese binding site 9 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn300
b:17.4
occ:1.00
|
NE2
|
E:HIS170
|
2.2
|
17.4
|
1.0
|
CE1
|
E:HIS170
|
3.1
|
17.4
|
1.0
|
CD2
|
E:HIS170
|
3.2
|
17.4
|
1.0
|
OD2
|
E:ASP108
|
4.0
|
17.4
|
1.0
|
ND1
|
E:HIS170
|
4.2
|
17.4
|
1.0
|
CG
|
E:HIS170
|
4.3
|
17.4
|
1.0
|
CD1
|
E:LEU107
|
4.9
|
17.4
|
1.0
|
|
Manganese binding site 10 out
of 32 in 2f1d
Go back to
Manganese Binding Sites List in 2f1d
Manganese binding site 10 out
of 32 in the X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase
 Mono view
 Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 10 of X-Ray Structure of Imidazoleglycerol-Phosphate Dehydratase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mn301
b:17.4
occ:1.00
|
OE1
|
E:GLU173
|
2.1
|
17.4
|
1.0
|
NE2
|
E:HIS47
|
2.3
|
17.4
|
1.0
|
NE2
|
E:HIS169
|
2.3
|
17.4
|
1.0
|
CD
|
E:GLU173
|
3.0
|
17.4
|
1.0
|
CE1
|
E:HIS47
|
3.1
|
17.4
|
1.0
|
CE1
|
E:HIS169
|
3.1
|
17.4
|
1.0
|
OE2
|
E:GLU173
|
3.3
|
17.4
|
1.0
|
CD2
|
E:HIS47
|
3.3
|
17.4
|
1.0
|
CD2
|
E:HIS169
|
3.4
|
17.4
|
1.0
|
ND1
|
E:HIS47
|
4.3
|
17.4
|
1.0
|
ND1
|
E:HIS169
|
4.3
|
17.4
|
1.0
|
CG
|
E:GLU173
|
4.4
|
17.4
|
1.0
|
CG
|
E:HIS47
|
4.4
|
17.4
|
1.0
|
CG
|
E:HIS169
|
4.5
|
17.4
|
1.0
|
|
Reference:
S.E.Glynn,
P.J.Baker,
S.E.Sedelnikova,
C.L.Davies,
T.C.Eadsforth,
C.W.Levy,
H.F.Rodgers,
G.M.Blackburn,
T.R.Hawkes,
R.Viner,
D.W.Rice.
Structure and Mechanism of Imidazoleglycerol-Phosphate Dehydratase. Structure V. 13 1809 2005.
ISSN: ISSN 0969-2126
PubMed: 16338409
DOI: 10.1016/J.STR.2005.08.012
Page generated: Sat Oct 5 14:01:10 2024
|