Iron in PDB 1sp8: 4-Hydroxyphenylpyruvate Dioxygenase
Protein crystallography data
The structure of 4-Hydroxyphenylpyruvate Dioxygenase, PDB code: 1sp8
was solved by
I.M.Fritze,
L.Linden,
J.Freigang,
G.Auerbach,
R.Huber,
S.Steinbacher,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.84 /
2.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.000,
110.900,
174.800,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
27.5 /
32.4
|
Iron Binding Sites:
The binding sites of Iron atom in the 4-Hydroxyphenylpyruvate Dioxygenase
(pdb code 1sp8). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
4-Hydroxyphenylpyruvate Dioxygenase, PDB code: 1sp8:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1sp8
Go back to
Iron Binding Sites List in 1sp8
Iron binding site 1 out
of 4 in the 4-Hydroxyphenylpyruvate Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of 4-Hydroxyphenylpyruvate Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:76.3
occ:1.00
|
OE1
|
A:GLU387
|
2.1
|
55.9
|
1.0
|
O
|
A:HOH501
|
2.1
|
61.5
|
1.0
|
O
|
A:HOH502
|
2.1
|
57.4
|
1.0
|
NE2
|
A:HIS219
|
2.1
|
52.7
|
1.0
|
NE2
|
A:HIS301
|
2.2
|
51.4
|
1.0
|
CE1
|
A:HIS301
|
3.0
|
29.7
|
1.0
|
CE1
|
A:HIS219
|
3.0
|
37.2
|
1.0
|
CD
|
A:GLU387
|
3.2
|
40.4
|
1.0
|
CD2
|
A:HIS219
|
3.2
|
39.4
|
1.0
|
CD2
|
A:HIS301
|
3.3
|
32.8
|
1.0
|
OE2
|
A:GLU387
|
3.6
|
36.3
|
1.0
|
ND1
|
A:HIS219
|
4.2
|
39.8
|
1.0
|
ND1
|
A:HIS301
|
4.2
|
31.2
|
1.0
|
CG
|
A:HIS219
|
4.3
|
40.3
|
1.0
|
CG
|
A:HIS301
|
4.4
|
35.2
|
1.0
|
CG
|
A:GLU387
|
4.5
|
35.3
|
1.0
|
CB
|
A:ALA303
|
4.5
|
28.7
|
1.0
|
CG2
|
A:VAL221
|
4.5
|
37.9
|
1.0
|
CE1
|
A:PHE374
|
4.6
|
41.1
|
1.0
|
CB
|
A:GLU387
|
4.7
|
33.4
|
1.0
|
CD1
|
A:PHE412
|
4.7
|
39.4
|
1.0
|
O
|
A:HOH718
|
4.8
|
59.0
|
1.0
|
CZ
|
A:PHE374
|
4.8
|
38.0
|
1.0
|
O
|
A:PHE412
|
4.9
|
49.1
|
1.0
|
|
Iron binding site 2 out
of 4 in 1sp8
Go back to
Iron Binding Sites List in 1sp8
Iron binding site 2 out
of 4 in the 4-Hydroxyphenylpyruvate Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of 4-Hydroxyphenylpyruvate Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:62.5
occ:1.00
|
O
|
B:HOH501
|
2.1
|
51.5
|
1.0
|
O
|
B:HOH502
|
2.1
|
56.0
|
1.0
|
OE1
|
B:GLU387
|
2.1
|
41.3
|
1.0
|
O
|
B:HOH503
|
2.1
|
52.8
|
1.0
|
NE2
|
B:HIS219
|
2.1
|
40.0
|
1.0
|
NE2
|
B:HIS301
|
2.1
|
39.8
|
1.0
|
CE1
|
B:HIS301
|
2.9
|
35.1
|
1.0
|
CE1
|
B:HIS219
|
3.0
|
37.0
|
1.0
|
CD2
|
B:HIS219
|
3.2
|
36.9
|
1.0
|
CD
|
B:GLU387
|
3.2
|
40.8
|
1.0
|
CD2
|
B:HIS301
|
3.3
|
36.5
|
1.0
|
OE2
|
B:GLU387
|
3.7
|
38.9
|
1.0
|
ND1
|
B:HIS301
|
4.1
|
35.5
|
1.0
|
ND1
|
B:HIS219
|
4.2
|
38.6
|
1.0
|
CG
|
B:HIS219
|
4.3
|
35.6
|
1.0
|
CG
|
B:HIS301
|
4.3
|
33.9
|
1.0
|
CB
|
B:ALA303
|
4.4
|
26.5
|
1.0
|
CG2
|
B:VAL221
|
4.4
|
31.0
|
1.0
|
CE1
|
B:PHE374
|
4.4
|
40.4
|
1.0
|
CG
|
B:GLU387
|
4.5
|
35.5
|
1.0
|
CB
|
B:GLU387
|
4.6
|
35.0
|
1.0
|
CZ
|
B:PHE374
|
4.7
|
37.2
|
1.0
|
|
Iron binding site 3 out
of 4 in 1sp8
Go back to
Iron Binding Sites List in 1sp8
Iron binding site 3 out
of 4 in the 4-Hydroxyphenylpyruvate Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of 4-Hydroxyphenylpyruvate Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe500
b:40.8
occ:1.00
|
O
|
C:HOH502
|
2.1
|
51.8
|
1.0
|
O
|
C:HOH501
|
2.1
|
50.2
|
1.0
|
O
|
C:HOH503
|
2.1
|
50.0
|
1.0
|
OE1
|
C:GLU387
|
2.1
|
47.2
|
1.0
|
NE2
|
C:HIS219
|
2.1
|
46.5
|
1.0
|
NE2
|
C:HIS301
|
2.2
|
44.4
|
1.0
|
CE1
|
C:HIS301
|
3.0
|
34.5
|
1.0
|
CE1
|
C:HIS219
|
3.0
|
41.9
|
1.0
|
CD
|
C:GLU387
|
3.2
|
41.0
|
1.0
|
CD2
|
C:HIS219
|
3.2
|
40.8
|
1.0
|
CD2
|
C:HIS301
|
3.3
|
34.1
|
1.0
|
OE2
|
C:GLU387
|
3.6
|
43.2
|
1.0
|
ND1
|
C:HIS301
|
4.2
|
39.5
|
1.0
|
ND1
|
C:HIS219
|
4.2
|
44.0
|
1.0
|
CG
|
C:HIS219
|
4.3
|
41.1
|
1.0
|
CG
|
C:HIS301
|
4.3
|
37.8
|
1.0
|
CE1
|
C:PHE374
|
4.5
|
39.5
|
1.0
|
CG
|
C:GLU387
|
4.5
|
37.4
|
1.0
|
CB
|
C:ALA303
|
4.6
|
28.9
|
1.0
|
O
|
C:HOH660
|
4.6
|
62.1
|
1.0
|
CG2
|
C:VAL221
|
4.7
|
35.8
|
1.0
|
CZ
|
C:PHE374
|
4.7
|
41.4
|
1.0
|
CB
|
C:GLU387
|
4.7
|
29.5
|
1.0
|
O
|
C:PHE412
|
4.8
|
46.5
|
1.0
|
|
Iron binding site 4 out
of 4 in 1sp8
Go back to
Iron Binding Sites List in 1sp8
Iron binding site 4 out
of 4 in the 4-Hydroxyphenylpyruvate Dioxygenase
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of 4-Hydroxyphenylpyruvate Dioxygenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe500
b:62.5
occ:1.00
|
OE1
|
D:GLU387
|
2.1
|
43.0
|
1.0
|
O
|
D:HOH501
|
2.1
|
51.0
|
1.0
|
O
|
D:HOH502
|
2.1
|
56.2
|
1.0
|
NE2
|
D:HIS219
|
2.1
|
39.8
|
1.0
|
O
|
D:HOH503
|
2.1
|
53.2
|
1.0
|
NE2
|
D:HIS301
|
2.2
|
37.2
|
1.0
|
CE1
|
D:HIS301
|
3.0
|
29.2
|
1.0
|
CE1
|
D:HIS219
|
3.1
|
36.7
|
1.0
|
CD2
|
D:HIS219
|
3.1
|
33.0
|
1.0
|
CD
|
D:GLU387
|
3.2
|
43.9
|
1.0
|
CD2
|
D:HIS301
|
3.2
|
32.7
|
1.0
|
OE2
|
D:GLU387
|
3.6
|
46.4
|
1.0
|
ND1
|
D:HIS301
|
4.2
|
31.1
|
1.0
|
ND1
|
D:HIS219
|
4.2
|
34.4
|
1.0
|
CG
|
D:HIS219
|
4.3
|
33.7
|
1.0
|
CG
|
D:HIS301
|
4.3
|
27.4
|
1.0
|
CE1
|
D:PHE374
|
4.4
|
40.8
|
1.0
|
CG2
|
D:VAL221
|
4.4
|
31.5
|
1.0
|
CG
|
D:GLU387
|
4.5
|
38.7
|
1.0
|
CB
|
D:ALA303
|
4.5
|
27.6
|
1.0
|
CB
|
D:GLU387
|
4.7
|
35.5
|
1.0
|
CZ
|
D:PHE374
|
4.8
|
38.1
|
1.0
|
CD1
|
D:PHE412
|
5.0
|
42.3
|
1.0
|
O
|
D:PHE412
|
5.0
|
44.1
|
1.0
|
|
Reference:
I.M.Fritze,
L.Linden,
J.Freigang,
G.Auerbach,
R.Huber,
S.Steinbacher.
The Crystal Structures of Zea Mays and Arabidopsis 4-Hydroxyphenylpyruvate Dioxygenase Plant Physiol. V. 134 1388 2004.
ISSN: ISSN 0032-0889
PubMed: 15084729
DOI: 10.1104/PP.103.034082
Page generated: Sat Aug 3 14:47:48 2024
|