Iron in PDB 1oqb: The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
Enzymatic activity of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
All present enzymatic activity of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).:
1.14.19.2;
Protein crystallography data
The structure of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean)., PDB code: 1oqb
was solved by
M.Moche,
J.Shanklin,
A.K.Ghoshal,
Y.Lindqvist,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.80
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
81.908,
145.791,
192.424,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.4 /
24.8
|
Iron Binding Sites:
The binding sites of Iron atom in the The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
(pdb code 1oqb). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean)., PDB code: 1oqb:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1oqb
Go back to
Iron Binding Sites List in 1oqb
Iron binding site 1 out
of 6 in the The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe364
b:53.7
occ:1.00
|
OE1
|
A:GLU143
|
2.3
|
30.2
|
1.0
|
OE1
|
A:GLU105
|
2.4
|
31.6
|
1.0
|
ND1
|
A:HIS146
|
2.5
|
28.4
|
1.0
|
OE2
|
A:GLU229
|
2.8
|
31.8
|
1.0
|
OE2
|
A:GLU105
|
2.8
|
33.3
|
1.0
|
CD
|
A:GLU105
|
2.9
|
31.3
|
1.0
|
CD
|
A:GLU229
|
3.0
|
32.5
|
1.0
|
CE1
|
A:HIS146
|
3.1
|
28.9
|
1.0
|
CD
|
A:GLU143
|
3.2
|
29.2
|
1.0
|
OE1
|
A:GLU229
|
3.4
|
34.6
|
1.0
|
OE2
|
A:GLU143
|
3.4
|
29.8
|
1.0
|
CG
|
A:HIS146
|
3.6
|
27.5
|
1.0
|
CG
|
A:GLU229
|
3.8
|
29.4
|
1.0
|
O
|
A:HOH501
|
3.9
|
28.5
|
1.0
|
CB
|
A:HIS146
|
4.1
|
26.6
|
1.0
|
NE2
|
A:HIS146
|
4.4
|
29.1
|
1.0
|
CG
|
A:GLU105
|
4.4
|
29.8
|
1.0
|
OG1
|
A:THR199
|
4.6
|
29.5
|
1.0
|
CD2
|
A:HIS146
|
4.6
|
29.3
|
1.0
|
CG
|
A:GLU143
|
4.6
|
27.7
|
1.0
|
CG2
|
A:ILE225
|
4.7
|
26.6
|
1.0
|
OE1
|
A:GLU196
|
4.9
|
33.3
|
1.0
|
O
|
A:GLU143
|
5.0
|
26.4
|
1.0
|
CB
|
A:GLU143
|
5.0
|
26.7
|
1.0
|
|
Iron binding site 2 out
of 6 in 1oqb
Go back to
Iron Binding Sites List in 1oqb
Iron binding site 2 out
of 6 in the The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe364
b:53.7
occ:1.00
|
OE1
|
B:GLU143
|
2.4
|
30.1
|
1.0
|
ND1
|
B:HIS146
|
2.5
|
28.4
|
1.0
|
OE1
|
B:GLU105
|
2.5
|
31.5
|
1.0
|
OE2
|
B:GLU229
|
2.7
|
31.7
|
1.0
|
OE2
|
B:GLU105
|
2.7
|
33.8
|
1.0
|
CD
|
B:GLU105
|
3.0
|
31.3
|
1.0
|
CD
|
B:GLU229
|
3.0
|
32.6
|
1.0
|
CE1
|
B:HIS146
|
3.1
|
28.9
|
1.0
|
CD
|
B:GLU143
|
3.3
|
29.3
|
1.0
|
OE2
|
B:GLU143
|
3.4
|
29.9
|
1.0
|
OE1
|
B:GLU229
|
3.5
|
34.4
|
1.0
|
CG
|
B:HIS146
|
3.6
|
27.6
|
1.0
|
CG
|
B:GLU229
|
3.7
|
29.5
|
1.0
|
O
|
B:HOH502
|
3.8
|
27.4
|
1.0
|
CB
|
B:HIS146
|
4.1
|
26.5
|
1.0
|
NE2
|
B:HIS146
|
4.4
|
29.1
|
1.0
|
CG
|
B:GLU105
|
4.5
|
29.8
|
1.0
|
CG2
|
B:ILE225
|
4.6
|
26.6
|
1.0
|
OG1
|
B:THR199
|
4.6
|
29.6
|
1.0
|
CD2
|
B:HIS146
|
4.6
|
29.4
|
1.0
|
CG
|
B:GLU143
|
4.7
|
27.9
|
1.0
|
OE1
|
B:GLU196
|
4.9
|
33.5
|
1.0
|
|
Iron binding site 3 out
of 6 in 1oqb
Go back to
Iron Binding Sites List in 1oqb
Iron binding site 3 out
of 6 in the The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe364
b:53.8
occ:1.00
|
OE1
|
C:GLU143
|
2.4
|
30.4
|
1.0
|
ND1
|
C:HIS146
|
2.5
|
28.5
|
1.0
|
OE1
|
C:GLU105
|
2.5
|
31.7
|
1.0
|
OE2
|
C:GLU105
|
2.7
|
33.6
|
1.0
|
OE2
|
C:GLU229
|
2.8
|
31.8
|
1.0
|
CD
|
C:GLU105
|
2.9
|
31.4
|
1.0
|
CD
|
C:GLU229
|
3.0
|
32.6
|
1.0
|
CE1
|
C:HIS146
|
3.1
|
28.7
|
1.0
|
CD
|
C:GLU143
|
3.3
|
29.4
|
1.0
|
OE1
|
C:GLU229
|
3.4
|
34.5
|
1.0
|
OE2
|
C:GLU143
|
3.5
|
29.7
|
1.0
|
CG
|
C:HIS146
|
3.6
|
27.6
|
1.0
|
CG
|
C:GLU229
|
3.7
|
29.3
|
1.0
|
O
|
C:HOH503
|
4.0
|
34.6
|
1.0
|
CB
|
C:HIS146
|
4.1
|
26.6
|
1.0
|
NE2
|
C:HIS146
|
4.3
|
28.9
|
1.0
|
CG
|
C:GLU105
|
4.4
|
29.7
|
1.0
|
CG2
|
C:ILE225
|
4.5
|
26.7
|
1.0
|
OG1
|
C:THR199
|
4.5
|
29.8
|
1.0
|
CD2
|
C:HIS146
|
4.6
|
29.2
|
1.0
|
CG
|
C:GLU143
|
4.7
|
27.9
|
1.0
|
OE1
|
C:GLU196
|
4.8
|
33.4
|
1.0
|
|
Iron binding site 4 out
of 6 in 1oqb
Go back to
Iron Binding Sites List in 1oqb
Iron binding site 4 out
of 6 in the The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe364
b:54.0
occ:1.00
|
OE1
|
D:GLU143
|
2.4
|
30.3
|
1.0
|
OE1
|
D:GLU105
|
2.4
|
31.7
|
1.0
|
ND1
|
D:HIS146
|
2.4
|
28.5
|
1.0
|
OE2
|
D:GLU105
|
2.7
|
33.8
|
1.0
|
OE2
|
D:GLU229
|
2.8
|
31.8
|
1.0
|
CD
|
D:GLU105
|
2.9
|
31.5
|
1.0
|
CD
|
D:GLU229
|
3.1
|
32.7
|
1.0
|
CE1
|
D:HIS146
|
3.1
|
28.8
|
1.0
|
CD
|
D:GLU143
|
3.3
|
29.3
|
1.0
|
OE2
|
D:GLU143
|
3.5
|
29.8
|
1.0
|
OE1
|
D:GLU229
|
3.5
|
34.6
|
1.0
|
CG
|
D:HIS146
|
3.6
|
27.6
|
1.0
|
CG
|
D:GLU229
|
3.8
|
29.5
|
1.0
|
CB
|
D:HIS146
|
4.0
|
26.4
|
1.0
|
NE2
|
D:HIS146
|
4.4
|
28.9
|
1.0
|
CG
|
D:GLU105
|
4.4
|
29.7
|
1.0
|
CG2
|
D:ILE225
|
4.6
|
26.6
|
1.0
|
CD2
|
D:HIS146
|
4.6
|
29.4
|
1.0
|
O
|
D:HOH504
|
4.6
|
36.3
|
1.0
|
CG
|
D:GLU143
|
4.6
|
27.9
|
1.0
|
OG1
|
D:THR199
|
4.7
|
29.7
|
1.0
|
OE1
|
D:GLU196
|
4.9
|
33.5
|
1.0
|
CB
|
D:GLU143
|
5.0
|
26.8
|
1.0
|
|
Iron binding site 5 out
of 6 in 1oqb
Go back to
Iron Binding Sites List in 1oqb
Iron binding site 5 out
of 6 in the The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe364
b:53.9
occ:1.00
|
OE1
|
E:GLU143
|
2.4
|
30.3
|
1.0
|
ND1
|
E:HIS146
|
2.4
|
28.6
|
1.0
|
OE1
|
E:GLU105
|
2.5
|
31.6
|
1.0
|
OE2
|
E:GLU105
|
2.8
|
33.4
|
1.0
|
OE2
|
E:GLU229
|
2.9
|
31.9
|
1.0
|
CD
|
E:GLU105
|
3.0
|
31.3
|
1.0
|
CD
|
E:GLU229
|
3.0
|
32.5
|
1.0
|
CE1
|
E:HIS146
|
3.1
|
28.9
|
1.0
|
CD
|
E:GLU143
|
3.3
|
29.3
|
1.0
|
OE1
|
E:GLU229
|
3.4
|
34.4
|
1.0
|
CG
|
E:HIS146
|
3.5
|
27.5
|
1.0
|
OE2
|
E:GLU143
|
3.5
|
29.6
|
1.0
|
CG
|
E:GLU229
|
3.7
|
29.5
|
1.0
|
CB
|
E:HIS146
|
4.0
|
26.5
|
1.0
|
NE2
|
E:HIS146
|
4.3
|
29.0
|
1.0
|
CG
|
E:GLU105
|
4.5
|
29.9
|
1.0
|
CG2
|
E:ILE225
|
4.5
|
26.6
|
1.0
|
CD2
|
E:HIS146
|
4.5
|
29.2
|
1.0
|
OG1
|
E:THR199
|
4.6
|
29.5
|
1.0
|
CG
|
E:GLU143
|
4.7
|
27.9
|
1.0
|
OE1
|
E:GLU196
|
4.9
|
33.5
|
1.0
|
|
Iron binding site 6 out
of 6 in 1oqb
Go back to
Iron Binding Sites List in 1oqb
Iron binding site 6 out
of 6 in the The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean).
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of The Crystal Structure of the One-Iron Form of the Di-Iron Center in Stearoyl Acyl Carrier Protein Desaturase From Ricinus Communis (Castor Bean). within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe364
b:53.5
occ:1.00
|
ND1
|
F:HIS146
|
2.4
|
28.6
|
1.0
|
OE1
|
F:GLU143
|
2.5
|
30.2
|
1.0
|
OE1
|
F:GLU105
|
2.5
|
31.7
|
1.0
|
OE2
|
F:GLU229
|
2.8
|
31.9
|
1.0
|
OE2
|
F:GLU105
|
2.8
|
33.3
|
1.0
|
CD
|
F:GLU229
|
3.0
|
32.6
|
1.0
|
CD
|
F:GLU105
|
3.0
|
31.3
|
1.0
|
CE1
|
F:HIS146
|
3.1
|
28.9
|
1.0
|
CD
|
F:GLU143
|
3.3
|
29.4
|
1.0
|
OE1
|
F:GLU229
|
3.4
|
34.4
|
1.0
|
OE2
|
F:GLU143
|
3.5
|
29.8
|
1.0
|
CG
|
F:HIS146
|
3.6
|
27.5
|
1.0
|
CG
|
F:GLU229
|
3.6
|
29.6
|
1.0
|
CB
|
F:HIS146
|
4.1
|
26.4
|
1.0
|
O
|
F:HOH505
|
4.1
|
45.1
|
1.0
|
NE2
|
F:HIS146
|
4.3
|
28.9
|
1.0
|
CG2
|
F:ILE225
|
4.5
|
26.5
|
1.0
|
CG
|
F:GLU105
|
4.5
|
29.8
|
1.0
|
CD2
|
F:HIS146
|
4.5
|
29.2
|
1.0
|
OG1
|
F:THR199
|
4.5
|
29.5
|
1.0
|
CG
|
F:GLU143
|
4.7
|
28.0
|
1.0
|
OE1
|
F:GLU196
|
4.9
|
33.4
|
1.0
|
|
Reference:
M.Moche,
J.Shanklin,
A.Ghoshal,
Y.Lindqvist.
Azide and Acetate Complexes Plus Two Iron-Depleted Crystal Structures of the Di-Iron Enzyme DELTA9 Stearoyl-Acp Desaturase-Implications For Oxygen Activation and Catalytic Intermediates J.Biol.Chem. V. 278 25072 2003.
ISSN: ISSN 0021-9258
PubMed: 12704186
DOI: 10.1074/JBC.M301662200
Page generated: Sat Aug 3 12:34:18 2024
|