Iron in PDB 1oqr: Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution
Protein crystallography data
The structure of Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution, PDB code: 1oqr
was solved by
I.F.Sevrioukova,
C.Garcia,
H.Li,
B.Bhaskar,
T.L.Poulos,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
27.65 /
1.65
|
Space group
|
P 41 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
66.219,
66.219,
152.131,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.7 /
25.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution
(pdb code 1oqr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution, PDB code: 1oqr:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1oqr
Go back to
Iron Binding Sites List in 1oqr
Iron binding site 1 out
of 6 in the Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe107
b:18.2
occ:1.00
|
FE1
|
A:FES107
|
0.0
|
18.2
|
1.0
|
S1
|
A:FES107
|
2.2
|
18.3
|
1.0
|
S2
|
A:FES107
|
2.3
|
18.2
|
1.0
|
SG
|
A:CYS39
|
2.3
|
18.8
|
1.0
|
SG
|
A:CYS45
|
2.3
|
18.8
|
1.0
|
FE2
|
A:FES107
|
2.7
|
18.2
|
1.0
|
CB
|
A:CYS39
|
3.4
|
19.4
|
1.0
|
CB
|
A:CYS45
|
3.6
|
19.4
|
1.0
|
N
|
A:CYS45
|
3.6
|
19.7
|
1.0
|
N
|
A:CYS39
|
3.7
|
19.7
|
1.0
|
CA
|
A:CYS45
|
4.0
|
19.5
|
1.0
|
CA
|
A:CYS39
|
4.0
|
19.6
|
1.0
|
N
|
A:SER44
|
4.1
|
20.0
|
1.0
|
N
|
A:GLY41
|
4.2
|
19.8
|
1.0
|
N
|
A:ALA46
|
4.3
|
19.5
|
1.0
|
SG
|
A:CYS86
|
4.4
|
18.8
|
1.0
|
C
|
A:SER44
|
4.5
|
19.8
|
1.0
|
N
|
A:GLY40
|
4.5
|
19.6
|
1.0
|
C
|
A:CYS39
|
4.5
|
19.6
|
1.0
|
N
|
A:ALA43
|
4.6
|
20.1
|
1.0
|
SG
|
A:CYS48
|
4.6
|
18.5
|
1.0
|
C
|
A:CYS45
|
4.6
|
19.5
|
1.0
|
OG1
|
A:THR47
|
4.6
|
19.2
|
1.0
|
CA
|
A:GLY41
|
4.7
|
19.9
|
1.0
|
C
|
A:GLY37
|
4.7
|
20.0
|
1.0
|
N
|
A:ASP38
|
4.7
|
20.0
|
1.0
|
N
|
A:SER42
|
4.7
|
20.0
|
1.0
|
CA
|
A:ALA43
|
4.8
|
20.0
|
1.0
|
CA
|
A:GLY37
|
4.8
|
20.1
|
1.0
|
CA
|
A:SER44
|
4.8
|
19.9
|
1.0
|
N
|
A:THR47
|
4.8
|
19.3
|
1.0
|
C
|
A:ASP38
|
4.9
|
19.8
|
1.0
|
C
|
A:ALA43
|
4.9
|
20.0
|
1.0
|
|
Iron binding site 2 out
of 6 in 1oqr
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Iron Binding Sites List in 1oqr
Iron binding site 2 out
of 6 in the Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe107
b:18.2
occ:1.00
|
FE2
|
A:FES107
|
0.0
|
18.2
|
1.0
|
S1
|
A:FES107
|
2.2
|
18.3
|
1.0
|
S2
|
A:FES107
|
2.3
|
18.2
|
1.0
|
SG
|
A:CYS48
|
2.3
|
18.5
|
1.0
|
SG
|
A:CYS86
|
2.3
|
18.8
|
1.0
|
FE1
|
A:FES107
|
2.7
|
18.2
|
1.0
|
CB
|
A:CYS86
|
3.1
|
19.4
|
1.0
|
CB
|
A:CYS48
|
3.5
|
19.0
|
1.0
|
N
|
A:CYS86
|
4.2
|
19.6
|
1.0
|
CB
|
A:LEU84
|
4.3
|
20.0
|
1.0
|
CA
|
A:CYS86
|
4.3
|
19.6
|
1.0
|
CA
|
A:GLY41
|
4.4
|
19.9
|
1.0
|
SG
|
A:CYS39
|
4.5
|
18.8
|
1.0
|
SG
|
A:CYS45
|
4.5
|
18.8
|
1.0
|
N
|
A:CYS48
|
4.6
|
19.1
|
1.0
|
CA
|
A:CYS48
|
4.6
|
19.1
|
1.0
|
N
|
A:ALA43
|
4.7
|
20.1
|
1.0
|
N
|
A:GLY41
|
4.7
|
19.8
|
1.0
|
CA
|
A:ALA43
|
4.8
|
20.0
|
1.0
|
CD1
|
A:LEU84
|
4.9
|
20.0
|
1.0
|
CG
|
A:MET24
|
4.9
|
21.1
|
1.0
|
|
Iron binding site 3 out
of 6 in 1oqr
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Iron Binding Sites List in 1oqr
Iron binding site 3 out
of 6 in the Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe107
b:21.4
occ:1.00
|
FE1
|
B:FES107
|
0.0
|
21.4
|
1.0
|
S1
|
B:FES107
|
2.2
|
21.4
|
1.0
|
S2
|
B:FES107
|
2.2
|
21.2
|
1.0
|
SG
|
B:CYS39
|
2.3
|
22.0
|
1.0
|
SG
|
B:CYS45
|
2.3
|
21.7
|
1.0
|
FE2
|
B:FES107
|
2.7
|
21.2
|
1.0
|
CB
|
B:CYS39
|
3.4
|
22.7
|
1.0
|
CB
|
B:CYS45
|
3.5
|
21.9
|
1.0
|
N
|
B:CYS45
|
3.7
|
22.1
|
1.0
|
N
|
B:CYS39
|
3.7
|
23.0
|
1.0
|
CA
|
B:CYS45
|
4.0
|
21.9
|
1.0
|
CA
|
B:CYS39
|
4.0
|
22.8
|
1.0
|
N
|
B:GLY41
|
4.1
|
22.8
|
1.0
|
N
|
B:SER44
|
4.2
|
22.4
|
1.0
|
N
|
B:ALA46
|
4.2
|
21.8
|
1.0
|
N
|
B:GLY40
|
4.4
|
22.9
|
1.0
|
SG
|
B:CYS86
|
4.4
|
21.1
|
1.0
|
C
|
B:CYS39
|
4.5
|
22.9
|
1.0
|
C
|
B:CYS45
|
4.5
|
21.9
|
1.0
|
CA
|
B:GLY41
|
4.5
|
22.8
|
1.0
|
N
|
B:ALA43
|
4.6
|
22.6
|
1.0
|
SG
|
B:CYS48
|
4.6
|
21.1
|
1.0
|
C
|
B:SER44
|
4.6
|
22.2
|
1.0
|
N
|
B:ASP38
|
4.7
|
23.4
|
1.0
|
OG1
|
B:THR47
|
4.7
|
21.3
|
1.0
|
C
|
B:GLY37
|
4.7
|
23.6
|
1.0
|
N
|
B:SER42
|
4.7
|
22.8
|
1.0
|
CA
|
B:ALA43
|
4.8
|
22.6
|
1.0
|
N
|
B:THR47
|
4.8
|
21.4
|
1.0
|
CA
|
B:GLY37
|
4.8
|
23.7
|
1.0
|
C
|
B:ASP38
|
4.9
|
23.2
|
1.0
|
|
Iron binding site 4 out
of 6 in 1oqr
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Iron Binding Sites List in 1oqr
Iron binding site 4 out
of 6 in the Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe107
b:21.2
occ:1.00
|
FE2
|
B:FES107
|
0.0
|
21.2
|
1.0
|
S1
|
B:FES107
|
2.3
|
21.4
|
1.0
|
S2
|
B:FES107
|
2.3
|
21.2
|
1.0
|
SG
|
B:CYS48
|
2.3
|
21.1
|
1.0
|
SG
|
B:CYS86
|
2.3
|
21.1
|
1.0
|
FE1
|
B:FES107
|
2.7
|
21.4
|
1.0
|
CB
|
B:CYS86
|
3.1
|
21.1
|
1.0
|
CB
|
B:CYS48
|
3.4
|
21.1
|
1.0
|
N
|
B:CYS86
|
4.2
|
21.0
|
1.0
|
CB
|
B:LEU84
|
4.3
|
20.9
|
1.0
|
CA
|
B:CYS86
|
4.3
|
21.1
|
1.0
|
CA
|
B:GLY41
|
4.3
|
22.8
|
1.0
|
SG
|
B:CYS39
|
4.5
|
22.0
|
1.0
|
SG
|
B:CYS45
|
4.6
|
21.7
|
1.0
|
N
|
B:CYS48
|
4.6
|
21.2
|
1.0
|
CA
|
B:CYS48
|
4.6
|
21.1
|
1.0
|
N
|
B:GLY41
|
4.7
|
22.8
|
1.0
|
N
|
B:ALA43
|
4.8
|
22.6
|
1.0
|
CA
|
B:ALA43
|
4.9
|
22.6
|
1.0
|
CG
|
B:MET24
|
4.9
|
21.6
|
1.0
|
CD1
|
B:LEU84
|
5.0
|
20.9
|
1.0
|
C
|
B:GLY41
|
5.0
|
22.8
|
1.0
|
|
Iron binding site 5 out
of 6 in 1oqr
Go back to
Iron Binding Sites List in 1oqr
Iron binding site 5 out
of 6 in the Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe107
b:15.9
occ:1.00
|
FE1
|
C:FES107
|
0.0
|
15.9
|
1.0
|
S1
|
C:FES107
|
2.2
|
16.1
|
1.0
|
S2
|
C:FES107
|
2.2
|
16.0
|
1.0
|
SG
|
C:CYS45
|
2.4
|
20.5
|
1.0
|
SG
|
C:CYS39
|
2.4
|
20.3
|
1.0
|
FE2
|
C:FES107
|
2.7
|
15.9
|
1.0
|
CB
|
C:CYS39
|
3.4
|
20.6
|
1.0
|
N
|
C:CYS45
|
3.5
|
20.8
|
1.0
|
CB
|
C:CYS45
|
3.6
|
20.6
|
1.0
|
N
|
C:CYS39
|
3.7
|
20.8
|
1.0
|
CA
|
C:CYS45
|
3.9
|
20.6
|
1.0
|
N
|
C:ALA46
|
4.0
|
20.5
|
1.0
|
CA
|
C:CYS39
|
4.0
|
20.7
|
1.0
|
N
|
C:SER44
|
4.1
|
20.9
|
1.0
|
N
|
C:GLY41
|
4.2
|
20.6
|
1.0
|
C
|
C:CYS45
|
4.3
|
20.6
|
1.0
|
N
|
C:GLY40
|
4.5
|
20.6
|
1.0
|
N
|
C:ALA43
|
4.5
|
20.8
|
1.0
|
SG
|
C:CYS86
|
4.5
|
19.2
|
1.0
|
C
|
C:CYS39
|
4.5
|
20.6
|
1.0
|
C
|
C:SER44
|
4.6
|
20.8
|
1.0
|
CA
|
C:GLY41
|
4.6
|
20.6
|
1.0
|
N
|
C:THR47
|
4.6
|
20.1
|
1.0
|
C
|
C:GLY37
|
4.6
|
21.0
|
1.0
|
SG
|
C:CYS48
|
4.6
|
19.4
|
1.0
|
N
|
C:ASP38
|
4.7
|
20.9
|
1.0
|
OG1
|
C:THR47
|
4.7
|
19.9
|
1.0
|
CA
|
C:ALA43
|
4.7
|
20.8
|
1.0
|
CA
|
C:GLY37
|
4.7
|
21.0
|
1.0
|
N
|
C:SER42
|
4.7
|
20.7
|
1.0
|
C
|
C:ALA43
|
4.9
|
20.9
|
1.0
|
C
|
C:ASP38
|
4.9
|
20.9
|
1.0
|
CA
|
C:SER44
|
4.9
|
20.9
|
1.0
|
|
Iron binding site 6 out
of 6 in 1oqr
Go back to
Iron Binding Sites List in 1oqr
Iron binding site 6 out
of 6 in the Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of C73S Mutant of Putidaredoxin, A [2FE- 2S] Ferredoxin From Pseudomonas Putida, at 1.65A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe107
b:15.9
occ:1.00
|
FE2
|
C:FES107
|
0.0
|
15.9
|
1.0
|
S1
|
C:FES107
|
2.2
|
16.1
|
1.0
|
S2
|
C:FES107
|
2.2
|
16.0
|
1.0
|
SG
|
C:CYS48
|
2.4
|
19.4
|
1.0
|
SG
|
C:CYS86
|
2.4
|
19.2
|
1.0
|
FE1
|
C:FES107
|
2.7
|
15.9
|
1.0
|
CB
|
C:CYS86
|
3.2
|
19.4
|
1.0
|
CB
|
C:CYS48
|
3.4
|
19.7
|
1.0
|
N
|
C:CYS86
|
4.3
|
19.4
|
1.0
|
CB
|
C:LEU84
|
4.3
|
19.5
|
1.0
|
CA
|
C:CYS86
|
4.3
|
19.4
|
1.0
|
CA
|
C:GLY41
|
4.4
|
20.6
|
1.0
|
N
|
C:CYS48
|
4.5
|
19.8
|
1.0
|
SG
|
C:CYS39
|
4.5
|
20.3
|
1.0
|
SG
|
C:CYS45
|
4.6
|
20.5
|
1.0
|
CA
|
C:CYS48
|
4.6
|
19.7
|
1.0
|
N
|
C:ALA43
|
4.6
|
20.8
|
1.0
|
CA
|
C:ALA43
|
4.7
|
20.8
|
1.0
|
N
|
C:GLY41
|
4.8
|
20.6
|
1.0
|
CD1
|
C:LEU84
|
4.9
|
19.5
|
1.0
|
N
|
C:ALA46
|
4.9
|
20.5
|
1.0
|
C
|
C:GLY41
|
4.9
|
20.7
|
1.0
|
|
Reference:
I.F.Sevrioukova,
C.Garcia,
H.Li,
B.Bhaskar,
T.L.Poulos.
Crystal Structure of Putidaredoxin, the [2FE-2S] Component of the P450CAM Monooxygenase System From Pseudomonas Putida J.Mol.Biol. V. 333 377 2003.
ISSN: ISSN 0022-2836
PubMed: 14529624
DOI: 10.1016/J.JMB.2003.08.028
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