Iron in PDB 1siz: Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
Protein crystallography data
The structure of Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus, PDB code: 1siz
was solved by
M.S.Nielsen,
P.Harris,
H.E.M.Christensen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.00 /
2.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
47.447,
51.637,
54.549,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.9 /
28.9
|
Other elements in 1siz:
The structure of Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
(pdb code 1siz). 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 the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus, PDB code: 1siz:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1siz
Go back to
Iron Binding Sites List in 1siz
Iron binding site 1 out
of 6 in the Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
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 the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe70
b:27.9
occ:1.00
|
FE1
|
A:F3S70
|
0.0
|
27.9
|
1.0
|
S1
|
A:F3S70
|
2.2
|
33.8
|
1.0
|
S2
|
A:F3S70
|
2.3
|
27.6
|
1.0
|
S3
|
A:F3S70
|
2.3
|
31.3
|
1.0
|
SG
|
A:CYS11
|
2.4
|
33.3
|
1.0
|
FE3
|
A:F3S70
|
2.7
|
32.6
|
1.0
|
FE4
|
A:F3S70
|
2.8
|
32.0
|
1.0
|
CB
|
A:CYS11
|
3.4
|
27.2
|
1.0
|
S4
|
A:F3S70
|
3.8
|
30.3
|
1.0
|
CA
|
A:CYS11
|
3.8
|
30.8
|
1.0
|
CB
|
A:ALA33
|
3.8
|
32.9
|
1.0
|
N
|
A:GLY13
|
3.9
|
33.4
|
1.0
|
N
|
A:ILE12
|
3.9
|
28.1
|
1.0
|
N
|
A:ALA33
|
4.2
|
32.4
|
1.0
|
N
|
A:ASP14
|
4.3
|
34.6
|
1.0
|
C
|
A:CYS11
|
4.3
|
30.9
|
1.0
|
CA
|
A:GLY13
|
4.4
|
33.6
|
1.0
|
CA
|
A:ALA33
|
4.6
|
32.8
|
1.0
|
SG
|
A:CYS17
|
4.7
|
32.3
|
1.0
|
SG
|
A:CYS56
|
4.7
|
25.2
|
1.0
|
CG1
|
A:VAL6
|
4.7
|
21.7
|
1.0
|
N
|
A:ALA15
|
4.8
|
29.0
|
1.0
|
C
|
A:GLY13
|
4.8
|
30.3
|
1.0
|
C
|
A:ILE12
|
4.8
|
33.9
|
1.0
|
CB
|
A:ALA60
|
4.9
|
21.4
|
1.0
|
|
Iron binding site 2 out
of 6 in 1siz
Go back to
Iron Binding Sites List in 1siz
Iron binding site 2 out
of 6 in the Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
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 the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe70
b:32.6
occ:1.00
|
FE3
|
A:F3S70
|
0.0
|
32.6
|
1.0
|
SG
|
A:CYS17
|
2.2
|
32.3
|
1.0
|
S4
|
A:F3S70
|
2.2
|
30.3
|
1.0
|
S1
|
A:F3S70
|
2.3
|
33.8
|
1.0
|
S3
|
A:F3S70
|
2.3
|
31.3
|
1.0
|
FE1
|
A:F3S70
|
2.7
|
27.9
|
1.0
|
FE4
|
A:F3S70
|
2.8
|
32.0
|
1.0
|
CB
|
A:CYS17
|
3.2
|
36.2
|
1.0
|
CB
|
A:ALA33
|
3.6
|
32.9
|
1.0
|
S2
|
A:F3S70
|
3.9
|
27.6
|
1.0
|
N
|
A:CYS17
|
3.9
|
34.4
|
1.0
|
N
|
A:ALA15
|
4.0
|
29.0
|
1.0
|
CA
|
A:ALA15
|
4.2
|
27.7
|
1.0
|
CA
|
A:CYS17
|
4.2
|
31.3
|
1.0
|
N
|
A:ILE16
|
4.4
|
36.4
|
1.0
|
C
|
A:ALA15
|
4.5
|
32.6
|
1.0
|
CD1
|
A:ILE61
|
4.6
|
25.0
|
1.0
|
SG
|
A:CYS56
|
4.8
|
25.2
|
1.0
|
SG
|
A:CYS11
|
4.9
|
33.3
|
1.0
|
CA
|
A:ALA33
|
4.9
|
32.8
|
1.0
|
N
|
A:ALA18
|
4.9
|
32.3
|
1.0
|
|
Iron binding site 3 out
of 6 in 1siz
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Iron Binding Sites List in 1siz
Iron binding site 3 out
of 6 in the Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
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 the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe70
b:32.0
occ:1.00
|
FE4
|
A:F3S70
|
0.0
|
32.0
|
1.0
|
S4
|
A:F3S70
|
2.2
|
30.3
|
1.0
|
SG
|
A:CYS56
|
2.3
|
25.2
|
1.0
|
S3
|
A:F3S70
|
2.3
|
31.3
|
1.0
|
S2
|
A:F3S70
|
2.3
|
27.6
|
1.0
|
FE1
|
A:F3S70
|
2.8
|
27.9
|
1.0
|
FE3
|
A:F3S70
|
2.8
|
32.6
|
1.0
|
CB
|
A:CYS56
|
3.3
|
29.4
|
1.0
|
CA
|
A:CYS56
|
3.9
|
23.1
|
1.0
|
S1
|
A:F3S70
|
3.9
|
33.8
|
1.0
|
CD
|
A:PRO57
|
4.2
|
17.0
|
1.0
|
CG2
|
A:VAL58
|
4.4
|
29.8
|
1.0
|
CB
|
A:ALA60
|
4.6
|
21.4
|
1.0
|
CD1
|
A:ILE61
|
4.6
|
25.0
|
1.0
|
C
|
A:CYS56
|
4.6
|
25.0
|
1.0
|
N
|
A:PRO57
|
4.7
|
25.0
|
1.0
|
CB
|
A:ASP14
|
4.7
|
41.5
|
1.0
|
SG
|
A:CYS17
|
4.8
|
32.3
|
1.0
|
CG1
|
A:ILE61
|
4.9
|
31.4
|
1.0
|
CG
|
A:PRO57
|
4.9
|
23.1
|
1.0
|
|
Iron binding site 4 out
of 6 in 1siz
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Iron Binding Sites List in 1siz
Iron binding site 4 out
of 6 in the Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
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 the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe71
b:26.9
occ:1.00
|
FE1
|
C:F3S71
|
0.0
|
26.9
|
1.0
|
S1
|
C:F3S71
|
2.2
|
34.1
|
1.0
|
S2
|
C:F3S71
|
2.3
|
26.8
|
1.0
|
S3
|
C:F3S71
|
2.3
|
29.1
|
1.0
|
SG
|
C:CYS11
|
2.7
|
27.5
|
1.0
|
FE3
|
C:F3S71
|
2.7
|
28.0
|
1.0
|
FE4
|
C:F3S71
|
2.7
|
30.9
|
1.0
|
CB
|
C:CYS11
|
3.4
|
15.0
|
1.0
|
CB
|
C:ALA33
|
3.7
|
39.1
|
1.0
|
S4
|
C:F3S71
|
3.8
|
30.9
|
1.0
|
CA
|
C:CYS11
|
3.8
|
25.6
|
1.0
|
N
|
C:GLY13
|
3.9
|
26.8
|
1.0
|
N
|
C:ILE12
|
4.1
|
27.9
|
1.0
|
N
|
C:ALA33
|
4.2
|
34.9
|
1.0
|
N
|
C:ASP14
|
4.3
|
36.2
|
1.0
|
CA
|
C:GLY13
|
4.3
|
31.3
|
1.0
|
C
|
C:CYS11
|
4.4
|
28.6
|
1.0
|
CA
|
C:ALA33
|
4.6
|
34.8
|
1.0
|
SG
|
C:CYS17
|
4.7
|
31.0
|
1.0
|
CG1
|
C:VAL6
|
4.7
|
17.9
|
1.0
|
N
|
C:ALA15
|
4.7
|
31.0
|
1.0
|
C
|
C:GLY13
|
4.8
|
30.7
|
1.0
|
SG
|
C:CYS56
|
4.8
|
27.8
|
1.0
|
CB
|
C:ALA60
|
4.9
|
27.4
|
1.0
|
C
|
C:ILE12
|
4.9
|
27.8
|
1.0
|
|
Iron binding site 5 out
of 6 in 1siz
Go back to
Iron Binding Sites List in 1siz
Iron binding site 5 out
of 6 in the Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
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 the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe71
b:28.0
occ:1.00
|
FE3
|
C:F3S71
|
0.0
|
28.0
|
1.0
|
S4
|
C:F3S71
|
2.2
|
30.9
|
1.0
|
SG
|
C:CYS17
|
2.2
|
31.0
|
1.0
|
S1
|
C:F3S71
|
2.3
|
34.1
|
1.0
|
S3
|
C:F3S71
|
2.3
|
29.1
|
1.0
|
FE1
|
C:F3S71
|
2.7
|
26.9
|
1.0
|
FE4
|
C:F3S71
|
2.8
|
30.9
|
1.0
|
CB
|
C:CYS17
|
3.3
|
35.5
|
1.0
|
CB
|
C:ALA33
|
3.7
|
39.1
|
1.0
|
N
|
C:CYS17
|
3.8
|
37.4
|
1.0
|
S2
|
C:F3S71
|
3.9
|
26.8
|
1.0
|
N
|
C:ALA15
|
3.9
|
31.0
|
1.0
|
CA
|
C:ALA15
|
4.1
|
30.8
|
1.0
|
CA
|
C:CYS17
|
4.2
|
34.4
|
1.0
|
N
|
C:ILE16
|
4.3
|
35.7
|
1.0
|
C
|
C:ALA15
|
4.4
|
33.0
|
1.0
|
CD1
|
C:ILE61
|
4.6
|
29.5
|
1.0
|
SG
|
C:CYS56
|
4.9
|
27.8
|
1.0
|
CE
|
C:MET27
|
5.0
|
57.3
|
1.0
|
C
|
C:ILE16
|
5.0
|
38.2
|
1.0
|
N
|
C:ALA18
|
5.0
|
35.9
|
1.0
|
N
|
C:ASP14
|
5.0
|
36.2
|
1.0
|
|
Iron binding site 6 out
of 6 in 1siz
Go back to
Iron Binding Sites List in 1siz
Iron binding site 6 out
of 6 in the Crystal Structure of the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
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 the [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe71
b:30.9
occ:1.00
|
FE4
|
C:F3S71
|
0.0
|
30.9
|
1.0
|
S4
|
C:F3S71
|
2.2
|
30.9
|
1.0
|
S3
|
C:F3S71
|
2.3
|
29.1
|
1.0
|
S2
|
C:F3S71
|
2.3
|
26.8
|
1.0
|
SG
|
C:CYS56
|
2.3
|
27.8
|
1.0
|
FE1
|
C:F3S71
|
2.7
|
26.9
|
1.0
|
FE3
|
C:F3S71
|
2.8
|
28.0
|
1.0
|
CB
|
C:CYS56
|
3.3
|
27.2
|
1.0
|
S1
|
C:F3S71
|
4.0
|
34.1
|
1.0
|
CA
|
C:CYS56
|
4.0
|
22.9
|
1.0
|
CD
|
C:PRO57
|
4.4
|
21.9
|
1.0
|
CG2
|
C:VAL58
|
4.5
|
24.1
|
1.0
|
CB
|
C:ALA60
|
4.5
|
27.4
|
1.0
|
CD1
|
C:ILE61
|
4.6
|
29.5
|
1.0
|
C
|
C:CYS56
|
4.7
|
22.6
|
1.0
|
N
|
C:PRO57
|
4.7
|
26.0
|
1.0
|
SG
|
C:CYS17
|
4.7
|
31.0
|
1.0
|
CB
|
C:ASP14
|
4.7
|
44.4
|
1.0
|
CG1
|
C:ILE61
|
4.9
|
32.8
|
1.0
|
|
Reference:
M.S.Nielsen,
P.Harris,
B.L.Ooi,
H.E.M.Christensen.
The 1.5 A Resolution Crystal Structure of [FE3S4]-Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus Biochemistry V. 43 5188 2004.
ISSN: ISSN 0006-2960
PubMed: 15122884
DOI: 10.1021/BI049942X
Page generated: Sat Aug 3 14:42:29 2024
|