Iron in PDB 1sj1: The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
Protein crystallography data
The structure of The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus, PDB code: 1sj1
was solved by
M.S.Nielsen,
P.Harris,
B.L.Ooi,
H.E.Christensen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.64 /
1.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
31.230,
47.511,
52.029,
90.00,
103.86,
90.00
|
R / Rfree (%)
|
19.4 /
22.3
|
Other elements in 1sj1:
The structure of The 1.5 A Resolution Crystal Structure of [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 The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus
(pdb code 1sj1). 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 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus, PDB code: 1sj1:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 1sj1
Go back to
Iron Binding Sites List in 1sj1
Iron binding site 1 out
of 6 in the The 1.5 A Resolution Crystal Structure of [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 The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe70
b:10.1
occ:1.00
|
FE1
|
A:F3S70
|
0.0
|
10.1
|
1.0
|
S1
|
A:F3S70
|
2.2
|
10.2
|
1.0
|
SG
|
A:CYS11
|
2.3
|
11.8
|
1.0
|
S2
|
A:F3S70
|
2.3
|
10.7
|
1.0
|
S3
|
A:F3S70
|
2.3
|
9.9
|
1.0
|
FE3
|
A:F3S70
|
2.7
|
10.9
|
1.0
|
FE4
|
A:F3S70
|
2.7
|
10.0
|
1.0
|
CB
|
A:CYS11
|
3.3
|
10.7
|
1.0
|
N
|
A:GLY13
|
3.8
|
8.0
|
1.0
|
CA
|
A:CYS11
|
3.8
|
11.4
|
1.0
|
O
|
A:HOH145
|
3.8
|
22.9
|
1.0
|
S4
|
A:F3S70
|
3.8
|
11.1
|
1.0
|
N
|
A:ILE12
|
4.1
|
9.2
|
1.0
|
CA
|
A:GLY13
|
4.1
|
10.1
|
1.0
|
N
|
A:ASP14
|
4.2
|
13.8
|
1.0
|
CB
|
A:ALA33
|
4.3
|
8.6
|
1.0
|
C
|
A:CYS11
|
4.3
|
12.9
|
1.0
|
N
|
A:ALA33
|
4.4
|
11.1
|
1.0
|
SG
|
A:CYS56
|
4.7
|
11.1
|
1.0
|
C
|
A:GLY13
|
4.7
|
9.3
|
1.0
|
CB
|
A:ALA60
|
4.7
|
10.6
|
1.0
|
SG
|
A:CYS17
|
4.8
|
9.7
|
1.0
|
CG1
|
A:VAL6
|
4.8
|
8.7
|
1.0
|
N
|
A:ALA15
|
4.8
|
12.1
|
1.0
|
C
|
A:ILE12
|
4.9
|
10.3
|
1.0
|
CA
|
A:ALA33
|
5.0
|
9.6
|
1.0
|
|
Iron binding site 2 out
of 6 in 1sj1
Go back to
Iron Binding Sites List in 1sj1
Iron binding site 2 out
of 6 in the The 1.5 A Resolution Crystal Structure of [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 The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe70
b:10.9
occ:1.00
|
FE3
|
A:F3S70
|
0.0
|
10.9
|
1.0
|
S1
|
A:F3S70
|
2.3
|
10.2
|
1.0
|
S4
|
A:F3S70
|
2.3
|
11.1
|
1.0
|
S3
|
A:F3S70
|
2.3
|
9.9
|
1.0
|
SG
|
A:CYS17
|
2.3
|
9.7
|
1.0
|
FE1
|
A:F3S70
|
2.7
|
10.1
|
1.0
|
FE4
|
A:F3S70
|
2.8
|
10.0
|
1.0
|
O
|
A:HOH145
|
2.9
|
22.9
|
1.0
|
CB
|
A:CYS17
|
3.4
|
7.2
|
1.0
|
CB
|
A:ALA33
|
3.8
|
8.6
|
1.0
|
S2
|
A:F3S70
|
4.0
|
10.7
|
1.0
|
N
|
A:CYS17
|
4.1
|
9.7
|
1.0
|
N
|
A:ALA15
|
4.1
|
12.1
|
1.0
|
CA
|
A:ALA15
|
4.3
|
11.9
|
1.0
|
CA
|
A:CYS17
|
4.4
|
10.9
|
1.0
|
CD1
|
A:ILE61
|
4.4
|
10.3
|
1.0
|
SG
|
A:CYS11
|
4.7
|
11.8
|
1.0
|
N
|
A:ILE16
|
4.7
|
10.6
|
1.0
|
C
|
A:ALA15
|
4.7
|
12.4
|
1.0
|
SG
|
A:CYS56
|
4.8
|
11.1
|
1.0
|
|
Iron binding site 3 out
of 6 in 1sj1
Go back to
Iron Binding Sites List in 1sj1
Iron binding site 3 out
of 6 in the The 1.5 A Resolution Crystal Structure of [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 The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe70
b:10.0
occ:1.00
|
FE4
|
A:F3S70
|
0.0
|
10.0
|
1.0
|
SG
|
A:CYS56
|
2.2
|
11.1
|
1.0
|
S4
|
A:F3S70
|
2.2
|
11.1
|
1.0
|
S2
|
A:F3S70
|
2.3
|
10.7
|
1.0
|
S3
|
A:F3S70
|
2.4
|
9.9
|
1.0
|
O
|
A:HOH145
|
2.6
|
22.9
|
1.0
|
FE1
|
A:F3S70
|
2.7
|
10.1
|
1.0
|
FE3
|
A:F3S70
|
2.8
|
10.9
|
1.0
|
CB
|
A:CYS56
|
3.2
|
9.3
|
1.0
|
S1
|
A:F3S70
|
3.9
|
10.2
|
1.0
|
CA
|
A:CYS56
|
3.9
|
11.7
|
1.0
|
CB
|
A:ALA60
|
4.3
|
10.6
|
1.0
|
CD
|
A:PRO57
|
4.3
|
9.0
|
1.0
|
CD1
|
A:ILE61
|
4.6
|
10.3
|
1.0
|
CG2
|
A:VAL58
|
4.6
|
10.4
|
1.0
|
C
|
A:CYS56
|
4.6
|
10.4
|
1.0
|
N
|
A:PRO57
|
4.7
|
8.4
|
1.0
|
CB
|
A:ASP14
|
4.7
|
14.8
|
1.0
|
SG
|
A:CYS11
|
4.8
|
11.8
|
1.0
|
CG1
|
A:ILE61
|
4.9
|
10.3
|
1.0
|
SG
|
A:CYS17
|
4.9
|
9.7
|
1.0
|
N
|
A:ALA60
|
5.0
|
12.3
|
1.0
|
|
Iron binding site 4 out
of 6 in 1sj1
Go back to
Iron Binding Sites List in 1sj1
Iron binding site 4 out
of 6 in the The 1.5 A Resolution Crystal Structure of [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 The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe70
b:10.3
occ:1.00
|
FE1
|
B:F3S70
|
0.0
|
10.3
|
1.0
|
S1
|
B:F3S70
|
2.2
|
10.7
|
1.0
|
SG
|
B:CYS11
|
2.3
|
11.7
|
1.0
|
S2
|
B:F3S70
|
2.3
|
11.6
|
1.0
|
S3
|
B:F3S70
|
2.4
|
10.1
|
1.0
|
FE4
|
B:F3S70
|
2.7
|
10.5
|
1.0
|
FE3
|
B:F3S70
|
2.7
|
10.2
|
1.0
|
O
|
B:HOH77
|
2.9
|
22.4
|
1.0
|
CB
|
B:CYS11
|
3.4
|
12.6
|
1.0
|
N
|
B:GLY13
|
3.8
|
12.4
|
1.0
|
CA
|
B:CYS11
|
3.8
|
10.8
|
1.0
|
S4
|
B:F3S70
|
3.9
|
11.4
|
1.0
|
N
|
B:ILE12
|
4.1
|
10.2
|
1.0
|
CA
|
B:GLY13
|
4.1
|
11.1
|
1.0
|
N
|
B:ASP14
|
4.3
|
11.9
|
1.0
|
C
|
B:CYS11
|
4.3
|
12.5
|
1.0
|
N
|
B:ALA33
|
4.4
|
9.7
|
1.0
|
CB
|
B:ALA33
|
4.4
|
7.4
|
1.0
|
SG
|
B:CYS56
|
4.7
|
9.9
|
1.0
|
C
|
B:GLY13
|
4.7
|
11.5
|
1.0
|
CB
|
B:ALA60
|
4.7
|
10.0
|
1.0
|
SG
|
B:CYS17
|
4.8
|
9.3
|
1.0
|
CG1
|
B:VAL6
|
4.8
|
11.1
|
1.0
|
C
|
B:ILE12
|
4.8
|
10.2
|
1.0
|
N
|
B:ALA15
|
4.9
|
11.3
|
1.0
|
|
Iron binding site 5 out
of 6 in 1sj1
Go back to
Iron Binding Sites List in 1sj1
Iron binding site 5 out
of 6 in the The 1.5 A Resolution Crystal Structure of [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 The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe70
b:10.2
occ:1.00
|
FE3
|
B:F3S70
|
0.0
|
10.2
|
1.0
|
S4
|
B:F3S70
|
2.2
|
11.4
|
1.0
|
SG
|
B:CYS17
|
2.3
|
9.3
|
1.0
|
S1
|
B:F3S70
|
2.3
|
10.7
|
1.0
|
S3
|
B:F3S70
|
2.4
|
10.1
|
1.0
|
O
|
B:HOH77
|
2.6
|
22.4
|
1.0
|
FE1
|
B:F3S70
|
2.7
|
10.3
|
1.0
|
FE4
|
B:F3S70
|
2.7
|
10.5
|
1.0
|
CB
|
B:CYS17
|
3.3
|
8.7
|
1.0
|
S2
|
B:F3S70
|
3.9
|
11.6
|
1.0
|
CB
|
B:ALA33
|
3.9
|
7.4
|
1.0
|
N
|
B:CYS17
|
4.0
|
10.5
|
1.0
|
N
|
B:ALA15
|
4.1
|
11.3
|
1.0
|
CA
|
B:ALA15
|
4.3
|
9.4
|
1.0
|
CA
|
B:CYS17
|
4.3
|
10.1
|
1.0
|
CD1
|
B:ILE61
|
4.4
|
9.4
|
1.0
|
N
|
B:ILE16
|
4.6
|
12.0
|
1.0
|
C
|
B:ALA15
|
4.6
|
10.8
|
1.0
|
SG
|
B:CYS11
|
4.7
|
11.7
|
1.0
|
SG
|
B:CYS56
|
4.8
|
9.9
|
1.0
|
|
Iron binding site 6 out
of 6 in 1sj1
Go back to
Iron Binding Sites List in 1sj1
Iron binding site 6 out
of 6 in the The 1.5 A Resolution Crystal Structure of [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 The 1.5 A Resolution Crystal Structure of [FE3S4]- Ferredoxin From the Hyperthermophilic Archaeon Pyrococcus Furiosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe70
b:10.5
occ:1.00
|
FE4
|
B:F3S70
|
0.0
|
10.5
|
1.0
|
SG
|
B:CYS56
|
2.3
|
9.9
|
1.0
|
S3
|
B:F3S70
|
2.3
|
10.1
|
1.0
|
S4
|
B:F3S70
|
2.3
|
11.4
|
1.0
|
S2
|
B:F3S70
|
2.3
|
11.6
|
1.0
|
O
|
B:HOH77
|
2.5
|
22.4
|
1.0
|
FE1
|
B:F3S70
|
2.7
|
10.3
|
1.0
|
FE3
|
B:F3S70
|
2.7
|
10.2
|
1.0
|
CB
|
B:CYS56
|
3.3
|
9.0
|
1.0
|
S1
|
B:F3S70
|
3.9
|
10.7
|
1.0
|
CA
|
B:CYS56
|
4.0
|
12.5
|
1.0
|
CD
|
B:PRO57
|
4.3
|
9.9
|
1.0
|
CB
|
B:ALA60
|
4.3
|
10.0
|
1.0
|
CG2
|
B:VAL58
|
4.4
|
10.8
|
1.0
|
CD1
|
B:ILE61
|
4.6
|
9.4
|
1.0
|
C
|
B:CYS56
|
4.7
|
10.3
|
1.0
|
CB
|
B:ASP14
|
4.7
|
14.0
|
1.0
|
N
|
B:PRO57
|
4.7
|
8.7
|
1.0
|
SG
|
B:CYS11
|
4.8
|
11.7
|
1.0
|
SG
|
B:CYS17
|
4.9
|
9.3
|
1.0
|
CG1
|
B:ILE61
|
4.9
|
10.7
|
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 14:42:39 2024
|