Iron in PDB 1rfk: Crystal Structure of 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus
Protein crystallography data
The structure of Crystal Structure of 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus, PDB code: 1rfk
was solved by
A.Fish,
R.Nechushtai,
O.Livnah,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.25
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
28.450,
50.934,
110.913,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.1 /
24.7
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus
(pdb code 1rfk). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus, PDB code: 1rfk:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 1rfk
Go back to
Iron Binding Sites List in 1rfk
Iron binding site 1 out
of 4 in the Crystal Structure of 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus
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 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe100
b:8.6
occ:1.00
|
FE1
|
A:FES100
|
0.0
|
8.6
|
1.0
|
S2
|
A:FES100
|
2.2
|
8.9
|
1.0
|
S1
|
A:FES100
|
2.2
|
8.1
|
1.0
|
SG
|
A:CYS46
|
2.3
|
9.8
|
1.0
|
SG
|
A:CYS41
|
2.3
|
9.1
|
1.0
|
FE2
|
A:FES100
|
2.7
|
7.4
|
1.0
|
CB
|
A:CYS46
|
3.4
|
12.5
|
1.0
|
N
|
A:CYS41
|
3.6
|
8.5
|
1.0
|
CB
|
A:CYS41
|
3.6
|
9.2
|
1.0
|
N
|
A:CYS46
|
3.6
|
10.0
|
1.0
|
N
|
A:ARG42
|
3.8
|
7.8
|
1.0
|
CA
|
A:CYS46
|
3.8
|
8.6
|
1.0
|
CA
|
A:CYS41
|
4.0
|
8.0
|
1.0
|
C
|
A:CYS46
|
4.0
|
9.6
|
1.0
|
O
|
A:CYS46
|
4.1
|
12.2
|
1.0
|
OG
|
A:SER40
|
4.2
|
10.6
|
0.5
|
N
|
A:ALA45
|
4.3
|
9.0
|
1.0
|
C
|
A:CYS41
|
4.3
|
9.9
|
1.0
|
N
|
A:GLY44
|
4.4
|
10.0
|
1.0
|
SG
|
A:CYS79
|
4.4
|
7.0
|
1.0
|
N
|
A:ALA43
|
4.5
|
8.4
|
1.0
|
C
|
A:ALA45
|
4.5
|
9.5
|
1.0
|
SG
|
A:CYS49
|
4.5
|
7.7
|
1.0
|
C
|
A:SER40
|
4.6
|
7.9
|
1.0
|
N
|
A:THR48
|
4.6
|
7.8
|
1.0
|
CA
|
A:ARG42
|
4.7
|
6.2
|
1.0
|
N
|
A:SER40
|
4.7
|
8.9
|
1.0
|
N
|
A:SER47
|
4.7
|
10.9
|
1.0
|
C
|
A:GLY44
|
4.9
|
11.2
|
1.0
|
CA
|
A:GLY44
|
4.9
|
8.2
|
1.0
|
CA
|
A:ALA45
|
5.0
|
9.9
|
1.0
|
CB
|
A:THR48
|
5.0
|
9.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 1rfk
Go back to
Iron Binding Sites List in 1rfk
Iron binding site 2 out
of 4 in the Crystal Structure of 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus
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 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe100
b:7.4
occ:1.00
|
FE2
|
A:FES100
|
0.0
|
7.4
|
1.0
|
S2
|
A:FES100
|
2.2
|
8.9
|
1.0
|
S1
|
A:FES100
|
2.2
|
8.1
|
1.0
|
SG
|
A:CYS49
|
2.2
|
7.7
|
1.0
|
SG
|
A:CYS79
|
2.3
|
7.0
|
1.0
|
FE1
|
A:FES100
|
2.7
|
8.6
|
1.0
|
CB
|
A:CYS79
|
3.3
|
9.4
|
1.0
|
CB
|
A:CYS49
|
3.3
|
10.2
|
1.0
|
N
|
A:CYS79
|
4.2
|
6.4
|
1.0
|
N
|
A:CYS49
|
4.3
|
7.3
|
1.0
|
N
|
A:GLY44
|
4.3
|
10.0
|
1.0
|
CA
|
A:CYS79
|
4.3
|
7.8
|
1.0
|
N
|
A:ARG42
|
4.4
|
7.8
|
1.0
|
CA
|
A:CYS49
|
4.4
|
7.9
|
1.0
|
SG
|
A:CYS41
|
4.4
|
9.1
|
1.0
|
CA
|
A:ARG42
|
4.4
|
6.2
|
1.0
|
CB
|
A:LEU77
|
4.5
|
7.5
|
1.0
|
SG
|
A:CYS46
|
4.6
|
9.8
|
1.0
|
N
|
A:ALA43
|
4.6
|
8.4
|
1.0
|
CA
|
A:GLY44
|
4.7
|
8.2
|
1.0
|
O
|
A:CYS46
|
4.8
|
12.2
|
1.0
|
C
|
A:ARG42
|
4.9
|
6.5
|
1.0
|
|
Iron binding site 3 out
of 4 in 1rfk
Go back to
Iron Binding Sites List in 1rfk
Iron binding site 3 out
of 4 in the Crystal Structure of 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus
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 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe300
b:11.0
occ:1.00
|
FE1
|
B:FES300
|
0.0
|
11.0
|
1.0
|
S2
|
B:FES300
|
2.2
|
10.5
|
1.0
|
S1
|
B:FES300
|
2.3
|
10.9
|
1.0
|
SG
|
B:CYS246
|
2.3
|
12.1
|
1.0
|
SG
|
B:CYS241
|
2.3
|
10.7
|
1.0
|
FE2
|
B:FES300
|
2.7
|
10.1
|
1.0
|
CB
|
B:CYS246
|
3.4
|
15.6
|
1.0
|
CB
|
B:CYS241
|
3.4
|
10.7
|
1.0
|
N
|
B:CYS241
|
3.5
|
10.4
|
1.0
|
N
|
B:CYS246
|
3.5
|
14.2
|
1.0
|
N
|
B:ARG242
|
3.8
|
12.5
|
1.0
|
CA
|
B:CYS246
|
3.8
|
13.2
|
1.0
|
CA
|
B:CYS241
|
3.9
|
13.1
|
1.0
|
C
|
B:CYS246
|
4.1
|
13.9
|
1.0
|
O
|
B:CYS246
|
4.1
|
14.9
|
1.0
|
OG
|
B:SER240
|
4.2
|
15.0
|
0.3
|
N
|
B:ALA245
|
4.2
|
12.8
|
1.0
|
C
|
B:CYS241
|
4.3
|
13.3
|
1.0
|
SG
|
B:CYS279
|
4.4
|
10.2
|
1.0
|
N
|
B:GLY244
|
4.4
|
10.2
|
1.0
|
C
|
B:ALA245
|
4.5
|
15.4
|
1.0
|
N
|
B:ALA243
|
4.5
|
11.6
|
1.0
|
C
|
B:SER240
|
4.6
|
12.3
|
1.0
|
N
|
B:THR248
|
4.6
|
12.6
|
1.0
|
SG
|
B:CYS249
|
4.6
|
10.7
|
1.0
|
CA
|
B:ARG242
|
4.6
|
12.1
|
1.0
|
N
|
B:SER240
|
4.6
|
12.5
|
1.0
|
N
|
B:SER247
|
4.8
|
13.1
|
1.0
|
CA
|
B:GLY244
|
4.8
|
9.0
|
1.0
|
C
|
B:GLY244
|
4.9
|
10.2
|
1.0
|
CA
|
B:ALA245
|
4.9
|
10.0
|
1.0
|
CB
|
B:SER240
|
4.9
|
14.5
|
1.0
|
CB
|
B:THR248
|
4.9
|
13.2
|
1.0
|
CA
|
B:SER240
|
5.0
|
12.9
|
1.0
|
|
Iron binding site 4 out
of 4 in 1rfk
Go back to
Iron Binding Sites List in 1rfk
Iron binding site 4 out
of 4 in the Crystal Structure of 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus
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 2FE2S Ferredoxin From Thermophilic Cyanobacterium Mastigocladus Laminosus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe300
b:10.1
occ:1.00
|
FE2
|
B:FES300
|
0.0
|
10.1
|
1.0
|
S2
|
B:FES300
|
2.2
|
10.5
|
1.0
|
S1
|
B:FES300
|
2.2
|
10.9
|
1.0
|
SG
|
B:CYS249
|
2.2
|
10.7
|
1.0
|
SG
|
B:CYS279
|
2.3
|
10.2
|
1.0
|
FE1
|
B:FES300
|
2.7
|
11.0
|
1.0
|
CB
|
B:CYS249
|
3.2
|
10.8
|
1.0
|
CB
|
B:CYS279
|
3.3
|
11.8
|
1.0
|
N
|
B:CYS279
|
4.2
|
9.8
|
1.0
|
N
|
B:CYS249
|
4.3
|
12.9
|
1.0
|
N
|
B:GLY244
|
4.3
|
10.2
|
1.0
|
CA
|
B:CYS249
|
4.3
|
11.9
|
1.0
|
CA
|
B:CYS279
|
4.4
|
11.4
|
1.0
|
SG
|
B:CYS241
|
4.4
|
10.7
|
1.0
|
N
|
B:ARG242
|
4.4
|
12.5
|
1.0
|
CA
|
B:ARG242
|
4.4
|
12.1
|
1.0
|
CB
|
B:LEU277
|
4.5
|
9.5
|
1.0
|
CA
|
B:GLY244
|
4.6
|
9.0
|
1.0
|
SG
|
B:CYS246
|
4.6
|
12.1
|
1.0
|
N
|
B:ALA243
|
4.7
|
11.6
|
1.0
|
C
|
B:ARG242
|
4.9
|
10.0
|
1.0
|
O
|
B:CYS246
|
4.9
|
14.9
|
1.0
|
|
Reference:
A.Fish,
T.Danieli,
I.Ohad,
R.Nechushtai,
O.Livnah.
Structural Basis For the Thermostability of Ferredoxin From the Cyanobacterium Mastigocladus Laminosus. J.Mol.Biol. V. 350 599 2005.
ISSN: ISSN 0022-2836
PubMed: 15961101
DOI: 10.1016/J.JMB.2005.04.071
Page generated: Sat Aug 3 14:15:28 2024
|