Iron in PDB 4jy9: X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters
Protein crystallography data
The structure of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters, PDB code: 4jy9
was solved by
Y.Nicolet,
R.Rohac,
L.Martin,
J.C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
58.22 /
1.60
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.247,
78.950,
86.145,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
10.2 /
15.6
|
Other elements in 4jy9:
The structure of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters
(pdb code 4jy9). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the
X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters, PDB code: 4jy9:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4jy9
Go back to
Iron Binding Sites List in 4jy9
Iron binding site 1 out
of 6 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:11.2
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
11.2
|
1.0
|
S4
|
A:SF4401
|
2.2
|
11.3
|
1.0
|
S2
|
A:SF4401
|
2.3
|
11.6
|
1.0
|
S3
|
A:SF4401
|
2.3
|
10.8
|
1.0
|
SG
|
A:CYS67
|
2.4
|
12.1
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
10.9
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
10.8
|
1.0
|
FE2
|
A:SF4401
|
2.9
|
11.7
|
1.0
|
CB
|
A:CYS67
|
3.2
|
11.5
|
1.0
|
S1
|
A:SF4401
|
3.9
|
10.5
|
1.0
|
O
|
A:HOH567
|
3.9
|
16.4
|
1.0
|
O
|
A:SAH402
|
4.1
|
12.2
|
1.0
|
N
|
A:CYS67
|
4.3
|
12.2
|
1.0
|
CA
|
A:CYS67
|
4.3
|
10.7
|
1.0
|
CB
|
A:LYS65
|
4.4
|
11.2
|
1.0
|
CB
|
A:CYS70
|
4.5
|
11.0
|
1.0
|
NH2
|
A:ARG172
|
4.5
|
12.1
|
1.0
|
OH
|
A:TYR69
|
4.6
|
12.2
|
1.0
|
SG
|
A:CYS70
|
4.6
|
11.1
|
1.0
|
SG
|
A:CYS63
|
4.7
|
11.1
|
1.0
|
O
|
A:HOH520
|
4.9
|
13.9
|
1.0
|
CE1
|
A:TYR69
|
4.9
|
10.1
|
1.0
|
CD
|
A:LYS65
|
5.0
|
12.3
|
1.0
|
N
|
A:SAH402
|
5.0
|
10.7
|
1.0
|
|
Iron binding site 2 out
of 6 in 4jy9
Go back to
Iron Binding Sites List in 4jy9
Iron binding site 2 out
of 6 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:11.7
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
11.7
|
1.0
|
O
|
A:SAH402
|
2.2
|
12.2
|
1.0
|
N
|
A:SAH402
|
2.3
|
10.7
|
1.0
|
S3
|
A:SF4401
|
2.3
|
10.8
|
1.0
|
S4
|
A:SF4401
|
2.4
|
11.3
|
1.0
|
S1
|
A:SF4401
|
2.4
|
10.5
|
1.0
|
FE4
|
A:SF4401
|
2.8
|
10.8
|
1.0
|
FE3
|
A:SF4401
|
2.9
|
10.9
|
1.0
|
FE1
|
A:SF4401
|
2.9
|
11.2
|
1.0
|
C
|
A:SAH402
|
3.0
|
11.5
|
1.0
|
CA
|
A:SAH402
|
3.2
|
11.7
|
1.0
|
SD
|
A:SAH402
|
3.3
|
19.5
|
1.0
|
CG
|
A:SAH402
|
3.7
|
17.0
|
1.0
|
CB
|
A:SAH402
|
4.0
|
14.4
|
1.0
|
S2
|
A:SF4401
|
4.1
|
11.6
|
1.0
|
O
|
A:HOH567
|
4.1
|
16.4
|
1.0
|
O
|
A:HOH520
|
4.1
|
13.9
|
1.0
|
OXT
|
A:SAH402
|
4.2
|
10.6
|
1.0
|
SG
|
A:CYS63
|
4.8
|
11.1
|
1.0
|
SG
|
A:CYS70
|
4.9
|
11.1
|
1.0
|
C5'
|
A:SAH402
|
5.0
|
23.3
|
1.0
|
|
Iron binding site 3 out
of 6 in 4jy9
Go back to
Iron Binding Sites List in 4jy9
Iron binding site 3 out
of 6 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:10.9
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
10.9
|
1.0
|
S2
|
A:SF4401
|
2.3
|
11.6
|
1.0
|
SG
|
A:CYS63
|
2.3
|
11.1
|
1.0
|
S1
|
A:SF4401
|
2.3
|
10.5
|
1.0
|
S4
|
A:SF4401
|
2.3
|
11.3
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
10.8
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
11.2
|
1.0
|
FE2
|
A:SF4401
|
2.9
|
11.7
|
1.0
|
CB
|
A:CYS63
|
3.4
|
11.1
|
1.0
|
S3
|
A:SF4401
|
3.9
|
10.8
|
1.0
|
N
|
A:SAH402
|
4.1
|
10.7
|
1.0
|
CB
|
A:LYS65
|
4.3
|
11.2
|
1.0
|
N
|
A:GLU110
|
4.4
|
9.2
|
1.0
|
CA
|
A:GLY109
|
4.6
|
9.8
|
1.0
|
O
|
A:LYS65
|
4.7
|
12.6
|
1.0
|
SG
|
A:CYS70
|
4.7
|
11.1
|
1.0
|
CA
|
A:CYS63
|
4.8
|
10.4
|
1.0
|
SG
|
A:CYS67
|
4.8
|
12.1
|
1.0
|
N
|
A:LYS65
|
4.8
|
10.3
|
1.0
|
C
|
A:LYS65
|
4.8
|
11.0
|
1.0
|
CB
|
A:LEU72
|
4.9
|
12.7
|
1.0
|
CA
|
A:LYS65
|
4.9
|
10.1
|
1.0
|
O
|
A:SAH402
|
4.9
|
12.2
|
1.0
|
CG
|
A:GLU110
|
5.0
|
8.5
|
1.0
|
O
|
A:LEU72
|
5.0
|
11.1
|
1.0
|
|
Iron binding site 4 out
of 6 in 4jy9
Go back to
Iron Binding Sites List in 4jy9
Iron binding site 4 out
of 6 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe401
b:10.8
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
10.8
|
1.0
|
S1
|
A:SF4401
|
2.2
|
10.5
|
1.0
|
SG
|
A:CYS70
|
2.3
|
11.1
|
1.0
|
S3
|
A:SF4401
|
2.3
|
10.8
|
1.0
|
S2
|
A:SF4401
|
2.3
|
11.6
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
10.9
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
11.2
|
1.0
|
FE2
|
A:SF4401
|
2.8
|
11.7
|
1.0
|
CB
|
A:CYS70
|
3.1
|
11.0
|
1.0
|
S4
|
A:SF4401
|
3.8
|
11.3
|
1.0
|
CB
|
A:LEU72
|
4.3
|
12.7
|
1.0
|
SD
|
A:SAH402
|
4.4
|
19.5
|
1.0
|
CD2
|
A:LEU305
|
4.5
|
21.8
|
1.0
|
CA
|
A:CYS70
|
4.5
|
9.2
|
1.0
|
CB
|
A:CYS67
|
4.8
|
11.5
|
1.0
|
N
|
A:ARG73
|
4.8
|
10.0
|
1.0
|
SG
|
A:CYS67
|
4.8
|
12.1
|
1.0
|
N
|
A:SAH402
|
4.8
|
10.7
|
1.0
|
C
|
A:LEU72
|
4.8
|
9.0
|
1.0
|
O
|
A:SAH402
|
4.8
|
12.2
|
1.0
|
SG
|
A:CYS63
|
4.8
|
11.1
|
1.0
|
N
|
A:LEU72
|
4.9
|
10.9
|
1.0
|
CA
|
A:LEU72
|
4.9
|
11.0
|
1.0
|
CG
|
A:LEU72
|
4.9
|
18.1
|
1.0
|
|
Iron binding site 5 out
of 6 in 4jy9
Go back to
Iron Binding Sites List in 4jy9
Iron binding site 5 out
of 6 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe409
b:13.1
occ:0.70
|
FE1
|
A:FES409
|
0.0
|
13.1
|
0.7
|
S2
|
A:FES409
|
2.2
|
12.5
|
0.7
|
S1
|
A:FES409
|
2.3
|
18.0
|
0.7
|
SG
|
A:CYS311
|
2.4
|
20.2
|
1.0
|
SG
|
A:CYS319
|
2.5
|
16.5
|
1.0
|
FE2
|
A:FES409
|
2.7
|
14.9
|
0.7
|
CB
|
A:CYS311
|
3.3
|
17.1
|
1.0
|
CB
|
A:CYS319
|
3.4
|
11.7
|
1.0
|
O
|
A:HOH622
|
3.8
|
18.4
|
1.0
|
CA
|
A:CYS319
|
3.8
|
10.5
|
1.0
|
O
|
A:HOH501
|
4.0
|
15.1
|
0.7
|
CA
|
A:CYS311
|
4.2
|
15.4
|
1.0
|
N
|
A:CYS319
|
4.5
|
10.1
|
1.0
|
NH1
|
A:ARG279
|
4.7
|
16.5
|
1.0
|
CB
|
A:CYS322
|
4.7
|
13.5
|
1.0
|
SG
|
A:CYS322
|
4.7
|
17.4
|
1.0
|
NH2
|
A:ARG279
|
4.8
|
20.0
|
1.0
|
O
|
A:HOH799
|
4.9
|
40.8
|
1.0
|
C
|
A:CYS319
|
5.0
|
10.1
|
1.0
|
N
|
A:CYS311
|
5.0
|
16.8
|
1.0
|
|
Iron binding site 6 out
of 6 in 4jy9
Go back to
Iron Binding Sites List in 4jy9
Iron binding site 6 out
of 6 in the X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters
 Mono view
 Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe409
b:14.9
occ:0.70
|
FE2
|
A:FES409
|
0.0
|
14.9
|
0.7
|
O
|
A:HOH501
|
2.1
|
15.1
|
0.7
|
S2
|
A:FES409
|
2.2
|
12.5
|
0.7
|
S1
|
A:FES409
|
2.2
|
18.0
|
0.7
|
SG
|
A:CYS322
|
2.3
|
17.4
|
1.0
|
FE1
|
A:FES409
|
2.7
|
13.1
|
0.7
|
CB
|
A:CYS322
|
3.1
|
13.5
|
1.0
|
NH2
|
A:ARG279
|
4.0
|
20.0
|
1.0
|
SG
|
A:CYS311
|
4.3
|
20.2
|
1.0
|
CA
|
A:CYS322
|
4.5
|
9.9
|
1.0
|
C
|
A:CYS322
|
4.8
|
10.0
|
1.0
|
NH1
|
A:ARG279
|
4.8
|
16.5
|
1.0
|
O
|
A:HOH799
|
4.9
|
40.8
|
1.0
|
CZ
|
A:ARG279
|
4.9
|
16.7
|
1.0
|
CA
|
A:CYS319
|
4.9
|
10.5
|
1.0
|
SG
|
A:CYS319
|
4.9
|
16.5
|
1.0
|
|
Reference:
Y.Nicolet,
R.Rohac,
L.Martin,
J.C.Fontecilla-Camps.
X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters. Proc.Natl.Acad.Sci.Usa V. 110 7188 2013.
ISSN: ISSN 0027-8424
PubMed: 23596207
DOI: 10.1073/PNAS.1302388110
Page generated: Mon Aug 5 04:53:35 2024
|