Iron in PDB 4jxc: 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: 4jxc
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)
|
58.12 /
1.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.132,
78.729,
86.209,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
12.1 /
16.6
|
Other elements in 4jxc:
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 4jxc). 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: 4jxc:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
Iron binding site 1 out
of 6 in 4jxc
Go back to
Iron Binding Sites List in 4jxc
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:9.2
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
9.2
|
1.0
|
S4
|
A:SF4401
|
2.3
|
9.3
|
1.0
|
S2
|
A:SF4401
|
2.3
|
9.7
|
1.0
|
S3
|
A:SF4401
|
2.3
|
9.3
|
1.0
|
SG
|
A:CYS67
|
2.3
|
10.7
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
9.6
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
9.5
|
1.0
|
FE2
|
A:SF4401
|
2.9
|
10.1
|
1.0
|
CB
|
A:CYS67
|
3.3
|
10.0
|
1.0
|
S1
|
A:SF4401
|
3.9
|
8.9
|
1.0
|
O
|
A:HOH567
|
3.9
|
11.4
|
1.0
|
O
|
A:SAM402
|
4.2
|
10.0
|
1.0
|
N
|
A:CYS67
|
4.2
|
8.4
|
1.0
|
CA
|
A:CYS67
|
4.4
|
8.3
|
1.0
|
CB
|
A:LYS65
|
4.4
|
7.4
|
1.0
|
CB
|
A:CYS70
|
4.4
|
9.6
|
1.0
|
NH2
|
A:ARG172
|
4.5
|
9.8
|
1.0
|
OH
|
A:TYR69
|
4.6
|
10.1
|
1.0
|
SG
|
A:CYS70
|
4.6
|
10.2
|
1.0
|
SG
|
A:CYS63
|
4.7
|
9.2
|
1.0
|
CE1
|
A:TYR69
|
4.8
|
8.4
|
1.0
|
O
|
A:HOH519
|
4.9
|
9.8
|
1.0
|
N
|
A:SAM402
|
5.0
|
9.8
|
1.0
|
CZ
|
A:TYR69
|
5.0
|
8.7
|
1.0
|
|
Iron binding site 2 out
of 6 in 4jxc
Go back to
Iron Binding Sites List in 4jxc
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:10.1
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
10.1
|
1.0
|
O
|
A:SAM402
|
2.3
|
10.0
|
1.0
|
N
|
A:SAM402
|
2.3
|
9.8
|
1.0
|
S3
|
A:SF4401
|
2.3
|
9.3
|
1.0
|
S4
|
A:SF4401
|
2.3
|
9.3
|
1.0
|
S1
|
A:SF4401
|
2.3
|
8.9
|
1.0
|
FE3
|
A:SF4401
|
2.8
|
9.5
|
1.0
|
FE4
|
A:SF4401
|
2.9
|
9.6
|
1.0
|
FE1
|
A:SF4401
|
2.9
|
9.2
|
1.0
|
C
|
A:SAM402
|
3.0
|
9.8
|
1.0
|
CA
|
A:SAM402
|
3.2
|
10.6
|
1.0
|
SD
|
A:SAM402
|
3.2
|
13.0
|
1.0
|
CG
|
A:SAM402
|
3.7
|
12.6
|
1.0
|
CB
|
A:SAM402
|
4.0
|
10.6
|
1.0
|
CE
|
A:SAM402
|
4.0
|
11.6
|
0.3
|
S2
|
A:SF4401
|
4.1
|
9.7
|
1.0
|
O
|
A:HOH567
|
4.1
|
11.4
|
1.0
|
O
|
A:HOH519
|
4.1
|
9.8
|
1.0
|
OXT
|
A:SAM402
|
4.2
|
11.5
|
1.0
|
SG
|
A:CYS63
|
4.7
|
9.2
|
1.0
|
SG
|
A:CYS70
|
4.9
|
10.2
|
1.0
|
C5'
|
A:SAM402
|
4.9
|
14.9
|
1.0
|
|
Iron binding site 3 out
of 6 in 4jxc
Go back to
Iron Binding Sites List in 4jxc
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:9.5
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
9.5
|
1.0
|
SG
|
A:CYS63
|
2.2
|
9.2
|
1.0
|
S2
|
A:SF4401
|
2.3
|
9.7
|
1.0
|
S1
|
A:SF4401
|
2.3
|
8.9
|
1.0
|
S4
|
A:SF4401
|
2.3
|
9.3
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
9.6
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
9.2
|
1.0
|
FE2
|
A:SF4401
|
2.8
|
10.1
|
1.0
|
CB
|
A:CYS63
|
3.4
|
8.7
|
1.0
|
S3
|
A:SF4401
|
3.9
|
9.3
|
1.0
|
N
|
A:SAM402
|
4.1
|
9.8
|
1.0
|
CB
|
A:LYS65
|
4.3
|
7.4
|
1.0
|
N
|
A:GLU110
|
4.4
|
7.0
|
1.0
|
CA
|
A:GLY109
|
4.6
|
6.6
|
1.0
|
O
|
A:LYS65
|
4.6
|
10.1
|
1.0
|
SG
|
A:CYS70
|
4.8
|
10.2
|
1.0
|
CA
|
A:CYS63
|
4.8
|
7.4
|
1.0
|
SG
|
A:CYS67
|
4.8
|
10.7
|
1.0
|
N
|
A:LYS65
|
4.8
|
8.1
|
1.0
|
C
|
A:LYS65
|
4.8
|
7.2
|
1.0
|
CA
|
A:LYS65
|
4.9
|
7.7
|
1.0
|
O
|
A:SAM402
|
4.9
|
10.0
|
1.0
|
CB
|
A:LEU72
|
4.9
|
8.9
|
1.0
|
CG
|
A:GLU110
|
5.0
|
7.1
|
1.0
|
|
Iron binding site 4 out
of 6 in 4jxc
Go back to
Iron Binding Sites List in 4jxc
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:9.6
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
9.6
|
1.0
|
S1
|
A:SF4401
|
2.3
|
8.9
|
1.0
|
SG
|
A:CYS70
|
2.3
|
10.2
|
1.0
|
S3
|
A:SF4401
|
2.3
|
9.3
|
1.0
|
S2
|
A:SF4401
|
2.3
|
9.7
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
9.5
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
9.2
|
1.0
|
FE2
|
A:SF4401
|
2.9
|
10.1
|
1.0
|
CB
|
A:CYS70
|
3.0
|
9.6
|
1.0
|
S4
|
A:SF4401
|
3.9
|
9.3
|
1.0
|
CE
|
A:SAM402
|
4.0
|
11.6
|
0.3
|
CB
|
A:LEU72
|
4.3
|
8.9
|
1.0
|
SD
|
A:SAM402
|
4.4
|
13.0
|
1.0
|
CA
|
A:CYS70
|
4.5
|
8.0
|
1.0
|
N
|
A:ARG73
|
4.8
|
7.5
|
1.0
|
SG
|
A:CYS67
|
4.8
|
10.7
|
1.0
|
CG
|
A:LEU72
|
4.8
|
12.5
|
1.0
|
SG
|
A:CYS63
|
4.8
|
9.2
|
1.0
|
CD2
|
A:LEU305
|
4.8
|
21.8
|
1.0
|
N
|
A:SAM402
|
4.8
|
9.8
|
1.0
|
CB
|
A:CYS67
|
4.8
|
10.0
|
1.0
|
O
|
A:SAM402
|
4.8
|
10.0
|
1.0
|
C
|
A:LEU72
|
4.8
|
7.3
|
1.0
|
N
|
A:LEU72
|
4.9
|
8.3
|
1.0
|
CA
|
A:LEU72
|
4.9
|
7.2
|
1.0
|
C
|
A:CYS70
|
5.0
|
7.5
|
1.0
|
|
Iron binding site 5 out
of 6 in 4jxc
Go back to
Iron Binding Sites List in 4jxc
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:18.6
occ:0.70
|
FE1
|
A:FES409
|
0.0
|
18.6
|
0.7
|
S2
|
A:FES409
|
2.2
|
20.9
|
0.7
|
S
|
A:H2S410
|
2.2
|
9.9
|
0.7
|
SG
|
A:CYS311
|
2.2
|
24.2
|
0.7
|
S1
|
A:FES409
|
2.2
|
17.6
|
0.7
|
FE2
|
A:FES409
|
2.7
|
20.0
|
0.7
|
CB
|
A:CYS311
|
3.3
|
18.4
|
1.0
|
SG
|
A:CYS319
|
3.4
|
14.3
|
1.0
|
O
|
A:HOH622
|
3.4
|
23.1
|
1.0
|
CB
|
A:CYS319
|
3.8
|
11.4
|
1.0
|
CA
|
A:CYS311
|
3.9
|
18.1
|
1.0
|
NH1
|
A:ARG279
|
4.3
|
19.6
|
1.0
|
N
|
A:CYS311
|
4.3
|
18.3
|
1.0
|
NH2
|
A:ARG279
|
4.4
|
18.2
|
1.0
|
CA
|
A:CYS319
|
4.4
|
9.9
|
1.0
|
S
|
A:H2S411
|
4.5
|
15.6
|
0.7
|
O
|
A:HOH800
|
4.8
|
47.8
|
1.0
|
CZ
|
A:ARG279
|
4.8
|
17.5
|
1.0
|
SG
|
A:CYS322
|
4.8
|
12.4
|
0.7
|
CD1
|
A:ILE310
|
4.9
|
24.3
|
0.7
|
|
Iron binding site 6 out
of 6 in 4jxc
Go back to
Iron Binding Sites List in 4jxc
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:20.0
occ:0.70
|
FE2
|
A:FES409
|
0.0
|
20.0
|
0.7
|
S1
|
A:FES409
|
2.2
|
17.6
|
0.7
|
S
|
A:H2S411
|
2.2
|
15.6
|
0.7
|
S2
|
A:FES409
|
2.2
|
20.9
|
0.7
|
NH2
|
A:ARG279
|
2.3
|
18.2
|
1.0
|
FE1
|
A:FES409
|
2.7
|
18.6
|
0.7
|
NH1
|
A:ARG279
|
3.0
|
19.6
|
1.0
|
CZ
|
A:ARG279
|
3.0
|
17.5
|
1.0
|
SG
|
A:CYS322
|
3.5
|
12.4
|
0.7
|
CG1
|
A:VAL323
|
4.2
|
10.2
|
1.0
|
CB
|
A:CYS322
|
4.3
|
9.4
|
0.7
|
NE
|
A:ARG279
|
4.3
|
14.0
|
1.0
|
CE
|
A:MET326
|
4.4
|
10.1
|
1.0
|
CB
|
A:CYS322
|
4.4
|
11.8
|
0.3
|
SG
|
A:CYS311
|
4.4
|
24.2
|
0.7
|
O
|
A:HOH622
|
4.4
|
23.1
|
1.0
|
S
|
A:H2S410
|
4.4
|
9.9
|
0.7
|
CD1
|
A:ILE310
|
4.7
|
24.3
|
0.7
|
|
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 04:53:11 2024
|