Iron in PDB 4jye: 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: 4jye
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)
|
43.30 /
1.65
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
51.196,
79.899,
86.594,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.7 /
19.2
|
Other elements in 4jye:
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 4jye). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 7 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: 4jye:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
Iron binding site 1 out
of 7 in 4jye
Go back to
Iron Binding Sites List in 4jye
Iron binding site 1 out
of 7 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:16.4
occ:1.00
|
FE1
|
A:SF4401
|
0.0
|
16.4
|
1.0
|
S4
|
A:SF4401
|
2.3
|
15.5
|
1.0
|
S2
|
A:SF4401
|
2.3
|
16.7
|
1.0
|
S3
|
A:SF4401
|
2.3
|
16.2
|
1.0
|
SG
|
A:CYS67
|
2.4
|
15.6
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
15.3
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
15.6
|
1.0
|
FE2
|
A:SF4401
|
2.9
|
15.8
|
1.0
|
CB
|
A:CYS67
|
3.2
|
14.9
|
1.0
|
S1
|
A:SF4401
|
3.9
|
15.6
|
1.0
|
O
|
A:HOH567
|
4.0
|
18.8
|
1.0
|
O
|
A:SAH402
|
4.2
|
16.3
|
1.0
|
N
|
A:CYS67
|
4.3
|
14.7
|
1.0
|
CA
|
A:CYS67
|
4.3
|
14.8
|
1.0
|
CB
|
A:LYS65
|
4.4
|
15.7
|
1.0
|
CB
|
A:CYS70
|
4.4
|
13.9
|
1.0
|
NH2
|
A:ARG172
|
4.5
|
15.0
|
1.0
|
SG
|
A:CYS70
|
4.6
|
15.2
|
1.0
|
OH
|
A:TYR69
|
4.7
|
17.2
|
1.0
|
SG
|
A:CYS63
|
4.7
|
14.2
|
1.0
|
CE1
|
A:TYR69
|
4.8
|
14.2
|
1.0
|
O
|
A:HOH520
|
4.8
|
16.2
|
1.0
|
CD
|
A:LYS65
|
5.0
|
15.0
|
1.0
|
N
|
A:SAH402
|
5.0
|
15.9
|
1.0
|
|
Iron binding site 2 out
of 7 in 4jye
Go back to
Iron Binding Sites List in 4jye
Iron binding site 2 out
of 7 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:15.8
occ:1.00
|
FE2
|
A:SF4401
|
0.0
|
15.8
|
1.0
|
O
|
A:SAH402
|
2.3
|
16.3
|
1.0
|
N
|
A:SAH402
|
2.3
|
15.9
|
1.0
|
S1
|
A:SF4401
|
2.3
|
15.6
|
1.0
|
S3
|
A:SF4401
|
2.3
|
16.2
|
1.0
|
S4
|
A:SF4401
|
2.3
|
15.5
|
1.0
|
FE4
|
A:SF4401
|
2.8
|
15.3
|
1.0
|
FE1
|
A:SF4401
|
2.9
|
16.4
|
1.0
|
FE3
|
A:SF4401
|
2.9
|
15.6
|
1.0
|
C
|
A:SAH402
|
3.1
|
16.1
|
1.0
|
CA
|
A:SAH402
|
3.2
|
16.3
|
1.0
|
SD
|
A:SAH402
|
3.4
|
19.9
|
1.0
|
CG
|
A:SAH402
|
3.7
|
19.0
|
1.0
|
CB
|
A:SAH402
|
4.0
|
16.5
|
1.0
|
S2
|
A:SF4401
|
4.1
|
16.7
|
1.0
|
O
|
A:HOH520
|
4.1
|
16.2
|
1.0
|
O
|
A:HOH567
|
4.2
|
18.8
|
1.0
|
OXT
|
A:SAH402
|
4.2
|
15.2
|
1.0
|
SG
|
A:CYS63
|
4.7
|
14.2
|
1.0
|
SG
|
A:CYS70
|
4.8
|
15.2
|
1.0
|
|
Iron binding site 3 out
of 7 in 4jye
Go back to
Iron Binding Sites List in 4jye
Iron binding site 3 out
of 7 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:15.6
occ:1.00
|
FE3
|
A:SF4401
|
0.0
|
15.6
|
1.0
|
SG
|
A:CYS63
|
2.3
|
14.2
|
1.0
|
S2
|
A:SF4401
|
2.3
|
16.7
|
1.0
|
S4
|
A:SF4401
|
2.3
|
15.5
|
1.0
|
S1
|
A:SF4401
|
2.3
|
15.6
|
1.0
|
FE4
|
A:SF4401
|
2.7
|
15.3
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
16.4
|
1.0
|
FE2
|
A:SF4401
|
2.9
|
15.8
|
1.0
|
CB
|
A:CYS63
|
3.4
|
14.6
|
1.0
|
S3
|
A:SF4401
|
3.9
|
16.2
|
1.0
|
N
|
A:SAH402
|
4.1
|
15.9
|
1.0
|
CB
|
A:LYS65
|
4.3
|
15.7
|
1.0
|
N
|
A:GLU110
|
4.4
|
12.9
|
1.0
|
CA
|
A:GLY109
|
4.6
|
11.5
|
1.0
|
SG
|
A:CYS70
|
4.7
|
15.2
|
1.0
|
O
|
A:LYS65
|
4.7
|
14.9
|
1.0
|
CA
|
A:CYS63
|
4.8
|
14.5
|
1.0
|
N
|
A:LYS65
|
4.8
|
14.6
|
1.0
|
CB
|
A:LEU72
|
4.8
|
14.7
|
1.0
|
SG
|
A:CYS67
|
4.9
|
15.6
|
1.0
|
CA
|
A:LYS65
|
4.9
|
14.5
|
1.0
|
C
|
A:LYS65
|
4.9
|
14.5
|
1.0
|
O
|
A:SAH402
|
4.9
|
16.3
|
1.0
|
|
Iron binding site 4 out
of 7 in 4jye
Go back to
Iron Binding Sites List in 4jye
Iron binding site 4 out
of 7 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:15.3
occ:1.00
|
FE4
|
A:SF4401
|
0.0
|
15.3
|
1.0
|
SG
|
A:CYS70
|
2.2
|
15.2
|
1.0
|
S1
|
A:SF4401
|
2.3
|
15.6
|
1.0
|
S3
|
A:SF4401
|
2.3
|
16.2
|
1.0
|
S2
|
A:SF4401
|
2.3
|
16.7
|
1.0
|
FE3
|
A:SF4401
|
2.7
|
15.6
|
1.0
|
FE1
|
A:SF4401
|
2.7
|
16.4
|
1.0
|
FE2
|
A:SF4401
|
2.8
|
15.8
|
1.0
|
CB
|
A:CYS70
|
3.0
|
13.9
|
1.0
|
S4
|
A:SF4401
|
3.8
|
15.5
|
1.0
|
CB
|
A:LEU72
|
4.3
|
14.7
|
1.0
|
CD2
|
A:LEU305
|
4.5
|
17.7
|
1.0
|
CA
|
A:CYS70
|
4.5
|
14.0
|
1.0
|
SD
|
A:SAH402
|
4.5
|
19.9
|
1.0
|
CB
|
A:CYS67
|
4.7
|
14.9
|
1.0
|
N
|
A:SAH402
|
4.8
|
15.9
|
1.0
|
N
|
A:ARG73
|
4.8
|
13.9
|
1.0
|
SG
|
A:CYS67
|
4.8
|
15.6
|
1.0
|
O
|
A:SAH402
|
4.8
|
16.3
|
1.0
|
SG
|
A:CYS63
|
4.8
|
14.2
|
1.0
|
N
|
A:LEU72
|
4.9
|
13.9
|
1.0
|
C
|
A:LEU72
|
4.9
|
13.7
|
1.0
|
CG
|
A:LEU72
|
4.9
|
17.1
|
1.0
|
CA
|
A:LEU72
|
4.9
|
14.2
|
1.0
|
|
Iron binding site 5 out
of 7 in 4jye
Go back to
Iron Binding Sites List in 4jye
Iron binding site 5 out
of 7 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:Fe408
b:14.7
occ:0.70
|
FE1
|
A:F3S408
|
0.0
|
14.7
|
0.7
|
S3
|
A:F3S408
|
2.3
|
19.9
|
0.7
|
S1
|
A:F3S408
|
2.3
|
13.9
|
0.7
|
SG
|
A:CYS319
|
2.3
|
11.5
|
0.7
|
SG
|
A:CYS311
|
2.3
|
22.9
|
1.0
|
FE3
|
A:F3S408
|
2.7
|
17.4
|
0.7
|
FE4
|
A:F3S408
|
2.8
|
24.0
|
0.4
|
CB
|
A:CYS311
|
3.2
|
24.0
|
1.0
|
CB
|
A:CYS319
|
3.3
|
12.0
|
1.0
|
O
|
A:HOH616
|
3.8
|
20.3
|
1.0
|
CA
|
A:CYS319
|
3.8
|
11.8
|
1.0
|
S4
|
A:F3S408
|
3.9
|
20.0
|
0.4
|
CA
|
A:CYS311
|
4.3
|
23.9
|
1.0
|
N
|
A:CYS319
|
4.5
|
12.1
|
1.0
|
CB
|
A:CYS322
|
4.6
|
13.3
|
0.2
|
CB
|
A:CYS322
|
4.6
|
13.1
|
0.8
|
SG
|
A:CYS322
|
4.7
|
17.2
|
0.2
|
SG
|
A:CYS322
|
4.7
|
17.5
|
0.8
|
NH1
|
A:ARG279
|
4.8
|
19.1
|
1.0
|
NH2
|
A:ARG279
|
4.9
|
19.9
|
1.0
|
O
|
A:HOH501
|
4.9
|
20.7
|
0.4
|
C
|
A:CYS319
|
5.0
|
12.1
|
1.0
|
C
|
A:ALA318
|
5.0
|
13.2
|
1.0
|
|
Iron binding site 6 out
of 7 in 4jye
Go back to
Iron Binding Sites List in 4jye
Iron binding site 6 out
of 7 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:Fe408
b:17.4
occ:0.70
|
FE3
|
A:F3S408
|
0.0
|
17.4
|
0.7
|
S1
|
A:F3S408
|
2.2
|
13.9
|
0.7
|
S4
|
A:F3S408
|
2.2
|
20.0
|
0.4
|
S3
|
A:F3S408
|
2.3
|
19.9
|
0.7
|
SG
|
A:CYS322
|
2.3
|
17.5
|
0.8
|
FE1
|
A:F3S408
|
2.7
|
14.7
|
0.7
|
FE4
|
A:F3S408
|
2.8
|
24.0
|
0.4
|
CB
|
A:CYS322
|
3.1
|
13.3
|
0.2
|
CB
|
A:CYS322
|
3.1
|
13.1
|
0.8
|
SG
|
A:CYS322
|
3.2
|
17.2
|
0.2
|
NH2
|
A:ARG279
|
4.1
|
19.9
|
1.0
|
SG
|
A:CYS311
|
4.1
|
22.9
|
1.0
|
CA
|
A:CYS322
|
4.5
|
13.0
|
0.2
|
CA
|
A:CYS322
|
4.6
|
12.9
|
0.8
|
SG
|
A:CYS319
|
4.8
|
11.5
|
0.7
|
O
|
A:HOH501
|
4.8
|
20.7
|
0.4
|
CA
|
A:CYS319
|
4.9
|
11.8
|
1.0
|
C
|
A:CYS322
|
4.9
|
12.6
|
1.0
|
|
Iron binding site 7 out
of 7 in 4jye
Go back to
Iron Binding Sites List in 4jye
Iron binding site 7 out
of 7 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 7 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:Fe408
b:24.0
occ:0.40
|
FE4
|
A:F3S408
|
0.0
|
24.0
|
0.4
|
S3
|
A:F3S408
|
2.2
|
19.9
|
0.7
|
S4
|
A:F3S408
|
2.3
|
20.0
|
0.4
|
O
|
A:HOH501
|
2.3
|
20.7
|
0.4
|
SG
|
A:CYS311
|
2.7
|
22.9
|
1.0
|
FE3
|
A:F3S408
|
2.8
|
17.4
|
0.7
|
FE1
|
A:F3S408
|
2.8
|
14.7
|
0.7
|
CB
|
A:CYS311
|
3.7
|
24.0
|
1.0
|
CA
|
A:CYS311
|
3.9
|
23.9
|
1.0
|
S1
|
A:F3S408
|
4.0
|
13.9
|
0.7
|
OE2
|
A:GLU314
|
4.2
|
25.6
|
0.3
|
N
|
A:CYS311
|
4.2
|
23.8
|
1.0
|
CG
|
A:GLU314
|
4.2
|
25.4
|
0.3
|
CG
|
A:GLU314
|
4.3
|
25.6
|
0.7
|
O
|
A:HOH717
|
4.5
|
32.9
|
1.0
|
CD
|
A:GLU314
|
4.6
|
25.8
|
0.3
|
SG
|
A:CYS322
|
4.8
|
17.5
|
0.8
|
SG
|
A:CYS319
|
4.9
|
11.5
|
0.7
|
NH2
|
A:ARG279
|
4.9
|
19.9
|
1.0
|
SG
|
A:CYS322
|
5.0
|
17.2
|
0.2
|
|
Reference:
Y.Nicolet,
R.Rohac,
L.Martin,
J.C.Fontecilla-Camps.
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ISSN: ISSN 0027-8424
PubMed: 23596207
DOI: 10.1073/PNAS.1302388110
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