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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:

Bromine (Br) 5 atoms

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

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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

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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

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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. 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 04:53:42 2024

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