Iron in PDB 4jy8: X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters

The structure of X-Ray Snapshots of Possible Intermediates in the Time Course of Synthesis and Degradation of Protein-Bound FE4S4 Clusters, PDB code: 4jy8 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)	43.24 / 2.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	82.430, 82.430, 217.340, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 24.1

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:

Chlorine

(Cl)

5 atoms

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 4jy8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 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: 4jy8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 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:76.8 occ:1.00 FE1 A:SF4401 0.0 76.8 1.0 SG A:CYS67 2.2 92.3 1.0 S4 A:SF4401 2.3 88.7 1.0 S3 A:SF4401 2.3 77.3 1.0 S2 A:SF4401 2.3 79.7 1.0 FE3 A:SF4401 2.7 70.7 1.0 FE2 A:SF4401 2.8 90.5 1.0 FE4 A:SF4401 2.8 75.1 1.0 CB A:CYS67 3.2 81.0 1.0 NH2 A:ARG172 3.7 76.5 1.0 S1 A:SF4401 4.0 65.7 1.0 NE A:ARG172 4.3 86.1 1.0 N A:CYS67 4.3 83.4 1.0 CA A:CYS67 4.4 80.9 1.0 CB A:LYS65 4.4 74.5 1.0 CZ A:ARG172 4.5 85.7 1.0 OH A:TYR69 4.5 91.6 1.0 SG A:CYS63 4.6 79.0 1.0 CB A:CYS70 4.8 99.4 1.0 SG A:CYS70 4.8 79.6 1.0 CD A:LYS65 4.9 73.9 1.0

Iron binding site 2 out of 8 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:90.5 occ:1.00 FE2 A:SF4401 0.0 90.5 1.0 S4 A:SF4401 2.3 88.7 1.0 S3 A:SF4401 2.3 77.3 1.0 S1 A:SF4401 2.3 65.7 1.0 FE4 A:SF4401 2.6 75.1 1.0 FE3 A:SF4401 2.7 70.7 1.0 FE1 A:SF4401 2.8 76.8 1.0 S A:H2S403 3.3 0.0 1.0 CL A:CL404 3.7 0.9 1.0 S2 A:SF4401 3.9 79.7 1.0 SG A:CYS63 4.6 79.0 1.0 SG A:CYS70 4.6 79.6 1.0 NH2 A:ARG172 4.8 76.5 1.0 SG A:CYS67 4.9 92.3 1.0 CA A:GLY109 5.0 65.5 1.0

Iron binding site 3 out of 8 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:70.7 occ:1.00 FE3 A:SF4401 0.0 70.7 1.0 SG A:CYS63 2.2 79.0 1.0 S2 A:SF4401 2.3 79.7 1.0 S1 A:SF4401 2.3 65.7 1.0 S4 A:SF4401 2.3 88.7 1.0 FE1 A:SF4401 2.7 76.8 1.0 FE4 A:SF4401 2.7 75.1 1.0 FE2 A:SF4401 2.7 90.5 1.0 CB A:CYS63 3.5 85.6 1.0 S3 A:SF4401 3.8 77.3 1.0 CB A:LYS65 4.3 74.5 1.0 N A:GLU110 4.3 65.9 1.0 CA A:GLY109 4.5 65.5 1.0 SG A:CYS70 4.6 79.6 1.0 SG A:CYS67 4.6 92.3 1.0 CA A:CYS63 4.8 73.3 1.0 O A:LYS65 4.9 75.6 1.0 N A:LYS65 4.9 75.0 1.0 C A:GLY109 4.9 79.5 1.0 CA A:LYS65 4.9 76.1 1.0 CG A:GLU110 4.9 65.6 1.0 CB A:LEU72 4.9 75.0 1.0 C A:LYS65 4.9 79.2 1.0

Iron binding site 4 out of 8 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:75.1 occ:1.00 FE4 A:SF4401 0.0 75.1 1.0 SG A:CYS70 2.2 79.6 1.0 S1 A:SF4401 2.3 65.7 1.0 S3 A:SF4401 2.3 77.3 1.0 S2 A:SF4401 2.3 79.7 1.0 FE2 A:SF4401 2.6 90.5 1.0 FE3 A:SF4401 2.7 70.7 1.0 FE1 A:SF4401 2.8 76.8 1.0 CB A:CYS70 3.0 99.4 1.0 S4 A:SF4401 3.9 88.7 1.0 CB A:LEU72 4.3 75.0 1.0 CB A:CYS67 4.4 81.0 1.0 SG A:CYS67 4.5 92.3 1.0 CA A:CYS70 4.6 53.1 1.0 SG A:CYS63 4.6 79.0 1.0 CD1 A:LEU72 4.8 71.9 1.0 CG A:LEU72 4.9 70.7 1.0 N A:ARG73 4.9 78.8 1.0 C A:LEU72 4.9 86.6 1.0 CE1 A:TYR69 4.9 85.5 1.0 N A:LEU72 4.9 82.4 1.0 CA A:LEU72 4.9 80.8 1.0

Iron binding site 5 out of 8 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:Fe402 b:64.0 occ:1.00 FE1 A:SF4402 0.0 64.0 1.0 OH A:TYR306 1.7 80.7 1.0 S3 A:SF4402 2.3 60.2 1.0 S2 A:SF4402 2.3 79.5 1.0 S4 A:SF4402 2.3 68.1 1.0 CZ A:TYR306 2.6 81.7 1.0 FE4 A:SF4402 2.6 59.9 1.0 FE3 A:SF4402 2.7 60.4 1.0 FE2 A:SF4402 2.8 60.1 1.0 CE2 A:TYR306 3.0 77.2 1.0 NH2 A:ARG279 3.7 0.6 1.0 CE1 A:TYR306 3.8 86.7 1.0 S1 A:SF4402 4.0 61.9 1.0 CZ A:ARG279 4.4 92.7 1.0 CD2 A:TYR306 4.4 77.0 1.0 CB A:CYS311 4.4 77.2 1.0 NH1 A:ARG279 4.5 89.7 1.0 CG A:GLN304 4.5 92.9 1.0 SG A:CYS311 4.6 82.2 1.0 SG A:CYS322 4.7 74.6 1.0 SG A:CYS319 4.8 79.9 0.9 CB A:GLN304 5.0 95.8 1.0

Iron binding site 6 out of 8 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:Fe402 b:60.1 occ:1.00 FE2 A:SF4402 0.0 60.1 1.0 S3 A:SF4402 2.3 60.2 1.0 S1 A:SF4402 2.3 61.9 1.0 S4 A:SF4402 2.3 68.1 1.0 SG A:CYS319 2.3 79.9 0.9 FE3 A:SF4402 2.6 60.4 1.0 FE4 A:SF4402 2.6 59.9 1.0 FE1 A:SF4402 2.8 64.0 1.0 CB A:CYS319 3.4 70.2 1.0 CA A:CYS319 3.8 89.5 1.0 S2 A:SF4402 3.9 79.5 1.0 OH A:TYR306 4.2 80.7 1.0 N A:CYS319 4.4 94.5 1.0 NH2 A:ARG300 4.5 72.8 1.0 CB A:CYS322 4.5 71.9 1.0 CD2 A:PHE313 4.6 89.0 1.0 SG A:CYS311 4.6 82.2 1.0 SG A:CYS322 4.6 74.6 1.0 CE2 A:PHE313 4.8 95.2 1.0 C A:ALA318 4.9 0.8 1.0

Iron binding site 7 out of 8 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:Fe402 b:60.4 occ:1.00 FE3 A:SF4402 0.0 60.4 1.0 SG A:CYS311 2.2 82.2 1.0 S4 A:SF4402 2.3 68.1 1.0 S1 A:SF4402 2.3 61.9 1.0 S2 A:SF4402 2.3 79.5 1.0 FE2 A:SF4402 2.6 60.1 1.0 FE4 A:SF4402 2.7 59.9 1.0 FE1 A:SF4402 2.7 64.0 1.0 CB A:CYS311 2.9 77.2 1.0 S3 A:SF4402 3.8 60.2 1.0 CD2 A:PHE313 4.1 89.0 1.0 OH A:TYR306 4.2 80.7 1.0 CE2 A:TYR306 4.2 77.2 1.0 CA A:CYS311 4.4 85.1 1.0 CE2 A:PHE313 4.6 95.2 1.0 CZ A:TYR306 4.7 81.7 1.0 C A:CYS311 4.8 87.0 1.0 SG A:CYS319 4.8 79.9 0.9 SG A:CYS322 4.9 74.6 1.0 CG A:PHE313 4.9 83.9 1.0 O A:CYS311 4.9 91.2 1.0

Iron binding site 8 out of 8 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 8 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:Fe402 b:59.9 occ:1.00 FE4 A:SF4402 0.0 59.9 1.0 S3 A:SF4402 2.3 60.2 1.0 S2 A:SF4402 2.3 79.5 1.0 S1 A:SF4402 2.3 61.9 1.0 SG A:CYS322 2.3 74.6 1.0 FE2 A:SF4402 2.6 60.1 1.0 FE1 A:SF4402 2.6 64.0 1.0 FE3 A:SF4402 2.7 60.4 1.0 CB A:CYS322 3.1 71.9 1.0 S4 A:SF4402 3.8 68.1 1.0 OH A:TYR306 4.2 80.7 1.0 NH2 A:ARG279 4.5 0.6 1.0 SG A:CYS311 4.5 82.2 1.0 CA A:CYS322 4.6 71.8 1.0 SG A:CYS319 4.6 79.9 0.9 CA A:CYS319 4.8 89.5 1.0 CB A:CYS319 5.0 70.2 1.0

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