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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:

Chlorine (Cl) 2 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 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

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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

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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

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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: Sun Dec 13 15:38:52 2020

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