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Iron in PDB 4jyf: 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: 4jyf 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 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.641, 78.762, 86.088, 90.00, 90.00, 90.00
R / Rfree (%) 13.3 / 16.6

Other elements in 4jyf:

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

Iron binding site 1 out of 4 in 4jyf

Go back to Iron Binding Sites List in 4jyf
Iron binding site 1 out of 4 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:12.3
occ:1.00
FE1 A:SF4401 0.0 12.3 1.0
S4 A:SF4401 2.3 12.8 1.0
S2 A:SF4401 2.3 12.8 1.0
SG A:CYS67 2.3 13.3 1.0
S3 A:SF4401 2.3 12.5 1.0
FE3 A:SF4401 2.7 12.1 1.0
FE4 A:SF4401 2.7 12.3 1.0
FE2 A:SF4401 2.9 13.0 1.0
CB A:CYS67 3.2 11.6 1.0
S1 A:SF4401 3.9 12.4 1.0
O A:HOH567 4.0 15.2 1.0
O A:SAH402 4.2 12.4 1.0
N A:CYS67 4.3 12.2 1.0
CB A:LYS65 4.4 11.6 1.0
CA A:CYS67 4.4 12.5 1.0
NH2 A:ARG172 4.5 14.1 1.0
CB A:CYS70 4.5 11.7 1.0
OH A:TYR69 4.6 13.6 1.0
SG A:CYS70 4.6 12.0 1.0
SG A:CYS63 4.7 12.0 1.0
O A:HOH519 4.9 14.2 1.0
CE1 A:TYR69 4.9 12.1 1.0
N A:SAH402 4.9 11.9 1.0
CD A:LYS65 5.0 12.2 1.0

Iron binding site 2 out of 4 in 4jyf

Go back to Iron Binding Sites List in 4jyf
Iron binding site 2 out of 4 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:13.0
occ:1.00
FE2 A:SF4401 0.0 13.0 1.0
N A:SAH402 2.2 11.9 1.0
O A:SAH402 2.3 12.4 1.0
S3 A:SF4401 2.3 12.5 1.0
S4 A:SF4401 2.4 12.8 1.0
S1 A:SF4401 2.4 12.4 1.0
FE4 A:SF4401 2.8 12.3 1.0
FE1 A:SF4401 2.9 12.3 1.0
FE3 A:SF4401 2.9 12.1 1.0
C A:SAH402 3.1 13.0 1.0
CA A:SAH402 3.1 12.5 1.0
SD A:SAH402 3.4 21.6 1.0
CG A:SAH402 3.7 17.5 1.0
CB A:SAH402 3.9 13.4 1.0
S2 A:SF4401 4.1 12.8 1.0
O A:HOH567 4.2 15.2 1.0
O A:HOH519 4.2 14.2 1.0
OXT A:SAH402 4.3 13.6 1.0
SG A:CYS63 4.7 12.0 1.0
SG A:CYS70 4.9 12.0 1.0

Iron binding site 3 out of 4 in 4jyf

Go back to Iron Binding Sites List in 4jyf
Iron binding site 3 out of 4 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:12.1
occ:1.00
FE3 A:SF4401 0.0 12.1 1.0
S2 A:SF4401 2.2 12.8 1.0
SG A:CYS63 2.3 12.0 1.0
S1 A:SF4401 2.3 12.4 1.0
S4 A:SF4401 2.3 12.8 1.0
FE4 A:SF4401 2.7 12.3 1.0
FE1 A:SF4401 2.7 12.3 1.0
FE2 A:SF4401 2.9 13.0 1.0
CB A:CYS63 3.4 12.2 1.0
S3 A:SF4401 3.9 12.5 1.0
N A:SAH402 4.1 11.9 1.0
CB A:LYS65 4.3 11.6 1.0
N A:GLU110 4.4 10.5 1.0
CA A:GLY109 4.6 11.0 1.0
O A:LYS65 4.6 14.1 1.0
SG A:CYS70 4.7 12.0 1.0
CA A:CYS63 4.8 11.2 1.0
SG A:CYS67 4.8 13.3 1.0
N A:LYS65 4.8 12.1 1.0
C A:LYS65 4.8 12.0 1.0
CA A:LYS65 4.9 12.0 1.0
CB A:LEU72 4.9 13.8 1.0
O A:LEU72 4.9 12.2 1.0
O A:SAH402 4.9 12.4 1.0

Iron binding site 4 out of 4 in 4jyf

Go back to Iron Binding Sites List in 4jyf
Iron binding site 4 out of 4 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:12.3
occ:1.00
FE4 A:SF4401 0.0 12.3 1.0
SG A:CYS70 2.2 12.0 1.0
S1 A:SF4401 2.2 12.4 1.0
S3 A:SF4401 2.3 12.5 1.0
S2 A:SF4401 2.3 12.8 1.0
FE3 A:SF4401 2.7 12.1 1.0
FE1 A:SF4401 2.7 12.3 1.0
FE2 A:SF4401 2.8 13.0 1.0
CB A:CYS70 3.1 11.7 1.0
S4 A:SF4401 3.9 12.8 1.0
CB A:LEU72 4.3 13.8 1.0
CD2 A:LEU305 4.4 17.6 1.0
CA A:CYS70 4.5 11.8 1.0
SD A:SAH402 4.6 21.6 1.0
N A:SAH402 4.7 11.9 1.0
CB A:CYS67 4.7 11.6 1.0
SG A:CYS67 4.8 13.3 1.0
N A:ARG73 4.8 12.3 1.0
C A:LEU72 4.8 12.3 1.0
SG A:CYS63 4.8 12.0 1.0
N A:LEU72 4.8 12.4 1.0
O A:SAH402 4.9 12.4 1.0
CA A:LEU72 4.9 12.6 1.0
CG A:LEU72 4.9 14.6 1.0
C A:CYS70 5.0 12.2 1.0

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 15:38:58 2020

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