Iron in PDB 5fex: Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction)

The structure of Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction), PDB code: 5fex was solved by R.Rohac, P.Amara, A.Benjdia, L.Martin, P.Ruffie, A.Favier, O.Berteau, J.M.Mouesca, J.C.Fontecilla-Camps, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.02 / 1.32
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.120, 79.460, 86.570, 90.00, 90.00, 90.00
R / Rfree (%)	11.3 / 14.7

The structure of Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Iron atom in the Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction) (pdb code 5fex). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction), PDB code: 5fex:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:13.3 occ:1.00 FE1 A:SF4401 0.0 13.3 1.0 S3 A:SF4401 2.2 12.9 1.0 SG A:CYS70 2.3 13.2 1.0 S2 A:SF4401 2.3 14.0 1.0 S4 A:SF4401 2.3 13.7 1.0 FE2 A:SF4401 2.7 12.8 1.0 FE3 A:SF4401 2.7 13.2 1.0 FE4 A:SF4401 2.8 14.3 1.0 CB A:CYS70 3.1 12.7 1.0 S1 A:SF4401 3.9 13.7 1.0 CB A:LEU72 4.2 13.9 1.0 SD A:MET411 4.2 17.6 1.0 CA A:CYS70 4.6 12.6 1.0 CE A:MET411 4.6 21.7 1.0 SG A:CYS67 4.8 14.5 1.0 N A:ARG73 4.8 12.3 1.0 C A:LEU72 4.8 12.2 1.0 SG A:CYS63 4.8 11.9 1.0 CB A:CYS67 4.8 12.7 1.0 N A:MET411 4.8 14.6 1.0 N A:LEU72 4.9 12.6 1.0 CA A:LEU72 4.9 12.8 1.0 OXT A:MET411 4.9 14.9 1.0 CG A:LEU72 4.9 16.2 1.0

Iron binding site 2 out of 4 in the Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.8 occ:1.00 FE2 A:SF4401 0.0 12.8 1.0 SG A:CYS63 2.2 11.9 1.0 S4 A:SF4401 2.3 13.7 1.0 S3 A:SF4401 2.3 12.9 1.0 S1 A:SF4401 2.3 13.7 1.0 FE1 A:SF4401 2.7 13.3 1.0 FE3 A:SF4401 2.7 13.2 1.0 FE4 A:SF4401 3.0 14.3 1.0 CB A:CYS63 3.3 12.4 1.0 S2 A:SF4401 3.9 14.0 1.0 N A:MET411 4.1 14.6 1.0 CB A:LYS65 4.2 11.6 1.0 N A:GLU110 4.4 10.6 1.0 O A:LYS65 4.6 14.9 1.0 CA A:GLY109 4.6 10.3 1.0 N A:LYS65 4.7 12.2 1.0 CA A:CYS63 4.8 11.5 1.0 SG A:CYS70 4.8 13.2 1.0 CA A:LYS65 4.8 12.5 1.0 C A:LYS65 4.8 12.2 1.0 SG A:CYS67 4.8 14.5 1.0 CB A:LEU72 4.9 13.9 1.0 OXT A:MET411 5.0 14.9 1.0

Iron binding site 3 out of 4 in the Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:13.2 occ:1.00 FE3 A:SF4401 0.0 13.2 1.0 S1 A:SF4401 2.3 13.7 1.0 S4 A:SF4401 2.3 13.7 1.0 S2 A:SF4401 2.3 14.0 1.0 SG A:CYS67 2.4 14.5 1.0 FE1 A:SF4401 2.7 13.3 1.0 FE2 A:SF4401 2.7 12.8 1.0 FE4 A:SF4401 2.9 14.3 1.0 CB A:CYS67 3.2 12.7 1.0 O A:HOH559 3.9 18.3 1.0 S3 A:SF4401 3.9 12.9 1.0 OXT A:MET411 4.2 14.9 1.0 N A:CYS67 4.3 13.0 1.0 CB A:LYS65 4.4 11.6 1.0 CA A:CYS67 4.4 12.3 1.0 NH2 A:ARG172 4.5 13.6 1.0 CB A:CYS70 4.5 12.7 1.0 SG A:CYS70 4.7 13.2 1.0 OH A:TYR69 4.7 14.2 1.0 SG A:CYS63 4.7 11.9 1.0 O A:HOH569 4.8 14.8 1.0 CE1 A:TYR69 4.9 13.3 1.0 N A:MET411 4.9 14.6 1.0 CD A:LYS65 5.0 12.9 1.0

Iron binding site 4 out of 4 in the Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hyde From T. Maritima in Complex with Se-Adenosyl-L-Selenocysteine (Tfinal of the Reaction) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:14.3 occ:1.00 FE4 A:SF4401 0.0 14.3 1.0 OXT A:MET411 2.2 14.9 1.0 N A:MET411 2.3 14.6 1.0 S2 A:SF4401 2.4 14.0 1.0 S3 A:SF4401 2.4 12.9 1.0 S1 A:SF4401 2.5 13.7 1.0 FE1 A:SF4401 2.8 13.3 1.0 SD A:MET411 2.9 17.6 1.0 FE3 A:SF4401 2.9 13.2 1.0 FE2 A:SF4401 3.0 12.8 1.0 C A:MET411 3.1 15.0 1.0 CA A:MET411 3.2 14.1 1.0 CE A:MET411 3.8 21.7 1.0 CG A:MET411 3.9 20.2 1.0 CB A:MET411 3.9 15.8 1.0 O A:HOH559 4.1 18.3 1.0 O A:HOH569 4.1 14.8 1.0 S4 A:SF4401 4.2 13.7 1.0 O A:MET411 4.3 15.6 1.0 SG A:CYS63 4.8 11.9 1.0 SG A:CYS70 4.9 13.2 1.0

R.Rohac, P.Amara, A.Benjdia, L.Martin, P.Ruffie, A.Favier, O.Berteau, J.M.Mouesca, J.C.Fontecilla-Camps, Y.Nicolet. Carbon-Sulfur Bond-Forming Reaction Catalysed By the Radical Sam Enzyme Hyde. Nat.Chem. V. 8 491 2016.
ISSN: ESSN 1755-4349
PubMed: 27102684
DOI: 10.1038/NCHEM.2490