Iron in PDB 5few: Hyde From T. Maritima in Complex with S-Adenosyl-L-Cysteine (Final Product)

The structure of Hyde From T. Maritima in Complex with S-Adenosyl-L-Cysteine (Final Product), PDB code: 5few 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)	43.90 / 1.17
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.990, 78.970, 86.270, 90.00, 90.00, 90.00
R / Rfree (%)	11 / 13.2

The structure of Hyde From T. Maritima in Complex with S-Adenosyl-L-Cysteine (Final Product) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Hyde From T. Maritima in Complex with S-Adenosyl-L-Cysteine (Final Product) (pdb code 5few). 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 S-Adenosyl-L-Cysteine (Final Product), PDB code: 5few:
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 S-Adenosyl-L-Cysteine (Final Product)


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 S-Adenosyl-L-Cysteine (Final Product) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.7 occ:1.00 FE1 A:SF4401 0.0 11.7 1.0 S3 A:SF4401 2.2 11.6 1.0 SG A:CYS70 2.3 11.8 1.0 S2 A:SF4401 2.3 12.7 1.0 S4 A:SF4401 2.3 12.0 1.0 FE2 A:SF4401 2.7 11.2 1.0 FE3 A:SF4401 2.7 11.6 1.0 FE4 A:SF4401 2.9 12.7 1.0 CB A:CYS70 3.1 11.4 1.0 S1 A:SF4401 3.8 12.1 1.0 SD A:SAH411 4.2 11.8 0.1 SD A:MET409 4.2 18.2 0.8 CB A:LEU72 4.3 11.7 1.0 CA A:CYS70 4.5 11.1 1.0 CE A:MET409 4.6 20.1 0.8 CB A:CYS67 4.7 11.7 1.0 SG A:CYS67 4.7 12.8 1.0 N A:ARG73 4.8 10.9 1.0 SG A:CYS63 4.8 10.9 1.0 N A:MET409 4.8 14.5 0.8 C A:LEU72 4.8 11.1 1.0 OXT A:MET409 4.8 14.8 0.8 N A:LEU72 4.8 10.7 1.0 CA A:LEU72 4.9 11.0 1.0 OXT A:SAH411 4.9 7.2 0.1 CD2 A:LEU305 4.9 24.1 1.0 N A:SAH411 5.0 12.5 0.1 CG A:LEU72 5.0 15.2 1.0

Iron binding site 2 out of 4 in the Hyde From T. Maritima in Complex with S-Adenosyl-L-Cysteine (Final Product)


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 S-Adenosyl-L-Cysteine (Final Product) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.2 occ:1.00 FE2 A:SF4401 0.0 11.2 1.0 SG A:CYS63 2.3 10.9 1.0 S4 A:SF4401 2.3 12.0 1.0 S3 A:SF4401 2.3 11.6 1.0 S1 A:SF4401 2.3 12.1 1.0 FE1 A:SF4401 2.7 11.7 1.0 FE3 A:SF4401 2.7 11.6 1.0 FE4 A:SF4401 2.9 12.7 1.0 CB A:CYS63 3.4 10.4 1.0 S2 A:SF4401 3.9 12.7 1.0 N A:MET409 4.1 14.5 0.8 N A:SAH411 4.2 12.5 0.1 CB A:LYS65 4.2 10.6 1.0 N A:GLU110 4.4 9.7 1.0 CA A:GLY109 4.6 9.6 1.0 O A:LYS65 4.6 13.1 1.0 CA A:CYS63 4.7 10.1 1.0 SG A:CYS70 4.8 11.8 1.0 N A:LYS65 4.8 10.2 1.0 SG A:CYS67 4.8 12.8 1.0 C A:LYS65 4.8 10.4 1.0 CA A:LYS65 4.8 10.6 1.0 OXT A:MET409 4.9 14.8 0.8 CB A:LEU72 5.0 11.7 1.0 OXT A:SAH411 5.0 7.2 0.1

Iron binding site 3 out of 4 in the Hyde From T. Maritima in Complex with S-Adenosyl-L-Cysteine (Final Product)


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 S-Adenosyl-L-Cysteine (Final Product) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:11.6 occ:1.00 FE3 A:SF4401 0.0 11.6 1.0 S1 A:SF4401 2.3 12.1 1.0 S4 A:SF4401 2.3 12.0 1.0 S2 A:SF4401 2.3 12.7 1.0 SG A:CYS67 2.3 12.8 1.0 FE1 A:SF4401 2.7 11.7 1.0 FE2 A:SF4401 2.7 11.2 1.0 FE4 A:SF4401 2.9 12.7 1.0 CB A:CYS67 3.2 11.7 1.0 O A:HOH571 3.9 19.0 1.0 S3 A:SF4401 3.9 11.6 1.0 OXT A:MET409 4.1 14.8 0.8 OXT A:SAH411 4.2 7.2 0.1 N A:CYS67 4.3 11.2 1.0 CA A:CYS67 4.3 11.2 1.0 CB A:LYS65 4.4 10.6 1.0 NH2 A:ARG172 4.4 13.2 1.0 CB A:CYS70 4.5 11.4 1.0 OH A:TYR69 4.6 15.0 1.0 SG A:CYS70 4.6 11.8 1.0 SG A:CYS63 4.7 10.9 1.0 O A:HOH555 4.9 13.9 1.0 CE1 A:TYR69 4.9 12.6 1.0 N A:MET409 4.9 14.5 0.8 CD A:LYS65 5.0 12.5 1.0

Iron binding site 4 out of 4 in the Hyde From T. Maritima in Complex with S-Adenosyl-L-Cysteine (Final Product)


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 S-Adenosyl-L-Cysteine (Final Product) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:12.7 occ:1.00 FE4 A:SF4401 0.0 12.7 1.0 OXT A:MET409 2.2 14.8 0.8 N A:MET409 2.2 14.5 0.8 OXT A:SAH411 2.3 7.2 0.1 S2 A:SF4401 2.4 12.7 1.0 N A:SAH411 2.4 12.5 0.1 S3 A:SF4401 2.4 11.6 1.0 S1 A:SF4401 2.4 12.1 1.0 SD A:SAH411 2.8 11.8 0.1 SD A:MET409 2.8 18.2 0.8 FE1 A:SF4401 2.9 11.7 1.0 FE3 A:SF4401 2.9 11.6 1.0 FE2 A:SF4401 2.9 11.2 1.0 C A:MET409 3.0 12.7 0.8 C A:SAH411 3.1 8.2 0.1 CA A:MET409 3.1 12.1 0.8 CA A:SAH411 3.2 11.1 0.1 CG A:SAH411 3.4 9.9 0.1 CE A:MET409 3.8 20.1 0.8 CB A:SAH411 3.8 12.0 0.1 CG A:MET409 3.9 19.4 0.8 CB A:MET409 4.0 15.5 0.8 O A:HOH571 4.1 19.0 1.0 S4 A:SF4401 4.2 12.0 1.0 O A:HOH555 4.2 13.9 1.0 O A:SAH411 4.3 5.8 0.1 O A:MET409 4.3 14.7 0.8 C5' A:SAH411 4.5 13.2 0.1 SG A:CYS63 4.8 10.9 1.0 SG A:CYS70 4.9 11.8 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