Iron in PDB 5fep: Hyde From T. Maritima in Complex with (2R,4R)-Metda

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Metda, PDB code: 5fep 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 / 1.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.160, 80.020, 86.360, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 18.8

The structure of Hyde From T. Maritima in Complex with (2R,4R)-Metda also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Hyde From T. Maritima in Complex with (2R,4R)-Metda (pdb code 5fep). 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 (2R,4R)-Metda, PDB code: 5fep:
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 (2R,4R)-Metda


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 (2R,4R)-Metda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:18.2 occ:1.00 FE1 A:SF4401 0.0 18.2 1.0 S3 A:SF4401 2.2 16.7 1.0 S2 A:SF4401 2.3 18.1 1.0 S4 A:SF4401 2.3 18.7 1.0 SG A:CYS70 2.3 17.8 1.0 FE2 A:SF4401 2.7 17.4 1.0 FE3 A:SF4401 2.7 17.9 1.0 FE4 A:SF4401 2.8 21.0 1.0 CB A:CYS70 3.1 18.5 1.0 CE A:SAM407 3.8 28.9 1.0 S1 A:SF4401 3.9 17.8 1.0 CB A:LEU72 4.2 19.4 1.0 SD A:SAM407 4.3 25.9 1.0 CA A:CYS70 4.6 18.1 1.0 OXT A:SAM407 4.8 22.8 1.0 N A:ARG73 4.8 17.5 1.0 SG A:CYS67 4.8 18.9 1.0 SG A:CYS63 4.8 16.0 1.0 C A:LEU72 4.8 18.5 1.0 CB A:CYS67 4.8 18.6 1.0 N A:LEU72 4.9 17.3 1.0 N A:SAM407 4.9 20.4 1.0 CA A:LEU72 4.9 17.4 1.0 CG A:LEU72 4.9 23.3 1.0

Iron binding site 2 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Metda


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 (2R,4R)-Metda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:17.4 occ:1.00 FE2 A:SF4401 0.0 17.4 1.0 SG A:CYS63 2.2 16.0 1.0 S4 A:SF4401 2.2 18.7 1.0 S3 A:SF4401 2.3 16.7 1.0 S1 A:SF4401 2.3 17.8 1.0 FE1 A:SF4401 2.7 18.2 1.0 FE3 A:SF4401 2.7 17.9 1.0 FE4 A:SF4401 2.8 21.0 1.0 CB A:CYS63 3.3 15.3 1.0 S2 A:SF4401 3.9 18.1 1.0 N A:SAM407 4.2 20.4 1.0 CB A:LYS65 4.2 15.7 1.0 N A:GLU110 4.4 14.4 1.0 CA A:GLY109 4.6 16.1 1.0 O A:LYS65 4.6 20.4 1.0 CA A:CYS63 4.8 15.2 1.0 SG A:CYS67 4.8 18.9 1.0 C A:LYS65 4.8 15.3 1.0 SG A:CYS70 4.8 17.8 1.0 N A:LYS65 4.8 16.6 1.0 OXT A:SAM407 4.8 22.8 1.0 CA A:LYS65 4.8 17.2 1.0 CB A:LEU72 4.9 19.4 1.0 O A:LEU72 5.0 17.6 1.0

Iron binding site 3 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Metda


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 (2R,4R)-Metda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:17.9 occ:1.00 FE3 A:SF4401 0.0 17.9 1.0 S1 A:SF4401 2.3 17.8 1.0 S2 A:SF4401 2.3 18.1 1.0 S4 A:SF4401 2.3 18.7 1.0 SG A:CYS67 2.3 18.9 1.0 FE1 A:SF4401 2.7 18.2 1.0 FE2 A:SF4401 2.7 17.4 1.0 FE4 A:SF4401 2.9 21.0 1.0 CB A:CYS67 3.2 18.6 1.0 O A:HOH659 3.8 22.6 1.0 S3 A:SF4401 3.9 16.7 1.0 OXT A:SAM407 4.2 22.8 1.0 N A:CYS67 4.3 18.3 1.0 CA A:CYS67 4.4 17.4 1.0 CB A:LYS65 4.4 15.7 1.0 CB A:CYS70 4.5 18.5 1.0 NH2 A:ARG172 4.5 17.1 1.0 OH A:TYR69 4.6 19.8 1.0 SG A:CYS70 4.7 17.8 1.0 SG A:CYS63 4.7 16.0 1.0 CE1 A:TYR69 4.8 19.8 1.0 O A:HOH569 4.9 19.9 1.0 NE A:ARG172 5.0 19.0 1.0 CZ A:TYR69 5.0 19.1 1.0

Iron binding site 4 out of 4 in the Hyde From T. Maritima in Complex with (2R,4R)-Metda


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 (2R,4R)-Metda within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:21.0 occ:1.00 FE4 A:SF4401 0.0 21.0 1.0 OXT A:SAM407 2.2 22.8 1.0 N A:SAM407 2.3 20.4 1.0 S3 A:SF4401 2.3 16.7 1.0 S1 A:SF4401 2.4 17.8 1.0 S2 A:SF4401 2.4 18.1 1.0 FE1 A:SF4401 2.8 18.2 1.0 FE2 A:SF4401 2.8 17.4 1.0 FE3 A:SF4401 2.9 17.9 1.0 C A:SAM407 3.1 25.9 1.0 SD A:SAM407 3.2 25.9 1.0 CA A:SAM407 3.3 23.0 1.0 CG A:SAM407 3.7 23.2 1.0 CE A:SAM407 3.9 28.9 1.0 S4 A:SF4401 4.0 18.7 1.0 CB A:SAM407 4.0 25.1 1.0 O A:HOH659 4.0 22.6 1.0 O A:HOH569 4.1 19.9 1.0 O A:SAM407 4.3 21.7 1.0 SG A:CYS63 4.7 16.0 1.0 C5' A:SAM407 4.9 23.0 1.0 SG A:CYS70 4.9 17.8 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