Iron in PDB 3iiz: X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine

The structure of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine, PDB code: 3iiz was solved by Y.Nicolet, P.Amara, J.M.Mouesca, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.16 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.628, 78.780, 85.943, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 18.4

The structure of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Iron atom in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine (pdb code 3iiz). 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 Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine, PDB code: 3iiz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2460 b:12.3 occ:1.00 FE1 A:SF42460 0.0 12.3 1.0 S4 A:SF42460 2.3 12.2 1.0 S2 A:SF42460 2.3 12.6 1.0 S3 A:SF42460 2.3 11.8 1.0 SG A:CYS67 2.3 13.0 1.0 FE3 A:SF42460 2.7 11.6 1.0 FE4 A:SF42460 2.7 12.0 1.0 FE2 A:SF42460 2.8 12.7 1.0 CB A:CYS67 3.2 11.3 1.0 S1 A:SF42460 3.9 12.1 1.0 O A:HOH514 3.9 16.1 1.0 O A:SAM1501 4.2 12.6 1.0 N A:CYS67 4.3 11.2 1.0 CA A:CYS67 4.3 11.1 1.0 CB A:LYS65 4.4 11.2 1.0 CB A:CYS70 4.4 11.4 1.0 NH2 A:ARG172 4.5 13.7 1.0 SG A:CYS70 4.6 13.3 1.0 OH A:TYR69 4.7 12.0 1.0 SG A:CYS63 4.7 11.8 1.0 CE1 A:TYR69 4.8 10.3 1.0 O A:HOH466 4.8 12.9 1.0 N A:SAM1501 5.0 13.0 1.0 CZ A:TYR69 5.0 10.8 1.0

Iron binding site 2 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2460 b:12.7 occ:1.00 FE2 A:SF42460 0.0 12.7 1.0 O A:SAM1501 2.3 12.6 1.0 S3 A:SF42460 2.3 11.8 1.0 S4 A:SF42460 2.3 12.2 1.0 N A:SAM1501 2.3 13.0 1.0 S1 A:SF42460 2.4 12.1 1.0 FE4 A:SF42460 2.8 12.0 1.0 FE1 A:SF42460 2.8 12.3 1.0 FE3 A:SF42460 2.8 11.6 1.0 C A:SAM1501 3.1 12.7 1.0 CA A:SAM1501 3.2 14.0 1.0 SD A:SAM1501 3.3 17.2 1.0 CG A:SAM1501 3.7 14.6 1.0 CB A:SAM1501 4.0 13.4 1.0 S2 A:SF42460 4.0 12.6 1.0 O A:HOH466 4.0 12.9 1.0 O A:HOH514 4.1 16.1 1.0 CE A:SAM1501 4.1 16.4 0.5 OXT A:SAM1501 4.2 12.4 1.0 SG A:CYS63 4.7 11.8 1.0 SG A:CYS70 4.9 13.3 1.0 C5' A:SAM1501 4.9 17.0 1.0 SG A:CYS67 5.0 13.0 1.0

Iron binding site 3 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2460 b:11.6 occ:1.00 FE3 A:SF42460 0.0 11.6 1.0 S2 A:SF42460 2.2 12.6 1.0 SG A:CYS63 2.3 11.8 1.0 S1 A:SF42460 2.3 12.1 1.0 S4 A:SF42460 2.3 12.2 1.0 FE4 A:SF42460 2.7 12.0 1.0 FE1 A:SF42460 2.7 12.3 1.0 FE2 A:SF42460 2.8 12.7 1.0 CB A:CYS63 3.4 10.6 1.0 S3 A:SF42460 3.9 11.8 1.0 N A:SAM1501 4.1 13.0 1.0 CB A:LYS65 4.3 11.2 1.0 N A:GLU110 4.4 8.7 1.0 O A:LYS65 4.6 11.8 1.0 CA A:GLY109 4.6 9.6 1.0 CA A:CYS63 4.7 10.0 1.0 SG A:CYS70 4.7 13.3 1.0 SG A:CYS67 4.8 13.0 1.0 N A:LYS65 4.8 11.1 1.0 C A:LYS65 4.8 11.1 1.0 CA A:LYS65 4.9 10.5 1.0 O A:SAM1501 4.9 12.6 1.0 O A:LEU72 5.0 10.8 1.0 CB A:LEU72 5.0 11.4 1.0

Iron binding site 4 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2460 b:12.0 occ:1.00 FE4 A:SF42460 0.0 12.0 1.0 S1 A:SF42460 2.2 12.1 1.0 SG A:CYS70 2.3 13.3 1.0 S3 A:SF42460 2.3 11.8 1.0 S2 A:SF42460 2.3 12.6 1.0 FE3 A:SF42460 2.7 11.6 1.0 FE1 A:SF42460 2.7 12.3 1.0 FE2 A:SF42460 2.8 12.7 1.0 CB A:CYS70 3.0 11.4 1.0 S4 A:SF42460 3.9 12.2 1.0 CE A:SAM1501 4.1 16.4 0.5 CB A:LEU72 4.3 11.4 1.0 SD A:SAM1501 4.4 17.2 1.0 CA A:CYS70 4.5 11.7 1.0 N A:ARG73 4.8 10.3 1.0 SG A:CYS67 4.8 13.0 1.0 CB A:CYS67 4.8 11.3 1.0 SG A:CYS63 4.8 11.8 1.0 N A:SAM1501 4.8 13.0 1.0 O A:SAM1501 4.8 12.6 1.0 C A:LEU72 4.8 10.3 1.0 N A:LEU72 4.9 11.1 1.0 CG A:LEU72 4.9 13.0 1.0 CD2 A:LEU305 4.9 23.1 1.0 CA A:LEU72 4.9 10.7 1.0 C A:CYS70 5.0 11.6 1.0

Iron binding site 5 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2648 b:19.7 occ:0.60 FE1 A:FES2648 0.0 19.7 0.6 SG A:CYS311 2.1 24.7 0.7 S A:H2S2649 2.1 15.4 0.9 S2 A:FES2648 2.2 21.3 0.6 S1 A:FES2648 2.2 18.4 0.6 FE2 A:FES2648 2.8 21.9 0.6 SG A:CYS319 3.2 14.8 1.0 CB A:CYS311 3.3 21.0 1.0 O A:HOH569 3.3 24.3 1.0 CB A:CYS319 3.7 11.0 1.0 CA A:CYS311 3.8 21.4 1.0 CA A:CYS319 4.3 10.9 1.0 N A:CYS311 4.3 21.6 1.0 NH1 A:ARG279 4.4 18.6 1.0 NH2 A:ARG279 4.5 16.9 1.0 S A:H2S2650 4.6 20.3 0.7 CZ A:ARG279 4.9 16.3 1.0 SG A:CYS322 5.0 15.1 0.7

Iron binding site 6 out of 6 in the X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of the Fefe-Hydrogenase Maturase Hyde From T. Maritima in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2648 b:21.9 occ:0.60 FE2 A:FES2648 0.0 21.9 0.6 S1 A:FES2648 2.2 18.4 0.6 S2 A:FES2648 2.2 21.3 0.6 NH2 A:ARG279 2.2 16.9 1.0 S A:H2S2650 2.3 20.3 0.7 FE1 A:FES2648 2.8 19.7 0.6 NH1 A:ARG279 2.9 18.6 1.0 CZ A:ARG279 2.9 16.3 1.0 SG A:CYS322 3.6 15.1 0.7 NE A:ARG279 4.2 15.2 1.0 CG1 A:VAL323 4.2 11.3 1.0 SG A:CYS311 4.2 24.7 0.7 O A:HOH569 4.4 24.3 1.0 CE A:MET326 4.4 11.1 1.0 CB A:CYS322 4.4 12.8 0.7 CB A:CYS322 4.4 13.2 0.3 S A:H2S2649 4.4 15.4 0.9 CD1 A:ILE310 4.6 22.6 0.7 O A:HOH585 4.8 25.1 1.0

Y.Nicolet, P.Amara, J.-M.Mouesca, J.C.Fontecilla-Camps. Unexpected Electron Transfer Mechanism Upon Adomet Cleavage in Radical Sam Proteins Proc.Natl.Acad.Sci.Usa 2009.
ISSN: ESSN 1091-6490
PubMed: 19706452
DOI: 10.1073/PNAS.0904385106