Iron in PDB 6vp4: Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG

All present enzymatic activity of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG:
1.13.12.19; 1.14.20.7;

The structure of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG, PDB code: 6vp4 was solved by K.M.Davis, R.A.Copeland, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.77 / 1.83
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.73, 78.807, 195.905, 90, 92.67, 90
R / Rfree (%)	17.5 / 19.7

The binding sites of Iron atom in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG (pdb code 6vp4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG, PDB code: 6vp4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:18.1 occ:1.00 O1 A:AKG402 2.1 20.2 1.0 NE2 A:HIS268 2.1 17.8 1.0 NE2 A:HIS189 2.1 17.1 1.0 OD1 A:ASP191 2.2 22.2 1.0 O5 A:AKG402 2.3 25.1 1.0 OD2 A:ASP191 2.8 21.8 1.0 CG A:ASP191 2.8 21.6 1.0 C1 A:AKG402 2.9 22.0 1.0 CE1 A:HIS189 3.0 20.9 1.0 C2 A:AKG402 3.0 24.3 1.0 CE1 A:HIS268 3.1 18.3 1.0 CD2 A:HIS268 3.1 17.5 1.0 CD2 A:HIS189 3.2 18.8 1.0 O2 A:AKG402 4.1 22.7 1.0 ND1 A:HIS189 4.2 16.9 1.0 CD A:ARG403 4.2 22.2 1.0 ND1 A:HIS268 4.2 17.6 1.0 CG A:HIS268 4.2 16.6 1.0 CG A:HIS189 4.3 16.7 1.0 CB A:ASP191 4.3 19.2 1.0 C3 A:AKG402 4.5 22.9 1.0 CE1 A:PHE283 4.6 18.0 1.0 CZ A:PHE283 4.6 18.7 1.0 NH2 A:ARG403 4.9 18.6 1.0 CG A:ARG403 4.9 22.2 1.0 N A:ASP191 5.0 19.2 1.0

Iron binding site 2 out of 4 in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:15.7 occ:1.00 O2 B:AKG402 2.0 16.7 1.0 NE2 B:HIS268 2.1 16.9 1.0 NE2 B:HIS189 2.1 14.8 1.0 OD2 B:ASP191 2.3 21.5 1.0 O5 B:AKG402 2.4 21.2 1.0 OD1 B:ASP191 2.8 19.6 1.0 CG B:ASP191 2.9 19.6 1.0 C1 B:AKG402 2.9 22.9 1.0 C2 B:AKG402 3.0 23.2 1.0 CE1 B:HIS189 3.0 16.7 1.0 CE1 B:HIS268 3.1 15.5 1.0 CD2 B:HIS268 3.1 16.3 1.0 CD2 B:HIS189 3.2 14.5 1.0 O1 B:AKG402 4.1 22.6 1.0 CD B:ARG403 4.2 17.6 1.0 ND1 B:HIS189 4.2 14.9 1.0 ND1 B:HIS268 4.2 13.8 1.0 CG B:HIS268 4.2 13.3 1.0 CG B:HIS189 4.3 14.5 1.0 CB B:ASP191 4.3 15.3 1.0 C3 B:AKG402 4.5 22.0 1.0 CE1 B:PHE283 4.6 16.3 1.0 CZ B:PHE283 4.7 17.6 1.0 NH1 B:ARG403 4.9 17.7 1.0 CG B:ARG403 4.9 15.4 1.0 N B:ASP191 5.0 15.4 1.0

Iron binding site 3 out of 4 in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:19.3 occ:1.00 O2 C:AKG402 2.1 23.7 1.0 NE2 C:HIS268 2.1 18.0 1.0 NE2 C:HIS189 2.2 18.3 1.0 OD2 C:ASP191 2.2 23.5 1.0 O5 C:AKG402 2.3 25.0 1.0 OD1 C:ASP191 2.7 21.3 1.0 CG C:ASP191 2.8 21.0 1.0 C1 C:AKG402 2.9 26.7 1.0 C2 C:AKG402 3.0 26.1 1.0 CE1 C:HIS189 3.1 17.0 1.0 CE1 C:HIS268 3.1 20.4 1.0 CD2 C:HIS268 3.1 18.6 1.0 CD2 C:HIS189 3.2 17.7 1.0 O1 C:AKG402 4.1 24.6 1.0 ND1 C:HIS268 4.2 18.3 1.0 ND1 C:HIS189 4.2 16.0 1.0 CD C:ARG403 4.2 20.2 1.0 CG C:HIS268 4.3 19.2 1.0 CB C:ASP191 4.3 18.5 1.0 CG C:HIS189 4.3 17.2 1.0 C3 C:AKG402 4.5 24.7 1.0 CE1 C:PHE283 4.6 17.7 1.0 CZ C:PHE283 4.6 20.7 1.0 N C:ASP191 4.9 20.1 1.0 CG C:ARG403 4.9 21.1 1.0 NH1 C:ARG403 5.0 20.1 1.0

Iron binding site 4 out of 4 in the Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ethylene Forming Enzyme (Efe) in Complex with Fe(II), L-Arginine, and 2OG within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:18.7 occ:1.00 OD2 D:ASP191 2.1 24.8 1.0 O1 D:AKG402 2.1 22.6 1.0 NE2 D:HIS189 2.1 17.8 1.0 NE2 D:HIS268 2.2 17.6 1.0 O5 D:AKG402 2.2 26.5 1.0 CG D:ASP191 2.8 21.5 1.0 OD1 D:ASP191 2.8 24.4 1.0 C1 D:AKG402 2.9 26.6 1.0 C2 D:AKG402 3.0 27.8 1.0 CE1 D:HIS189 3.1 18.3 1.0 CD2 D:HIS268 3.1 17.8 1.0 CD2 D:HIS189 3.2 18.0 1.0 CE1 D:HIS268 3.2 18.1 1.0 O2 D:AKG402 4.1 25.8 1.0 ND1 D:HIS189 4.2 17.2 1.0 CB D:ASP191 4.2 17.6 1.0 CG D:HIS189 4.3 18.4 1.0 CG D:HIS268 4.3 16.5 1.0 ND1 D:HIS268 4.3 17.1 1.0 CD D:ARG403 4.3 21.6 1.0 C3 D:AKG402 4.4 25.4 1.0 CE2 D:PHE283 4.6 20.3 1.0 CZ D:PHE283 4.7 18.4 1.0 NH2 D:ARG403 4.9 21.3 1.0 N D:ASP191 5.0 21.7 1.0

R.A.Copeland, K.M.Davis, T.K.C.Shoda, E.J.Blaesi, A.K.Boal, C.Krebs, J.M.Bollinger Jr.. An Iron(IV)-Oxo Intermediate Initiating L-Arginine Oxidation But Not Ethylene Production By the 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme To Be Published.