Iron in PDB 3dy5: Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla

All present enzymatic activity of Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla:
1.13.11.40; 4.2.1.92;

The structure of Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla, PDB code: 3dy5 was solved by N.C.Gilbert, M.Niebuhr, H.Tsuruta, M.E.Newcomer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.86 / 3.51
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	235.520, 77.493, 157.966, 90.00, 112.45, 90.00
R / Rfree (%)	27.3 / 32.2

The binding sites of Iron atom in the Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla (pdb code 3dy5). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla, PDB code: 3dy5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1099 b:2.0 occ:1.00 ND2 A:ASN947 1.8 2.0 1.0 NE2 A:HIS757 1.9 2.0 1.0 NE2 A:HIS943 2.0 2.0 1.0 OXT A:ILE1066 2.2 2.0 1.0 NE2 A:HIS762 2.3 2.0 1.0 CE1 A:HIS757 2.7 2.0 1.0 CE1 A:HIS943 2.8 2.0 1.0 C A:ILE1066 2.9 2.0 1.0 CD2 A:HIS757 3.0 2.0 1.0 CD2 A:HIS943 3.1 2.0 1.0 CE1 A:HIS762 3.1 2.0 1.0 CG A:ASN947 3.1 2.0 1.0 O A:ILE1066 3.2 2.0 1.0 CD2 A:HIS762 3.4 2.0 1.0 ND1 A:HIS757 3.9 2.0 1.0 OD1 A:ASN947 3.9 2.0 1.0 ND1 A:HIS943 4.0 2.0 1.0 CG A:HIS757 4.1 2.0 1.0 CB A:ASN947 4.1 2.0 1.0 CG A:HIS943 4.1 2.0 1.0 CA A:ILE1066 4.2 2.0 1.0 ND1 A:HIS762 4.3 2.0 1.0 N A:ILE1066 4.4 2.0 1.0 CG A:HIS762 4.4 2.0 1.0 CG2 A:THR1064 4.8 2.0 1.0

Iron binding site 2 out of 4 in the Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1099 b:18.6 occ:1.00 ND2 C:ASN947 1.8 2.0 1.0 NE2 C:HIS757 1.9 2.0 1.0 NE2 C:HIS943 2.0 2.0 1.0 NE2 C:HIS762 2.2 2.0 1.0 OXT C:ILE1066 2.4 2.0 1.0 CE1 C:HIS757 2.7 2.0 1.0 CE1 C:HIS943 2.8 2.0 1.0 CD2 C:HIS757 3.0 2.0 1.0 CE1 C:HIS762 3.1 2.0 1.0 CD2 C:HIS943 3.1 2.0 1.0 CG C:ASN947 3.1 2.0 1.0 CD2 C:HIS762 3.3 2.0 1.0 C C:ILE1066 3.5 2.0 1.0 OD1 C:ASN947 3.9 2.0 1.0 O C:ILE1066 3.9 2.0 1.0 ND1 C:HIS757 3.9 2.0 1.0 ND1 C:HIS943 4.0 2.0 1.0 CG C:HIS757 4.1 2.0 1.0 CB C:ASN947 4.1 2.0 1.0 CG C:HIS943 4.1 2.0 1.0 ND1 C:HIS762 4.2 2.0 1.0 CG C:HIS762 4.4 2.0 1.0 CA C:ILE1066 4.8 2.0 1.0 N C:ILE1066 4.9 2.0 1.0

Iron binding site 3 out of 4 in the Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1100 b:2.0 occ:1.00 FE A:HEM1100 0.0 2.0 1.0 OH A:TYR353 1.9 2.0 1.0 NC A:HEM1100 2.0 2.0 1.0 NB A:HEM1100 2.0 2.0 1.0 NA A:HEM1100 2.1 2.0 1.0 ND A:HEM1100 2.1 2.0 1.0 C1C A:HEM1100 3.0 2.0 1.0 C4C A:HEM1100 3.0 2.0 1.0 C4B A:HEM1100 3.0 2.0 1.0 C1B A:HEM1100 3.0 2.0 1.0 C1D A:HEM1100 3.1 2.0 1.0 CZ A:TYR353 3.1 2.0 1.0 C4A A:HEM1100 3.1 2.0 1.0 C4D A:HEM1100 3.1 2.0 1.0 C1A A:HEM1100 3.1 2.0 1.0 CHC A:HEM1100 3.4 2.0 1.0 CHD A:HEM1100 3.4 2.0 1.0 CHB A:HEM1100 3.4 2.0 1.0 CHA A:HEM1100 3.5 2.0 1.0 CE1 A:TYR353 3.7 2.0 1.0 CE2 A:TYR353 4.1 2.0 1.0 NH2 A:ARG349 4.1 2.0 1.0 OG1 A:THR66 4.1 2.0 1.0 C3C A:HEM1100 4.2 2.0 1.0 C2C A:HEM1100 4.2 2.0 1.0 NE A:ARG349 4.2 2.0 1.0 C3B A:HEM1100 4.2 2.0 1.0 CE1 A:HIS67 4.3 2.0 1.0 C2B A:HEM1100 4.3 2.0 1.0 C2D A:HEM1100 4.3 2.0 1.0 C3A A:HEM1100 4.3 2.0 1.0 C3D A:HEM1100 4.3 2.0 1.0 C2A A:HEM1100 4.3 2.0 1.0 CZ A:ARG349 4.4 2.0 1.0 ND1 A:HIS67 4.7 2.0 1.0

Iron binding site 4 out of 4 in the Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Allene Oxide Synthase 8R-Lipoxygenase From Plexaura Homomalla within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe1100 b:2.0 occ:1.00 FE C:HEM1100 0.0 2.0 1.0 NC C:HEM1100 2.0 2.0 1.0 OH C:TYR353 2.0 2.0 1.0 NB C:HEM1100 2.0 2.0 1.0 ND C:HEM1100 2.1 2.0 1.0 NA C:HEM1100 2.1 2.0 1.0 C1C C:HEM1100 3.0 2.0 1.0 C4C C:HEM1100 3.0 2.0 1.0 C4B C:HEM1100 3.0 2.0 1.0 C1D C:HEM1100 3.0 2.0 1.0 C1B C:HEM1100 3.0 2.0 1.0 CZ C:TYR353 3.1 2.0 1.0 C4A C:HEM1100 3.1 2.0 1.0 C4D C:HEM1100 3.2 2.0 1.0 C1A C:HEM1100 3.2 2.0 1.0 CHC C:HEM1100 3.3 2.0 1.0 CHD C:HEM1100 3.3 2.0 1.0 CHB C:HEM1100 3.5 2.0 1.0 CHA C:HEM1100 3.5 2.0 1.0 CE1 C:TYR353 3.7 2.0 1.0 NH2 C:ARG349 4.1 2.0 1.0 CE2 C:TYR353 4.1 2.0 1.0 OG1 C:THR66 4.1 2.0 1.0 C3C C:HEM1100 4.2 2.0 1.0 C2C C:HEM1100 4.2 2.0 1.0 C3B C:HEM1100 4.2 2.0 1.0 NE C:ARG349 4.2 2.0 1.0 C2B C:HEM1100 4.3 2.0 1.0 CE1 C:HIS67 4.3 2.0 1.0 C2D C:HEM1100 4.3 2.0 1.0 C3D C:HEM1100 4.4 2.0 1.0 C3A C:HEM1100 4.4 2.0 1.0 C2A C:HEM1100 4.4 2.0 1.0 CZ C:ARG349 4.5 2.0 1.0 ND1 C:HIS67 4.7 2.0 1.0

N.C.Gilbert, M.Niebuhr, H.Tsuruta, T.Bordelon, O.Ridderbusch, A.Dassey, A.R.Brash, S.G.Bartlett, M.E.Newcomer. A Covalent Linker Allows For Membrane Targeting of An Oxylipin Biosynthetic Complex. Biochemistry V. 47 10665 2008.
ISSN: ISSN 0006-2960
PubMed: 18785758
DOI: 10.1021/BI800751P