Iron in PDB 4m26: Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg

The structure of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg, PDB code: 4m26 was solved by C.Y.Chang, Y.C.Liu, S.Y.Lyu, C.C.Wu, T.L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.105, 116.697, 96.146, 90.00, 91.47, 90.00
R / Rfree (%)	20.8 / 26.5

The binding sites of Iron atom in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg (pdb code 4m26). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg, PDB code: 4m26:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:31.0 occ:1.00 O A:HOH637 2.0 32.2 1.0 O1 A:AKG403 2.1 33.4 1.0 NE2 A:HIS154 2.1 31.5 1.0 NE2 A:HIS303 2.1 26.8 1.0 OE1 A:GLU156 2.1 23.4 1.0 O5 A:AKG403 2.4 38.4 1.0 C1 A:AKG403 2.9 38.0 1.0 C2 A:AKG403 3.0 37.0 1.0 CD2 A:HIS303 3.1 26.6 1.0 CE1 A:HIS154 3.1 33.2 1.0 CD2 A:HIS154 3.1 33.8 1.0 CE1 A:HIS303 3.1 25.9 1.0 CD A:GLU156 3.2 26.2 1.0 OE2 A:GLU156 3.5 25.5 1.0 O2 A:AKG403 4.1 38.8 1.0 ND1 A:HIS154 4.2 35.4 1.0 ND1 A:HIS303 4.2 25.3 1.0 CG A:HIS303 4.2 26.3 1.0 CG A:HIS154 4.2 33.7 1.0 NH2 A:ARG321 4.3 31.1 1.0 CG A:GLU156 4.5 24.5 1.0 C3 A:AKG403 4.5 34.1 1.0 CB A:GLU156 4.8 24.5 1.0 O A:HIS303 5.0 31.4 1.0

Iron binding site 2 out of 5 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:55.0 occ:1.00 OD1 A:ASP157 2.1 35.0 1.0 O A:HOH643 2.3 41.5 1.0 NE2 A:HIS211 2.3 61.9 1.0 O A:HOH644 2.3 44.9 1.0 O A:HOH642 2.4 42.5 1.0 CG A:ASP157 3.2 30.9 1.0 CD2 A:HIS211 3.2 64.6 1.0 CE1 A:HIS211 3.3 63.5 1.0 OD2 A:ASP157 3.5 28.8 1.0 OG A:SER210 4.1 68.2 1.0 OD2 A:ASP208 4.1 71.3 1.0 NE2 A:GLN123 4.2 44.0 1.0 O A:HOH502 4.3 27.2 1.0 CG A:HIS211 4.4 66.5 1.0 ND1 A:HIS211 4.4 63.4 1.0 CB A:ASP157 4.5 28.6 1.0 CG A:ASP208 4.7 63.0 1.0 OE2 A:GLU156 4.8 25.5 1.0 CB A:ASP208 4.9 60.7 1.0 CA A:ASP157 4.9 27.8 1.0 CD A:GLN123 5.0 42.2 1.0

Iron binding site 3 out of 5 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:40.4 occ:1.00 NE2 B:HIS154 2.0 39.8 1.0 O1 B:AKG402 2.1 52.0 1.0 NE2 B:HIS303 2.2 29.9 1.0 OE1 B:GLU156 2.2 32.9 1.0 O B:HOH578 2.3 29.9 1.0 O5 B:AKG402 2.7 50.2 1.0 CE1 B:HIS154 2.8 42.2 1.0 C1 B:AKG402 3.0 54.0 1.0 CD2 B:HIS154 3.0 39.4 1.0 CE1 B:HIS303 3.1 28.9 1.0 CD B:GLU156 3.1 33.2 1.0 CD2 B:HIS303 3.2 28.6 1.0 C2 B:AKG402 3.2 52.3 1.0 OE2 B:GLU156 3.3 32.1 1.0 ND1 B:HIS154 4.0 42.2 1.0 O2 B:AKG402 4.1 57.1 1.0 CG B:HIS154 4.1 39.4 1.0 ND1 B:HIS303 4.2 28.7 1.0 CG B:HIS303 4.3 27.6 1.0 CG B:GLU156 4.5 32.8 1.0 CD2 B:LEU167 4.7 40.9 1.0 C3 B:AKG402 4.7 49.0 1.0 CB B:GLU156 4.9 32.4 1.0

Iron binding site 4 out of 5 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:30.7 occ:1.00 OB C:ZZU403 1.9 36.9 1.0 NE2 C:HIS303 1.9 23.3 1.0 NE2 C:HIS154 2.2 30.1 1.0 OE1 C:GLU156 2.2 30.4 1.0 O3 C:SIN402 2.2 38.2 1.0 O4 C:SIN402 2.7 39.2 1.0 C4 C:SIN402 2.8 39.6 1.0 CD2 C:HIS303 2.9 24.1 1.0 CE1 C:HIS303 3.0 24.1 1.0 CE1 C:HIS154 3.0 30.4 1.0 CD C:GLU156 3.1 31.4 1.0 CD2 C:HIS154 3.2 27.8 1.0 CB C:ZZU403 3.2 47.5 1.0 OE2 C:GLU156 3.3 37.5 1.0 CG C:ZZU403 3.9 47.2 1.0 ND1 C:HIS303 4.1 23.1 1.0 CG C:HIS303 4.1 23.2 1.0 ND1 C:HIS154 4.2 30.6 1.0 NH2 C:ARG321 4.3 58.2 1.0 C3 C:SIN402 4.3 37.2 1.0 CG C:HIS154 4.3 28.4 1.0 CA C:ZZU403 4.4 53.7 1.0 CD2 C:LEU167 4.5 32.3 1.0 CG C:GLU156 4.5 28.9 1.0 OXT C:ZZU403 4.7 61.6 1.0 N C:ZZU403 4.8 58.8 1.0 CB C:GLU156 4.8 27.2 1.0 C C:ZZU403 4.9 59.0 1.0 O C:HIS303 4.9 23.4 1.0

Iron binding site 5 out of 5 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe, Succinate, and (3S)-Hydroxy-L-Arg within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:31.4 occ:1.00 NE2 D:HIS303 2.0 26.9 1.0 OE1 D:GLU156 2.1 29.8 1.0 OB D:ZZU403 2.1 43.0 1.0 NE2 D:HIS154 2.1 30.5 1.0 O4 D:SIN402 2.1 37.2 1.0 O3 D:SIN402 2.5 35.9 1.0 C4 D:SIN402 2.6 38.8 1.0 CE1 D:HIS154 2.9 31.2 1.0 CE1 D:HIS303 3.0 30.6 1.0 CD D:GLU156 3.0 33.4 1.0 CD2 D:HIS303 3.0 27.6 1.0 OE2 D:GLU156 3.2 36.6 1.0 CD2 D:HIS154 3.2 30.8 1.0 CB D:ZZU403 3.4 48.6 1.0 CG D:ZZU403 4.0 47.7 1.0 ND1 D:HIS303 4.1 29.8 1.0 CG D:HIS303 4.1 28.4 1.0 C3 D:SIN402 4.1 37.1 1.0 ND1 D:HIS154 4.1 32.5 1.0 CG D:HIS154 4.3 31.5 1.0 CG D:GLU156 4.4 30.7 1.0 CA D:ZZU403 4.6 50.0 1.0 O D:HOH524 4.8 34.0 1.0 CB D:GLU156 4.8 30.3 1.0 N D:ZZU403 4.8 49.9 1.0 C2 D:SIN402 4.9 36.0 1.0 NH2 D:ARG321 5.0 53.0 1.0 CA D:GLU156 5.0 29.1 1.0

C.Y.Chang, S.Y.Lyu, Y.C.Liu, N.S.Hsu, C.C.Wu, C.F.Tang, K.H.Lin, J.Y.Ho, C.J.Wu, M.D.Tsai, T.L.Li. Biosynthesis of Streptolidine Involved Two Unexpected Intermediates Produced By A Dihydroxylase and A Cyclase Through Unusual Mechanisms. Angew.Chem.Int.Ed.Engl. V. 53 1943 2014.
ISSN: ISSN 1433-7851
PubMed: 24505011
DOI: 10.1002/ANIE.201307989