Iron in PDB 4m25: Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid

The structure of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid, PDB code: 4m25 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 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.205, 117.262, 96.556, 90.00, 91.86, 90.00
R / Rfree (%)	19.4 / 23.2

The binding sites of Iron atom in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid (pdb code 4m25). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid, PDB code: 4m25:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid


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 and Alpha-Ketoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:24.1 occ:1.00 NE2 A:HIS303 2.0 21.7 1.0 OE1 A:GLU156 2.1 19.8 1.0 O1 A:AKG403 2.2 25.6 1.0 NE2 A:HIS154 2.2 25.1 1.0 O A:HOH601 2.2 27.6 1.0 O5 A:AKG403 2.4 27.1 1.0 CE1 A:HIS303 2.8 21.7 1.0 C1 A:AKG403 3.0 26.6 1.0 CD2 A:HIS303 3.0 21.9 1.0 C2 A:AKG403 3.0 25.8 1.0 CD2 A:HIS154 3.1 24.9 1.0 CD A:GLU156 3.1 20.6 1.0 CE1 A:HIS154 3.2 25.6 1.0 OE2 A:GLU156 3.5 22.8 1.0 ND1 A:HIS303 4.0 20.1 1.0 CG A:HIS303 4.1 21.2 1.0 O2 A:AKG403 4.2 25.2 1.0 NH2 A:ARG321 4.2 26.1 1.0 CG A:HIS154 4.3 24.8 1.0 ND1 A:HIS154 4.3 25.6 1.0 O A:HOH704 4.3 34.4 1.0 O A:HOH628 4.3 39.6 1.0 CG A:GLU156 4.5 19.6 1.0 C3 A:AKG403 4.5 25.0 1.0 CB A:GLU156 4.8 20.2 1.0 O A:HIS303 5.0 24.0 1.0

Iron binding site 2 out of 8 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid


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 and Alpha-Ketoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe402 b:26.5 occ:1.00 OD1 A:ASP157 2.0 23.1 1.0 O A:HOH698 2.1 28.6 1.0 O A:HOH700 2.2 25.6 1.0 O A:HOH699 2.2 23.6 1.0 O A:HOH697 2.3 25.4 1.0 NE2 A:HIS211 2.3 28.6 1.0 CG A:ASP157 3.0 23.8 1.0 CD2 A:HIS211 3.3 31.8 1.0 CE1 A:HIS211 3.3 33.6 1.0 OD2 A:ASP157 3.4 23.5 1.0 O A:HOH705 4.0 33.0 1.0 O A:HOH634 4.1 24.5 1.0 O A:HOH506 4.2 23.2 1.0 NE2 A:GLN123 4.3 28.9 1.0 O A:HOH555 4.3 23.2 1.0 CB A:ASP157 4.4 22.3 1.0 O A:HOH856 4.4 46.8 1.0 O A:HOH696 4.4 34.2 1.0 CG A:HIS211 4.5 33.7 1.0 ND1 A:HIS211 4.5 31.9 1.0 OD2 A:ASP208 4.6 38.2 1.0 OE2 A:GLU156 4.6 22.8 1.0 CA A:ASP157 4.8 20.8 1.0 N A:ASP157 4.9 19.7 1.0 O A:HOH706 5.0 33.2 1.0

Iron binding site 3 out of 8 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid


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 and Alpha-Ketoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:30.4 occ:1.00 O1 B:AKG403 2.0 33.2 1.0 NE2 B:HIS154 2.1 30.1 1.0 NE2 B:HIS303 2.2 26.9 1.0 OE1 B:GLU156 2.2 24.9 1.0 O B:HOH645 2.2 32.6 1.0 O5 B:AKG403 2.4 29.4 1.0 C1 B:AKG403 2.8 36.4 1.0 CE1 B:HIS303 3.0 25.1 1.0 C2 B:AKG403 3.0 32.6 1.0 CE1 B:HIS154 3.1 32.0 1.0 CD B:GLU156 3.1 27.1 1.0 CD2 B:HIS154 3.1 28.7 1.0 CD2 B:HIS303 3.2 24.6 1.0 OE2 B:GLU156 3.4 29.5 1.0 O2 B:AKG403 4.0 31.5 1.0 ND1 B:HIS303 4.1 23.8 1.0 O B:HOH737 4.2 46.4 1.0 ND1 B:HIS154 4.2 31.6 1.0 CG B:HIS303 4.2 23.5 1.0 CG B:HIS154 4.3 29.7 1.0 NH2 B:ARG321 4.3 33.9 1.0 CG B:GLU156 4.5 24.2 1.0 CD1 B:LEU167 4.5 33.7 1.0 C3 B:AKG403 4.5 30.9 1.0 CB B:GLU156 4.8 25.5 1.0

Iron binding site 4 out of 8 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid


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 and Alpha-Ketoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:48.1 occ:1.00 OD1 B:ASP157 2.1 36.5 1.0 O B:HOH738 2.4 43.4 1.0 NE2 B:HIS211 2.6 76.3 1.0 CG B:ASP157 3.0 33.9 1.0 CE1 B:HIS211 3.3 76.3 1.0 OD2 B:ASP157 3.4 32.7 1.0 CD2 B:HIS211 3.7 78.8 1.0 O B:HOH651 3.8 33.0 1.0 NE2 B:GLN123 3.9 41.5 1.0 CB B:ASP157 4.4 30.1 1.0 O B:HOH652 4.5 40.2 1.0 ND1 B:HIS211 4.5 78.1 1.0 OE2 B:GLU156 4.6 29.5 1.0 CG B:HIS211 4.7 81.6 1.0 CA B:ASP157 4.8 28.2 1.0 N B:ASP157 4.8 29.0 1.0 CD B:GLN123 4.8 43.2 1.0 CB B:SER210 4.9 82.8 1.0 CB B:ASP208 4.9 79.8 1.0 OG B:SER210 5.0 81.7 1.0 OE1 B:GLN123 5.0 45.4 1.0 CE1 B:PHE159 5.0 33.4 1.0

Iron binding site 5 out of 8 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid


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 and Alpha-Ketoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:22.3 occ:1.00 NE2 C:HIS303 2.0 21.1 1.0 OE1 C:GLU156 2.1 20.7 1.0 O C:HOH669 2.1 24.7 1.0 NE2 C:HIS154 2.2 23.5 1.0 O1 C:AKG403 2.2 26.2 1.0 O5 C:AKG403 2.2 26.3 1.0 C1 C:AKG403 2.9 26.4 1.0 C2 C:AKG403 2.9 26.8 1.0 CD2 C:HIS303 3.0 18.3 1.0 CE1 C:HIS303 3.0 19.3 1.0 CD C:GLU156 3.1 21.6 1.0 CE1 C:HIS154 3.1 22.1 1.0 CD2 C:HIS154 3.1 22.7 1.0 OE2 C:GLU156 3.4 24.6 1.0 O2 C:AKG403 4.1 26.1 1.0 ND1 C:HIS303 4.1 19.0 1.0 CG C:HIS303 4.1 20.0 1.0 ND1 C:HIS154 4.3 23.8 1.0 O C:HOH726 4.3 41.8 1.0 CG C:HIS154 4.3 22.5 1.0 NH2 C:ARG321 4.3 34.4 1.0 O C:HOH724 4.4 42.9 1.0 C3 C:AKG403 4.4 27.5 1.0 CG C:GLU156 4.4 20.0 1.0 CD1 C:LEU167 4.5 24.5 1.0 CB C:GLU156 4.8 19.0 1.0 CD2 C:LEU151 5.0 41.0 1.0

Iron binding site 6 out of 8 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe402 b:48.9 occ:1.00 OD1 C:ASP157 2.1 29.1 1.0 O C:HOH730 2.3 45.4 1.0 O C:HOH728 2.4 40.0 1.0 CE1 C:HIS211 2.7 64.8 1.0 NE2 C:HIS211 2.7 63.8 1.0 CG C:ASP157 3.1 27.4 1.0 OD2 C:ASP157 3.5 26.9 1.0 O C:HOH598 3.7 31.8 1.0 OE1 C:GLN123 3.7 55.9 1.0 O C:HOH729 4.0 55.7 1.0 ND1 C:HIS211 4.0 72.8 1.0 CD2 C:HIS211 4.0 66.1 1.0 OE2 C:GLU156 4.4 24.6 1.0 O C:HOH731 4.4 32.8 1.0 CB C:ASP157 4.4 22.1 1.0 CG C:HIS211 4.7 73.8 1.0 CA C:ASP157 4.7 22.0 1.0 N C:ASP157 4.8 19.3 1.0 CD C:GLN123 4.9 51.6 1.0

Iron binding site 7 out of 8 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:23.8 occ:1.00 O1 D:AKG403 2.0 32.8 1.0 OE1 D:GLU156 2.1 23.7 1.0 NE2 D:HIS154 2.1 24.9 1.0 NE2 D:HIS303 2.1 25.1 1.0 O5 D:AKG403 2.2 27.9 1.0 O D:HOH501 2.2 31.7 1.0 C1 D:AKG403 2.8 29.2 1.0 C2 D:AKG403 2.9 28.3 1.0 CE1 D:HIS154 3.1 24.3 1.0 CD2 D:HIS303 3.1 25.8 1.0 CD D:GLU156 3.1 25.0 1.0 CE1 D:HIS303 3.1 24.9 1.0 CD2 D:HIS154 3.1 23.4 1.0 OE2 D:GLU156 3.4 25.2 1.0 O2 D:AKG403 4.0 28.1 1.0 ND1 D:HIS154 4.2 25.2 1.0 ND1 D:HIS303 4.2 23.8 1.0 CG D:HIS303 4.2 24.9 1.0 CG D:HIS154 4.3 25.1 1.0 NH2 D:ARG321 4.4 35.1 1.0 C3 D:AKG403 4.4 29.1 1.0 O D:HOH714 4.4 38.6 1.0 CG D:GLU156 4.4 20.9 1.0 CD1 D:LEU167 4.5 20.9 0.5 CB D:GLU156 4.7 20.8 1.0 O D:HOH632 4.7 50.0 1.0 O D:HIS303 5.0 24.8 1.0

Iron binding site 8 out of 8 in the Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Non-Heme Iron Oxygenase Orfp in Complex with Fe and Alpha-Ketoglutaric Acid within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe402 b:47.0 occ:1.00 OD1 D:ASP157 2.2 30.9 1.0 O D:HOH657 2.2 39.5 1.0 O D:HOH656 2.3 39.9 1.0 NE2 D:HIS211 2.5 42.9 1.0 CG D:ASP157 3.2 27.4 1.0 CD2 D:HIS211 3.4 43.0 1.0 CE1 D:HIS211 3.5 44.6 1.0 OD2 D:ASP157 3.6 26.9 1.0 O D:HOH515 3.7 30.2 1.0 NE2 D:GLN123 3.8 43.0 1.0 OE2 D:GLU156 4.3 25.2 1.0 OD2 D:ASP208 4.3 65.5 1.0 CB D:ASP157 4.5 24.4 1.0 CG D:ASP208 4.5 64.9 1.0 CG D:HIS211 4.6 45.9 1.0 ND1 D:HIS211 4.6 42.3 1.0 CD D:GLN123 4.7 40.6 1.0 CA D:ASP157 4.7 21.6 1.0 CB D:SER210 4.7 62.0 1.0 CB D:ASP208 4.8 58.5 1.0 N D:ASP157 4.8 22.7 1.0 OE1 D:GLN123 4.8 46.2 1.0 O D:HOH713 4.9 43.7 1.0 OG D:SER210 5.0 64.2 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