Iron in PDB 8h7v: Trans-3/4-Proline-Hydroxylase H11 with Akg

The structure of Trans-3/4-Proline-Hydroxylase H11 with Akg, PDB code: 8h7v was solved by W.M.Gong, X.Y.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.82 / 1.97
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.763, 106.763, 144.01, 90, 90, 90
R / Rfree (%)	13.5 / 17.5

The binding sites of Iron atom in the Trans-3/4-Proline-Hydroxylase H11 with Akg (pdb code 8h7v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Trans-3/4-Proline-Hydroxylase H11 with Akg, PDB code: 8h7v:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Trans-3/4-Proline-Hydroxylase H11 with Akg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Trans-3/4-Proline-Hydroxylase H11 with Akg within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:20.0 occ:0.50 O2 A:AKG501 2.0 37.4 1.0 NE2 A:HIS214 2.0 27.2 1.0 O5 A:AKG501 2.1 38.1 1.0 NE2 A:HIS114 2.2 33.2 1.0 OD1 A:ASP116 2.2 33.0 1.0 O A:HOH689 2.3 47.0 1.0 C1 A:AKG501 2.8 48.4 1.0 C2 A:AKG501 2.8 44.9 1.0 CE1 A:HIS214 2.9 31.2 1.0 CE1 A:HIS114 3.1 38.3 1.0 CD2 A:HIS214 3.1 28.9 1.0 CG A:ASP116 3.1 32.0 1.0 CD2 A:HIS114 3.2 35.6 1.0 OD2 A:ASP116 3.4 31.3 1.0 O1 A:AKG501 4.0 47.6 1.0 ND1 A:HIS214 4.0 32.2 1.0 CG A:HIS214 4.2 28.6 1.0 ND1 A:HIS114 4.2 36.0 1.0 C3 A:AKG501 4.3 47.4 1.0 CG A:HIS114 4.3 34.1 1.0 O A:HOH776 4.3 50.2 1.0 CB A:ASP116 4.5 28.8 1.0 O A:HOH772 4.6 49.5 1.0 CA A:ASP116 4.9 30.7 1.0 N A:ASP116 5.0 30.9 1.0 CE2 A:PHE208 5.0 26.1 1.0

Iron binding site 2 out of 2 in the Trans-3/4-Proline-Hydroxylase H11 with Akg


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Trans-3/4-Proline-Hydroxylase H11 with Akg within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:36.9 occ:0.50 NE2 B:HIS214 2.1 34.0 1.0 O1 B:AKG301 2.1 58.5 1.0 OD1 B:ASP116 2.1 40.4 1.0 O5 B:AKG301 2.1 66.2 1.0 NE2 B:HIS114 2.1 42.5 1.0 C1 B:AKG301 2.9 73.2 1.0 C2 B:AKG301 2.9 74.4 1.0 CE1 B:HIS214 2.9 35.6 1.0 CG B:ASP116 3.0 35.3 1.0 CE1 B:HIS114 3.1 48.7 1.0 CD2 B:HIS114 3.1 40.1 1.0 CD2 B:HIS214 3.2 34.7 1.0 OD2 B:ASP116 3.3 38.8 1.0 ND1 B:HIS214 4.0 36.0 1.0 O2 B:AKG301 4.0 71.3 1.0 ND1 B:HIS114 4.2 45.2 1.0 CG B:HIS214 4.2 32.4 1.0 CG B:HIS114 4.2 41.7 1.0 C3 B:AKG301 4.3 66.4 1.0 O B:HOH472 4.4 40.0 1.0 CG2 B:THR172 4.4 73.0 1.0 CB B:ASP116 4.4 31.2 1.0 O B:HOH507 4.5 53.2 1.0 CB B:THR172 4.5 80.3 1.0 CA B:ASP116 4.8 33.4 1.0 OG1 B:THR172 4.9 73.2 1.0 N B:ASP116 4.9 32.7 1.0 CE2 B:PHE208 4.9 24.6 1.0

X.Hu, X.Huang, J.Liu, P.Zheng, W.Gong, L.Yang. Structures of L-Proline Trans-Hydroxylase Reveal the Catalytic Specificity and Provide Deeper Insight Into Akg-Dependent Hydroxylation. Acta Crystallogr D Struct V. 79 318 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 36974966
DOI: 10.1107/S2059798323001936