Iron in PDB 8h7y: Trans-3/4-Proline-Hydroxylase H11 with Akg and L-Proline

The structure of Trans-3/4-Proline-Hydroxylase H11 with Akg and L-Proline, PDB code: 8h7y 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)	39.79 / 2.14
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	106.437, 106.437, 145.016, 90, 90, 90
R / Rfree (%)	15.2 / 21.6

The binding sites of Iron atom in the Trans-3/4-Proline-Hydroxylase H11 with Akg and L-Proline (pdb code 8h7y). 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 and L-Proline, PDB code: 8h7y:
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 and L-Proline


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 and L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:32.7 occ:1.00 O2 A:AKG302 2.0 34.4 1.0 NE2 A:HIS214 2.1 23.2 1.0 OD1 A:ASP116 2.1 28.1 1.0 O5 A:AKG302 2.1 35.5 1.0 NE2 A:HIS114 2.2 34.7 1.0 C1 A:AKG302 2.8 45.4 1.0 C2 A:AKG302 2.8 46.2 1.0 CE1 A:HIS214 3.1 32.0 1.0 CD2 A:HIS214 3.1 25.4 1.0 CG A:ASP116 3.1 31.1 1.0 CE1 A:HIS114 3.1 34.1 1.0 CD2 A:HIS114 3.2 33.9 1.0 OD2 A:ASP116 3.5 34.4 1.0 O1 A:AKG302 4.0 43.2 1.0 CG A:PRO303 4.1 33.4 1.0 O A:HOH437 4.2 47.4 1.0 ND1 A:HIS214 4.2 28.2 1.0 C3 A:AKG302 4.2 49.5 1.0 CG A:HIS214 4.2 25.7 1.0 ND1 A:HIS114 4.3 31.2 1.0 CG A:HIS114 4.3 35.4 1.0 CB A:PRO303 4.4 35.8 1.0 CD A:PRO303 4.4 37.1 1.0 CB A:ASP116 4.5 28.3 1.0 CA A:ASP116 4.9 28.7 1.0

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


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 and L-Proline within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:33.9 occ:1.00 O1 B:AKG302 1.9 32.4 1.0 O5 B:AKG302 2.0 40.9 1.0 OD1 B:ASP116 2.0 32.1 1.0 NE2 B:HIS214 2.0 24.9 1.0 NE2 B:HIS114 2.2 40.4 1.0 C1 B:AKG302 2.7 48.4 1.0 C2 B:AKG302 2.7 45.4 1.0 CE1 B:HIS214 3.0 28.9 1.0 CG B:ASP116 3.0 35.6 1.0 CD2 B:HIS214 3.1 28.6 1.0 CE1 B:HIS114 3.1 48.0 1.0 CD2 B:HIS114 3.1 39.1 1.0 OD2 B:ASP116 3.3 30.8 1.0 O2 B:AKG302 4.0 37.0 1.0 CG B:PRO303 4.1 35.8 1.0 ND1 B:HIS214 4.1 24.9 1.0 CG B:HIS214 4.2 28.5 1.0 C3 B:AKG302 4.2 45.7 1.0 ND1 B:HIS114 4.2 44.6 1.0 CG B:HIS114 4.2 40.4 1.0 CB B:ASP116 4.4 32.2 1.0 CB B:PRO303 4.4 41.7 1.0 CD B:PRO303 4.6 37.0 1.0 CA B:ASP116 4.8 34.5 1.0 CE2 B:PHE208 4.8 26.6 1.0 C4 B:AKG302 4.9 39.0 1.0 N B:ASP116 4.9 38.1 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