Iron in PDB 6fxt: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc:
1.14.11.4;

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc, PDB code: 6fxt was solved by L.Scietti, A.Chiapparino, F.De Giorgi, M.Fumagalli, L.Khoriauli, S.Nergadze, S.Basu, V.Olieric, B.Banushi, E.Giulotto, P.Gissen, F.Forneris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.50 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	97.744, 100.472, 225.394, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.8

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Iron atom in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc (pdb code 6fxt). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc, PDB code: 6fxt:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc


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 Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe805 b:54.6 occ:1.00 OD1 A:ASP669 2.4 68.9 1.0 O5 A:AKG803 2.5 60.9 1.0 O2 A:AKG803 2.5 60.8 1.0 NE2 A:HIS719 2.5 52.9 1.0 NE2 A:HIS667 2.5 63.9 1.0 OD2 A:ASP669 2.8 66.7 1.0 CE1 A:HIS719 2.8 52.6 1.0 CG A:ASP669 2.9 67.5 1.0 C2 A:AKG803 3.2 62.4 1.0 C1 A:AKG803 3.2 62.1 1.0 CD2 A:HIS667 3.3 63.6 1.0 CE1 A:HIS667 3.4 64.5 1.0 CD2 A:HIS719 3.7 54.4 1.0 ND1 A:HIS719 4.1 53.1 1.0 CG A:HIS667 4.3 64.4 1.0 CZ A:PHE735 4.3 52.7 1.0 CB A:ASP669 4.3 65.9 1.0 ND1 A:HIS667 4.3 65.0 1.0 CE1 A:PHE735 4.4 51.7 1.0 O1 A:AKG803 4.4 62.2 1.0 NE A:ARG599 4.5 57.5 1.0 CG A:HIS719 4.5 55.7 1.0 C3 A:AKG803 4.6 62.4 1.0 CA A:ASP669 4.8 62.6 1.0 N A:ASP669 4.9 63.8 1.0 CD A:ARG599 4.9 60.0 1.0 O A:HIS668 4.9 63.7 1.0 C A:HIS668 4.9 64.1 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc


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 Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glc within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe806 b:56.6 occ:1.00 NE2 A:HIS595 2.5 88.3 1.0 OD1 A:ASP597 2.5 91.3 1.0 NE2 A:HIS613 2.6 62.8 1.0 OD2 A:ASP611 2.6 67.0 1.0 OD1 A:ASP611 2.6 67.0 1.0 OD2 A:ASP597 2.7 93.8 1.0 CG A:ASP611 2.8 66.2 1.0 CG A:ASP597 2.9 91.5 1.0 CE1 A:HIS595 3.1 88.3 1.0 CD2 A:HIS613 3.3 61.9 1.0 CE1 A:HIS613 3.6 62.8 1.0 CD2 A:HIS595 3.7 91.1 1.0 CB A:ASP611 4.2 63.3 1.0 CG A:PHE652 4.2 57.0 1.0 OG1 A:THR609 4.2 60.9 1.0 CB A:ASP597 4.3 90.0 1.0 CD2 A:PHE652 4.4 56.5 1.0 ND1 A:HIS595 4.4 91.1 1.0 CD1 A:PHE652 4.4 57.3 1.0 CG A:HIS613 4.5 61.3 1.0 ND1 A:HIS613 4.6 61.5 1.0 CB A:PHE652 4.6 56.9 1.0 O A:GLU596 4.7 92.7 1.0 CE2 A:PHE652 4.7 56.7 1.0 CG A:HIS595 4.7 93.8 1.0 CE1 A:PHE652 4.7 57.4 1.0 O A:THR609 4.8 64.7 1.0 CA A:ASP597 4.8 89.1 1.0 OG A:SER591 4.8 78.9 1.0 CZ A:PHE652 4.8 57.3 1.0

L.Scietti, A.Chiapparino, F.De Giorgi, M.Fumagalli, L.Khoriauli, S.Nergadze, S.Basu, V.Olieric, L.Cucca, B.Banushi, A.Profumo, E.Giulotto, P.Gissen, F.Forneris. Molecular Architecture of the Multifunctional Collagen Lysyl Hydroxylase and Glycosyltransferase LH3. Nat Commun V. 9 3163 2018.
ISSN: ESSN 2041-1723
PubMed: 30089812
DOI: 10.1038/S41467-018-05631-5