Manganese in PDB 6fxm: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with MN2+

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

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with MN2+, PDB code: 6fxm 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)	37.37 / 2.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	97.270, 99.949, 225.138, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 25.2

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

Iron

(Fe)

1 atom

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

Manganese binding site 1 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn807 b:48.5 occ:1.00 OD2 A:ASP115 2.3 50.1 1.0 NE2 A:HIS253 2.3 42.8 1.0 OD1 A:ASP115 2.4 45.2 1.0 O A:HOH1032 2.4 41.1 1.0 OD2 A:ASP112 2.4 43.1 1.0 O A:HOH1137 2.5 54.4 1.0 CG A:ASP115 2.6 45.5 1.0 CG A:ASP112 3.3 48.1 1.0 CE1 A:HIS253 3.3 46.6 1.0 CD2 A:HIS253 3.3 41.4 1.0 CB A:ASP112 3.4 40.9 1.0 CB A:ASP115 4.1 38.4 1.0 ND1 A:HIS253 4.4 47.0 1.0 OD1 A:ASP112 4.4 51.9 1.0 CG A:HIS253 4.4 39.6 1.0 CA A:ASN255 4.9 40.2 1.0 O A:ASP115 4.9 39.9 1.0 CA A:ASP112 5.0 37.1 1.0 N A:ASP115 5.0 30.3 1.0 CA A:ASP115 5.0 39.2 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn808 b:89.5 occ:1.00 OD2 A:ASP597 1.9 1.0 1.0 OD2 A:ASP611 2.0 98.7 1.0 CG A:ASP611 2.5 71.4 1.0 OD1 A:ASP611 2.5 62.1 1.0 O A:HOH1007 2.6 55.3 1.0 CG A:ASP597 2.7 0.2 1.0 CE1 A:HIS613 2.7 50.9 1.0 OD1 A:ASP597 2.9 0.3 1.0 ND1 A:HIS613 3.6 55.4 1.0 NE2 A:HIS613 3.7 49.9 1.0 CB A:ASP611 3.9 58.3 1.0 CB A:ASP597 4.1 0.5 1.0 OG A:SER591 4.2 53.6 1.0 OG1 A:THR609 4.3 50.7 1.0 O A:THR609 4.3 59.3 1.0 CD2 A:PHE652 4.6 43.6 1.0 CA A:ASP597 4.7 0.3 1.0 CG A:PHE652 4.8 44.6 1.0 CG A:HIS613 4.8 53.5 1.0 N A:ASP597 4.8 0.7 1.0 CD2 A:HIS613 4.8 52.0 1.0 CA A:ASP611 5.0 52.7 1.0 CE2 A:PHE652 5.0 41.7 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