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Manganese in PDB 6fxx: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak

Enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak:
1.14.11.4;

Protein crystallography data

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak, PDB code: 6fxx 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) 49.34 / 3.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.679, 100.330, 225.954, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.8

Other elements in 6fxx:

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak also contains other interesting chemical elements:

Mercury (Hg) 3 atoms
Iron (Fe) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak (pdb code 6fxx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak, PDB code: 6fxx:

Manganese binding site 1 out of 1 in 6fxx

Go back to Manganese Binding Sites List in 6fxx
Manganese binding site 1 out of 1 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal, HG2+ Soak


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 FE2+, MN2+, Udp-Gal, HG2+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn807

b:48.2
occ:1.00
 O3B A:UDP806 1.9 78.1 1.0
O1A A:UDP806 2.0 68.2 1.0
OD2 A:ASP115 2.0 62.0 1.0
NE2 A:HIS253 2.3 61.4 1.0
OD1 A:ASP115 2.4 61.2 1.0
CG A:ASP115 2.5 61.2 1.0
OD2 A:ASP112 2.6 64.0 1.0
PB A:UDP806 3.1 77.6 1.0
PA A:UDP806 3.2 74.7 1.0
CD2 A:HIS253 3.3 59.9 1.0
CE1 A:HIS253 3.3 62.0 1.0
O3A A:UDP806 3.5 81.8 1.0
CG A:ASP112 3.5 67.4 1.0
CB A:ASP112 3.8 65.2 1.0
O2B A:UDP806 3.8 80.3 1.0
O3' A:UDP806 4.0 74.1 1.0
CB A:ASP115 4.0 60.5 1.0
O5' A:UDP806 4.1 80.6 1.0
O2A A:UDP806 4.3 79.2 1.0
O1B A:UDP806 4.3 87.9 1.0
C5' A:UDP806 4.3 84.6 1.0
ND1 A:HIS253 4.4 60.9 1.0
CG A:HIS253 4.5 59.5 1.0
CA A:ASN255 4.6 64.0 1.0
OD1 A:ASP112 4.7 70.0 1.0
C3' A:UDP806 4.8 75.4 1.0
CB A:ASN255 4.8 64.5 1.0
C4' A:UDP806 4.9 81.1 1.0
O A:GLY254 4.9 62.3 1.0
O A:ASP115 4.9 58.0 1.0
CA A:ASP115 5.0 59.3 1.0

Reference:

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
Page generated: Sat Aug 16 20:26:56 2025

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