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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6fxt:

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

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-Glc (pdb code 6fxt). 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-Glc, PDB code: 6fxt:

Manganese binding site 1 out of 1 in 6fxt

Go back to Manganese Binding Sites List in 6fxt
Manganese binding site 1 out of 1 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 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-Glc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn807

b:58.5
occ:1.00
 OD2 A:ASP115 2.0 65.5 1.0
O1B A:UDP804 2.0 61.9 1.0
O1A A:UDP804 2.1 62.3 1.0
NE2 A:HIS253 2.4 53.6 1.0
OD1 A:ASP115 2.4 59.6 1.0
CG A:ASP115 2.5 60.2 1.0
OD2 A:ASP112 2.6 58.2 1.0
PB A:UDP804 3.3 62.3 1.0
CD2 A:HIS253 3.3 52.4 1.0
CG A:ASP112 3.4 56.7 1.0
CE1 A:HIS253 3.4 54.2 1.0
PA A:UDP804 3.4 62.6 1.0
CB A:ASP112 3.5 52.6 1.0
O3A A:UDP804 3.7 61.4 1.0
O2B A:UDP804 3.8 63.8 1.0
NZ A:LYS259 3.8 55.8 1.0
O3' A:UDP804 4.0 62.3 1.0
CB A:ASP115 4.0 55.0 1.0
C5' A:UDP804 4.2 61.5 1.0
O5' A:UDP804 4.2 61.1 1.0
O2A A:UDP804 4.4 65.4 1.0
O3B A:UDP804 4.4 61.8 1.0
CG A:HIS253 4.5 51.5 1.0
ND1 A:HIS253 4.5 53.1 1.0
OD1 A:ASP112 4.5 57.4 1.0
CA A:ASN255 4.7 51.4 1.0
C3' A:UDP804 4.8 61.7 1.0
C4' A:UDP804 4.8 61.7 1.0
O A:GLY254 4.9 49.5 1.0
CA A:ASP115 4.9 51.5 1.0
N A:ASP115 4.9 51.0 1.0
O A:ASP115 5.0 48.6 1.0
CB A:ASN255 5.0 50.2 1.0
CA A:ASP112 5.0 51.0 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: Sun Oct 6 04:44:04 2024

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