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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6fxm:

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

Manganese Binding Sites:

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 6fxm

Go back to Manganese Binding Sites List in 6fxm
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 6fxm

Go back to Manganese Binding Sites List in 6fxm
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

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 04:39:38 2024

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