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Iron in PDB 6fxy: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal - Structure From Long-Wavelength S-Sad

Enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal - Structure From Long-Wavelength S-Sad

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal - Structure From Long-Wavelength S-Sad:
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 - Structure From Long-Wavelength S-Sad, PDB code: 6fxy 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) 112.37 / 2.14
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.040, 100.105, 224.743, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 23.1

Other elements in 6fxy:

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal - Structure From Long-Wavelength S-Sad also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal - Structure From Long-Wavelength S-Sad (pdb code 6fxy). 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-Gal - Structure From Long-Wavelength S-Sad, PDB code: 6fxy:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6fxy

Go back to Iron Binding Sites List in 6fxy
Iron binding site 1 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal - Structure From Long-Wavelength S-Sad


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-Gal - Structure From Long-Wavelength S-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe805

b:25.7
occ:1.00
NE2 A:HIS719 2.3 19.4 1.0
O5 A:AKG803 2.4 47.3 1.0
O2 A:AKG803 2.4 27.3 1.0
OD1 A:ASP669 2.4 32.1 1.0
NE2 A:HIS667 2.4 30.5 1.0
OD2 A:ASP669 2.9 34.0 1.0
CG A:ASP669 3.0 36.5 1.0
C2 A:AKG803 3.0 43.1 1.0
C1 A:AKG803 3.0 38.8 1.0
CD2 A:HIS719 3.2 22.7 1.0
CE1 A:HIS667 3.3 30.0 1.0
CE1 A:HIS719 3.3 33.2 1.0
CD2 A:HIS667 3.4 31.9 1.0
O A:HOH980 4.2 39.6 1.0
O1 A:AKG803 4.2 45.5 1.0
CG A:HIS719 4.3 28.7 1.0
ND1 A:HIS719 4.4 33.8 1.0
CZ A:PHE735 4.4 31.6 1.0
ND1 A:HIS667 4.4 27.5 1.0
CE1 A:PHE735 4.4 29.1 1.0
CB A:ASP669 4.5 34.9 1.0
NE A:ARG599 4.5 29.4 1.0
C3 A:AKG803 4.5 38.2 1.0
CG A:HIS667 4.5 28.5 1.0
CD2 A:LEU664 4.8 17.6 1.0
CD A:ARG599 4.8 28.0 1.0
C4 A:AKG803 5.0 35.9 1.0

Iron binding site 2 out of 2 in 6fxy

Go back to Iron Binding Sites List in 6fxy
Iron binding site 2 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal - Structure From Long-Wavelength S-Sad


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-Gal - Structure From Long-Wavelength S-Sad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe806

b:34.6
occ:1.00
NE2 A:HIS595 2.3 50.3 1.0
OD2 A:ASP611 2.5 33.4 1.0
OD1 A:ASP597 2.5 56.1 1.0
OD1 A:ASP611 2.6 31.1 1.0
NE2 A:HIS613 2.6 30.0 1.0
OD2 A:ASP597 2.7 54.3 1.0
CG A:ASP611 2.8 31.1 1.0
CG A:ASP597 2.9 55.2 1.0
CE1 A:HIS595 3.1 51.1 1.0
CD2 A:HIS613 3.3 29.3 1.0
CD2 A:HIS595 3.4 55.9 1.0
CE1 A:HIS613 3.7 33.0 1.0
CB A:ASP611 4.2 29.9 1.0
OG1 A:THR609 4.3 29.8 1.0
ND1 A:HIS595 4.3 56.4 1.0
CB A:ASP597 4.4 53.7 1.0
O A:THR609 4.4 35.7 1.0
OG A:SER591 4.5 52.9 1.0
CG A:HIS595 4.5 60.4 1.0
O A:GLU596 4.5 58.1 1.0
CG A:HIS613 4.5 30.6 1.0
CG A:PHE652 4.5 23.3 1.0
CD2 A:PHE652 4.6 22.2 1.0
ND1 A:HIS613 4.7 33.8 1.0
CB A:PHE652 4.8 24.8 1.0
CA A:ASP597 4.8 54.1 1.0
CD1 A:PHE652 4.9 25.1 1.0
CE2 A:PHE652 4.9 21.4 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 Dec 13 16:26:40 2020

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