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Iron 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
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, HG2+ Soak (pdb code 6fxx). 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, HG2+ Soak, PDB code: 6fxx:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6fxx

Go back to Iron Binding Sites List in 6fxx
Iron binding site 1 out of 2 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 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, HG2+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe808

b:57.5
occ:1.00
 O2 A:AKG805 1.9 54.7 1.0
NE2 A:HIS719 2.0 70.0 1.0
CE1 A:HIS719 2.1 69.9 1.0
OD1 A:ASP669 2.4 68.8 1.0
C1 A:AKG805 2.7 55.9 1.0
O5 A:AKG805 2.7 70.9 1.0
OD2 A:ASP669 2.8 67.1 1.0
NE2 A:HIS667 2.8 72.3 1.0
CG A:ASP669 2.9 67.8 1.0
C2 A:AKG805 3.0 61.9 1.0
CD2 A:HIS719 3.3 70.9 1.0
ND1 A:HIS719 3.4 70.7 1.0
CE1 A:HIS667 3.6 73.6 1.0
CD2 A:HIS667 3.8 73.3 1.0
O1 A:AKG805 3.8 47.8 1.0
CG A:HIS719 4.0 71.4 1.0
CE1 A:PHE735 4.1 65.4 1.0
CZ A:PHE735 4.2 66.7 1.0
NE A:ARG599 4.3 71.4 1.0
C3 A:AKG805 4.4 59.1 1.0
CB A:ASP669 4.4 67.7 1.0
ND1 A:HIS667 4.8 75.5 1.0
CG A:HIS667 4.8 75.3 1.0
CG2 A:THR674 4.9 72.1 1.0
CD A:ARG599 5.0 73.1 1.0
C4 A:AKG805 5.0 53.0 1.0

Iron binding site 2 out of 2 in 6fxx

Go back to Iron Binding Sites List in 6fxx
Iron binding site 2 out of 2 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 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, HG2+ Soak within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe809

b:77.0
occ:1.00
 NE2 A:HIS595 1.9 95.9 1.0
OD1 A:ASP597 1.9 98.1 1.0
OD2 A:ASP611 2.1 71.5 1.0
OD1 A:ASP611 2.4 72.7 1.0
CG A:ASP611 2.4 71.6 1.0
CE1 A:HIS595 2.7 93.8 1.0
CG A:ASP597 2.8 98.6 1.0
CE1 A:HIS613 2.8 70.2 1.0
CD2 A:HIS595 3.0 0.6 1.0
OD2 A:ASP597 3.0 97.9 1.0
ND1 A:HIS613 3.5 70.1 1.0
NE2 A:HIS613 3.8 69.0 1.0
CB A:ASP611 3.8 70.4 1.0
ND1 A:HIS595 3.9 0.0 1.0
CG A:HIS595 4.0 0.2 1.0
CG A:PHE652 4.2 66.1 1.0
CB A:ASP597 4.2 95.6 1.0
OG1 A:THR609 4.2 73.3 1.0
CD2 A:PHE652 4.3 66.6 1.0
CD1 A:PHE652 4.3 65.9 1.0
CE2 A:PHE652 4.6 66.9 1.0
CB A:PHE652 4.6 65.9 1.0
OG A:SER591 4.6 1.0 1.0
CE1 A:PHE652 4.6 66.2 1.0
CG A:HIS613 4.7 68.8 1.0
CZ A:PHE652 4.7 66.7 1.0
CA A:ASP597 4.8 0.1 1.0
CD2 A:HIS613 4.8 68.1 1.0
O A:THR609 4.9 77.6 1.0
CA A:ASP611 4.9 71.6 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: Tue Aug 6 18:47:56 2024

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