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Iron in PDB 6fxr: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal

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

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal:
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, PDB code: 6fxr 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) 48.90 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.801, 100.268, 224.895, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 23.7

Other elements in 6fxr:

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Gal 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 (pdb code 6fxr). 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, PDB code: 6fxr:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6fxr

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe805

b:35.7
occ:1.00
NE2 A:HIS719 1.9 55.6 1.0
OD1 A:ASP669 2.1 35.3 1.0
NE2 A:HIS667 2.1 42.4 1.0
O2 A:AKG803 2.2 46.3 1.0
O5 A:AKG803 2.2 48.1 1.0
CE1 A:HIS719 2.7 50.5 1.0
C1 A:AKG803 2.9 47.5 1.0
C2 A:AKG803 2.9 48.6 1.0
CG A:ASP669 2.9 37.6 1.0
OD2 A:ASP669 3.0 35.5 1.0
CE1 A:HIS667 3.0 42.6 1.0
CD2 A:HIS667 3.1 41.2 1.0
CD2 A:HIS719 3.1 50.1 1.0
ND1 A:HIS719 3.9 47.1 1.0
O1 A:AKG803 4.1 47.6 1.0
CG A:HIS719 4.1 46.7 1.0
ND1 A:HIS667 4.1 42.6 1.0
CG A:HIS667 4.2 42.6 1.0
O A:HOH1077 4.2 38.8 1.0
CB A:ASP669 4.3 39.1 1.0
C3 A:AKG803 4.4 50.1 1.0
NE A:ARG599 4.4 47.8 1.0
CZ A:PHE735 4.4 39.9 1.0
CE1 A:PHE735 4.5 38.7 1.0
CD A:ARG599 4.7 50.8 1.0
N A:ASP669 4.8 41.6 1.0
CA A:ASP669 4.8 41.6 1.0
C4 A:AKG803 4.9 52.1 1.0
CD2 A:LEU664 4.9 49.8 1.0

Iron binding site 2 out of 2 in 6fxr

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe806

b:58.6
occ:1.00
OD2 A:ASP611 1.9 79.3 1.0
NE2 A:HIS595 1.9 89.8 1.0
OD1 A:ASP597 2.0 90.0 1.0
NE2 A:HIS613 2.3 53.2 1.0
CG A:ASP611 2.5 67.4 1.0
CE1 A:HIS595 2.5 88.5 1.0
OD1 A:ASP611 2.7 66.5 1.0
CG A:ASP597 2.8 86.6 1.0
OD2 A:ASP597 2.9 86.2 1.0
CD2 A:HIS613 3.2 52.5 1.0
CD2 A:HIS595 3.2 90.1 1.0
CE1 A:HIS613 3.4 52.6 1.0
ND1 A:HIS595 3.8 89.9 1.0
CB A:ASP611 3.9 58.4 1.0
CG A:HIS595 4.1 90.5 1.0
CB A:ASP597 4.2 85.0 1.0
CG A:HIS613 4.4 51.1 1.0
CD2 A:PHE652 4.4 44.2 1.0
ND1 A:HIS613 4.4 53.2 1.0
CG A:PHE652 4.5 43.0 1.0
OG1 A:THR609 4.5 51.9 1.0
O A:THR609 4.6 52.8 1.0
O A:GLU596 4.6 87.0 1.0
OG A:SER591 4.7 52.9 1.0
CA A:ASP597 4.7 84.2 1.0
O A:HOH926 4.7 52.7 1.0
CE2 A:PHE652 4.8 46.1 1.0
CB A:PHE652 4.8 41.6 1.0
CD1 A:PHE652 4.8 44.2 1.0
N A:ASP597 4.9 86.6 1.0
C A:GLU596 4.9 88.4 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 16:26:37 2020

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