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

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

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid:
1.14.11.4; 2.4.1.50; 2.4.1.66;

Protein crystallography data

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid, PDB code: 6tes was solved by A.Chiapparino, F.De Giorgi, L.Scietti, S.Faravelli, T.Roscioli, F.Forneris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.10 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.202, 100.505, 224.745, 90, 90, 90
R / Rfree (%) 19 / 23.8

Other elements in 6tes:

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

Iron binding site 1 out of 2 in 6tes

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


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-Glucuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:30.0
occ:1.00
 NE2 A:HIS719 2.1 34.1 1.0
OD1 A:ASP669 2.2 32.9 1.0
O2 A:AKG1001 2.2 45.5 1.0
O5 A:AKG1001 2.4 62.4 1.0
NE2 A:HIS667 2.4 36.4 1.0
C1 A:AKG1001 2.7 47.5 1.0
C2 A:AKG1001 2.7 58.1 1.0
OD2 A:ASP669 2.8 35.8 1.0
CG A:ASP669 2.8 43.3 1.0
CE1 A:HIS719 3.1 36.3 1.0
CD2 A:HIS719 3.1 35.9 1.0
CD2 A:HIS667 3.2 34.2 1.0
CE1 A:HIS667 3.5 36.9 1.0
O1 A:AKG1001 3.9 50.7 1.0
O A:HOH1117 4.0 32.4 1.0
C3 A:AKG1001 4.0 58.8 1.0
ND1 A:HIS719 4.2 39.4 1.0
CG A:HIS719 4.2 36.5 1.0
CB A:ASP669 4.3 41.2 1.0
CG A:HIS667 4.4 37.2 1.0
ND1 A:HIS667 4.5 35.1 1.0
CZ A:PHE735 4.5 41.8 1.0
CE1 A:PHE735 4.6 36.1 1.0
NE A:ARG599 4.6 42.2 1.0
C4 A:AKG1001 4.6 55.9 1.0
N A:ASP669 4.8 38.2 1.0
CA A:ASP669 4.9 31.0 1.0
CD A:ARG599 4.9 43.1 1.0
CE1 A:HIS711 4.9 36.0 1.0

Iron binding site 2 out of 2 in 6tes

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


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-Glucuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1003

b:38.7
occ:1.00
 NE2 A:HIS595 2.3 59.3 1.0
OD2 A:ASP611 2.3 34.4 1.0
OD1 A:ASP597 2.4 72.9 1.0
OD1 A:ASP611 2.6 37.3 1.0
CE1 A:HIS613 2.6 41.7 1.0
OD2 A:ASP597 2.7 63.0 1.0
CG A:ASP611 2.7 36.6 1.0
CG A:ASP597 2.8 68.2 1.0
CD2 A:HIS595 3.2 60.3 1.0
CE1 A:HIS595 3.3 63.6 1.0
ND1 A:HIS613 3.5 43.8 1.0
NE2 A:HIS613 3.5 41.5 1.0
OG1 A:THR609 4.0 35.5 1.0
CB A:ASP611 4.2 33.2 1.0
CB A:ASP597 4.3 62.6 1.0
CG A:HIS595 4.4 68.3 1.0
OG A:SER591 4.4 50.6 1.0
O A:THR609 4.4 52.4 1.0
ND1 A:HIS595 4.4 67.5 1.0
CG A:PHE652 4.6 36.4 1.0
CD2 A:PHE652 4.7 37.0 1.0
CG A:HIS613 4.7 38.7 1.0
CD2 A:HIS613 4.7 41.6 1.0
O A:GLU596 4.7 71.3 1.0
CD1 A:PHE652 4.9 38.5 1.0
CA A:ASP597 4.9 67.0 1.0
CB A:PHE652 4.9 39.3 1.0

Reference:

A.Chiapparino, F.De Giorgi, L.Scietti, S.Faravelli, T.Roscioli, F.Forneris. A Cooperative Network of Molecular "Hot Spots" Highlights the Complexity of LH3 Collagen Glycosyltransferase Activities To Be Published.
Page generated: Wed Aug 7 10:46:08 2024

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