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Iron in PDB 6tez: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - VAL80LYS Mutant - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid

Enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - VAL80LYS Mutant - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - VAL80LYS Mutant - 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 - VAL80LYS Mutant - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid, PDB code: 6tez 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) 49.00 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.001, 99.77, 224.461, 90, 90, 90
R / Rfree (%) 19 / 22.8

Other elements in 6tez:

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - VAL80LYS Mutant - 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 - VAL80LYS Mutant - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid (pdb code 6tez). 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 - VAL80LYS Mutant - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid, PDB code: 6tez:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6tez

Go back to Iron Binding Sites List in 6tez
Iron binding site 1 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - VAL80LYS Mutant - 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 - VAL80LYS Mutant - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe805

b:27.9
occ:1.00
 O5 A:AKG804 2.3 63.1 1.0
O2 A:AKG804 2.4 53.5 1.0
NE2 A:HIS719 2.4 44.1 1.0
OD1 A:ASP669 2.4 37.9 1.0
NE2 A:HIS667 2.5 40.9 1.0
OD2 A:ASP669 2.6 30.6 1.0
CG A:ASP669 2.8 34.2 1.0
C1 A:AKG804 2.9 56.4 1.0
C2 A:AKG804 2.9 61.6 1.0
CD2 A:HIS719 3.0 44.2 1.0
CD2 A:HIS667 3.3 41.1 1.0
CE1 A:HIS667 3.4 41.4 1.0
CE1 A:HIS719 3.6 45.5 1.0
O1 A:AKG804 4.1 55.3 1.0
CB A:ASP669 4.2 33.8 1.0
CG A:HIS719 4.3 45.5 1.0
ND1 A:HIS667 4.4 41.9 1.0
CG A:HIS667 4.4 42.4 1.0
C3 A:AKG804 4.4 62.9 1.0
CE1 A:PHE735 4.5 30.0 1.0
ND1 A:HIS719 4.5 46.2 1.0
CZ A:PHE735 4.5 33.9 1.0
NE A:ARG599 4.6 41.6 1.0
O A:HIS668 4.8 40.1 1.0
CE1 A:HIS711 4.8 33.2 1.0
C A:HIS668 4.8 38.8 1.0
CA A:ASP669 4.8 35.5 1.0
N A:ASP669 4.8 36.9 1.0
CD A:ARG599 4.9 42.1 1.0

Iron binding site 2 out of 2 in 6tez

Go back to Iron Binding Sites List in 6tez
Iron binding site 2 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - VAL80LYS Mutant - 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 - VAL80LYS Mutant - Cocrystal with FE2+, MN2+, Udp-Glucuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe806

b:55.9
occ:1.00
 OD1 A:ASP597 2.5 79.8 1.0
NE2 A:HIS595 2.5 73.3 1.0
NE2 A:HIS613 2.5 45.2 1.0
OD2 A:ASP611 2.6 43.5 1.0
OD1 A:ASP611 2.7 44.5 1.0
OD2 A:ASP597 2.7 80.3 1.0
CG A:ASP611 2.8 43.0 1.0
CG A:ASP597 2.9 79.6 1.0
CE1 A:HIS595 3.2 73.2 1.0
CD2 A:HIS613 3.3 45.2 1.0
CE1 A:HIS613 3.5 44.6 1.0
CD2 A:HIS595 3.7 74.7 1.0
CG A:PHE652 3.9 38.3 1.0
CD2 A:PHE652 4.0 40.1 1.0
CB A:ASP611 4.0 40.5 1.0
OG1 A:THR609 4.1 49.9 1.0
CD1 A:PHE652 4.2 37.6 1.0
CE2 A:PHE652 4.3 39.6 1.0
CB A:PHE652 4.3 37.8 1.0
CB A:ASP597 4.4 79.0 1.0
CG A:HIS613 4.4 43.7 1.0
ND1 A:HIS595 4.5 75.4 1.0
ND1 A:HIS613 4.5 43.9 1.0
CE1 A:PHE652 4.5 38.2 1.0
CZ A:PHE652 4.5 38.8 1.0
CG A:HIS595 4.7 77.2 1.0
CA A:ASP597 4.9 77.8 1.0
O A:THR609 4.9 51.5 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 10:49:23 2024

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