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

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

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - VAL80LYS Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose:
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-Glucose, PDB code: 6tex 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 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 98.049, 100.409, 225.179, 90, 90, 90
R / Rfree (%) 17 / 22.6

Other elements in 6tex:

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

Iron binding site 1 out of 2 in 6tex

Go back to Iron Binding Sites List in 6tex
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-Glucose


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

b:28.8
occ:1.00
 O2 A:AKG803 2.2 42.8 1.0
NE2 A:HIS719 2.2 43.4 1.0
OD1 A:ASP669 2.2 46.0 1.0
NE2 A:HIS667 2.3 38.2 1.0
O5 A:AKG803 2.5 78.9 1.0
OD2 A:ASP669 2.6 35.1 1.0
CG A:ASP669 2.7 44.9 1.0
CE1 A:HIS719 2.7 35.5 1.0
C1 A:AKG803 2.7 52.8 1.0
C2 A:AKG803 2.8 73.2 1.0
CD2 A:HIS667 3.1 38.7 1.0
CE1 A:HIS667 3.2 46.1 1.0
CD2 A:HIS719 3.4 43.3 1.0
O1 A:AKG803 3.9 48.5 1.0
ND1 A:HIS719 3.9 42.8 1.0
C3 A:AKG803 4.1 76.1 1.0
CB A:ASP669 4.1 47.7 1.0
CG A:HIS667 4.2 40.5 1.0
ND1 A:HIS667 4.3 38.3 1.0
CG A:HIS719 4.3 44.3 1.0
CE1 A:PHE735 4.4 44.7 1.0
CZ A:PHE735 4.4 45.6 1.0
NE A:ARG599 4.5 42.0 1.0
CA A:ASP669 4.7 30.9 1.0
N A:ASP669 4.8 50.2 1.0
CE1 A:HIS711 4.8 44.4 1.0
C A:HIS668 4.8 43.5 1.0
CD A:ARG599 4.9 43.3 1.0
O A:HIS668 4.9 52.3 1.0
C4 A:AKG803 4.9 71.5 1.0

Iron binding site 2 out of 2 in 6tex

Go back to Iron Binding Sites List in 6tex
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-Glucose


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

b:46.5
occ:1.00
 NE2 A:HIS595 2.2 68.2 1.0
OD2 A:ASP611 2.3 41.6 1.0
OD1 A:ASP597 2.4 76.3 1.0
NE2 A:HIS613 2.5 51.7 1.0
OD1 A:ASP611 2.7 47.6 1.0
OD2 A:ASP597 2.8 74.0 1.0
CG A:ASP611 2.8 45.5 1.0
CE1 A:HIS595 2.9 69.8 1.0
CG A:ASP597 2.9 73.6 1.0
CD2 A:HIS613 3.4 51.2 1.0
CD2 A:HIS595 3.5 74.6 1.0
CE1 A:HIS613 3.5 51.9 1.0
ND1 A:HIS595 4.1 76.6 1.0
CB A:ASP611 4.3 41.5 1.0
CB A:ASP597 4.3 69.2 1.0
OG1 A:THR609 4.3 51.4 1.0
CG A:HIS595 4.4 80.3 1.0
OG A:SER591 4.4 60.5 1.0
CG A:HIS613 4.5 47.9 1.0
O A:THR609 4.5 61.8 1.0
O A:GLU596 4.5 83.0 1.0
ND1 A:HIS613 4.5 53.5 1.0
CD2 A:PHE652 4.6 47.3 1.0
CG A:PHE652 4.7 40.9 1.0
CA A:ASP597 4.8 74.2 1.0
CE2 A:PHE652 5.0 37.6 1.0
CD1 A:PHE652 5.0 40.8 1.0
CB A:PHE652 5.0 33.3 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 10:49:23 2024

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