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Iron in PDB 8one: Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose

Enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose

All present enzymatic activity of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER 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 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose, PDB code: 8one was solved by D.Mattoteia, M.De Marco, A.Pinnola, S.Faravelli, L.Scietti, F.Forneris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.44 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 97.09, 100.181, 223.794, 90, 90, 90
R / Rfree (%) 20.4 / 22.8

Other elements in 8one:

The structure of Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER 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 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose (pdb code 8one). 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 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose, PDB code: 8one:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 8one

Go back to Iron Binding Sites List in 8one
Iron binding site 1 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER 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 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1002

b:23.8
occ:1.00
 OD1 A:ASP669 2.5 32.1 1.0
O5 A:AKG1001 2.5 44.7 1.0
NE2 A:HIS719 2.6 25.3 1.0
O2 A:AKG1001 2.6 29.1 1.0
NE2 A:HIS667 2.6 31.0 1.0
OD2 A:ASP669 2.7 27.3 1.0
CG A:ASP669 2.9 34.2 1.0
C2 A:AKG1001 3.2 62.6 1.0
CD2 A:HIS667 3.3 29.1 1.0
C1 A:AKG1001 3.4 46.6 1.0
CE1 A:HIS719 3.4 31.8 1.0
CD2 A:HIS719 3.5 26.3 1.0
CE1 A:HIS667 3.6 41.4 1.0
O A:HOH1104 3.8 35.7 1.0
CZ A:PHE735 4.3 35.4 1.0
CE1 A:PHE735 4.3 22.6 1.0
CB A:ASP669 4.4 38.3 1.0
CG A:HIS667 4.4 34.7 1.0
ND1 A:HIS719 4.5 36.7 1.0
C3 A:AKG1001 4.5 58.9 1.0
ND1 A:HIS667 4.5 31.4 1.0
O1 A:AKG1001 4.6 74.8 1.0
CG A:HIS719 4.6 32.9 1.0
NE A:ARG599 4.6 33.0 1.0
O A:HIS668 4.7 40.4 1.0
C A:HIS668 4.9 34.6 1.0
CD A:ARG599 4.9 31.8 1.0
C4 A:AKG1001 5.0 48.4 1.0

Iron binding site 2 out of 2 in 8one

Go back to Iron Binding Sites List in 8one
Iron binding site 2 out of 2 in the Crystal Structure of Full-Length Human Lysyl Hydroxylase LH3 - ASP190SER 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 - ASP190SER Mutant - Cocrystal with FE2+, MN2+, Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe1003

b:31.6
occ:1.00
 OD1 A:ASP597 2.6 53.3 1.0
OD2 A:ASP611 2.6 44.6 1.0
OD1 A:ASP611 2.7 32.0 1.0
NE2 A:HIS595 2.7 44.9 1.0
NE2 A:HIS613 2.7 44.8 1.0
OD2 A:ASP597 2.7 39.0 1.0
CG A:ASP611 2.9 41.0 1.0
CG A:ASP597 3.0 50.8 1.0
CD2 A:HIS595 3.2 51.5 1.0
CE1 A:HIS613 3.4 35.6 1.0
CD2 A:HIS613 3.6 39.1 1.0
CE1 A:HIS595 3.9 60.1 1.0
OG1 A:THR609 4.1 32.0 1.0
CD2 A:PHE652 4.3 34.1 1.0
O A:THR609 4.3 44.2 1.0
CG A:PHE652 4.3 31.3 1.0
CB A:ASP611 4.3 31.9 1.0
ND1 A:HIS613 4.4 38.3 1.0
CB A:ASP597 4.4 42.7 1.0
CG A:HIS595 4.5 58.1 1.0
CG A:HIS613 4.6 30.6 1.0
OG A:SER591 4.6 53.0 1.0
O A:GLU596 4.6 52.2 1.0
CE2 A:PHE652 4.6 29.3 1.0
CD1 A:PHE652 4.6 33.5 1.0
CB A:PHE652 4.7 25.8 1.0
ND1 A:HIS595 4.8 68.2 1.0
CZ A:PHE652 4.9 31.3 1.0
CE1 A:PHE652 4.9 33.3 1.0
CA A:ASP597 5.0 44.0 1.0

Reference:

D.Mattoteia, A.Chiapparino, M.Fumagalli, M.De Marco, F.De Giorgi, L.Negro, A.Pinnola, S.Faravelli, T.Roscioli, L.Scietti, F.Forneris. Identification of Regulatory Molecular 'Hot Spots' For Lh/Plod Collagen Glycosyltransferase Activity Int J Mol Sci 2023.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS241311213
Page generated: Thu Aug 7 19:34:44 2025

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