Iron in PDB 8zgh: Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State

All present enzymatic activity of Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State:
1.14.11.4; 2.4.1.50; 2.4.1.66;

The structure of Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Iron atom in the Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State (pdb code 8zgh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State, PDB code: 8zgh:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:94.8 occ:1.00 O5 A:AKG802 2.5 80.0 1.0 OD2 A:ASP669 2.8 73.9 1.0 OD1 A:ASP669 3.0 73.9 1.0 CG A:ASP669 3.0 73.9 1.0 CE1 A:PHE735 3.1 69.3 1.0 CZ A:PHE735 3.2 69.3 1.0 CE1 A:HIS719 3.2 76.2 1.0 C2 A:AKG802 3.3 80.0 1.0 NE2 A:HIS719 3.5 76.2 1.0 O2 A:AKG802 3.6 80.0 1.0 CG2 A:THR674 3.9 68.9 1.0 C1 A:AKG802 3.9 80.0 1.0 OG1 A:THR674 4.0 68.9 1.0 CB A:THR674 4.0 68.9 1.0 CB A:ASP669 4.1 73.9 1.0 ND1 A:HIS719 4.3 76.2 1.0 CD1 A:PHE735 4.4 69.3 1.0 C3 A:AKG802 4.4 80.0 1.0 C4 A:AKG802 4.5 80.0 1.0 CE2 A:PHE735 4.5 69.3 1.0 CE1 A:HIS711 4.7 56.3 1.0 CD2 A:HIS719 4.7 76.2 1.0 NE2 A:HIS667 4.8 76.8 1.0

Iron binding site 2 out of 2 in the Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human Lysine O-Link Glycosylation Complex, LH3/COLGALT1 in Its Apo State within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe804 b:94.3 occ:1.00 O5 B:AKG803 2.8 73.7 1.0 OD2 B:ASP669 2.8 60.8 1.0 O2 B:AKG803 2.8 73.7 1.0 NE2 B:HIS719 2.9 65.8 1.0 CE1 B:HIS719 3.0 65.8 1.0 C1 B:AKG803 3.3 73.7 1.0 C2 B:AKG803 3.3 73.7 1.0 CG B:ASP669 3.6 60.8 1.0 OG1 B:THR674 3.7 51.7 1.0 OD1 B:ASP669 3.8 60.8 1.0 CE1 B:HIS711 3.9 48.4 1.0 CD2 B:HIS719 4.0 65.8 1.0 ND1 B:HIS719 4.1 65.8 1.0 CG2 B:THR674 4.1 51.7 1.0 NE2 B:HIS711 4.2 48.4 1.0 CB B:THR674 4.3 51.7 1.0 O1 B:AKG803 4.3 73.7 1.0 CE1 B:PHE735 4.5 57.1 1.0 NE2 B:HIS667 4.6 64.0 1.0 CG B:HIS719 4.6 65.8 1.0 C3 B:AKG803 4.6 73.7 1.0 CE1 B:HIS667 4.8 64.0 1.0 CB B:ASP669 4.8 60.8 1.0 CZ B:PHE735 5.0 57.1 1.0

J.Peng, W.Li, D.Yao, Y.Xia, Q.Wang, Y.Cai, S.Li, M.Cao, Y.Shen, P.Ma, R.Liao, J.Zhao, A.Qin, Y.Cao. The Structural Basis For the Human Procollagen Lysine Hydroxylation and Dual-Glycosylation. Nat Commun 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-57768-9