Manganese in PDB 7zvj: Homodimeric Structure of LARGE1

The structure of Homodimeric Structure of LARGE1, PDB code: 7zvj was solved by R.Diskin, M.Katz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.64 / 2.61
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	196.531, 107.377, 100.334, 90, 120.26, 90
R / Rfree (%)	21.5 / 27

The binding sites of Manganese atom in the Homodimeric Structure of LARGE1 (pdb code 7zvj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Homodimeric Structure of LARGE1, PDB code: 7zvj:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Homodimeric Structure of LARGE1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Homodimeric Structure of LARGE1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn803 b:123.4 occ:1.00 OD2 A:ASP565 2.9 90.3 1.0 CE1 A:HIS705 3.2 73.3 1.0 NE2 A:HIS708 3.3 74.1 1.0 CG A:ASP565 3.8 71.9 1.0 NE2 A:HIS705 3.9 69.2 1.0 CB A:ASP565 3.9 73.7 1.0 CE1 A:HIS708 4.0 81.1 1.0 OD2 A:ASP563 4.0 94.8 1.0 CD2 A:HIS708 4.3 75.2 1.0 ND1 A:HIS705 4.3 70.5 1.0 OD1 A:ASP565 4.9 68.3 1.0

Manganese binding site 2 out of 2 in the Homodimeric Structure of LARGE1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Homodimeric Structure of LARGE1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn804 b:122.9 occ:1.00 NE2 B:HIS708 3.1 82.8 1.0 NE2 B:HIS705 3.3 63.1 1.0 CE1 B:HIS708 3.8 88.1 1.0 OD2 B:ASP565 3.9 91.3 1.0 CD2 B:HIS705 4.0 67.4 1.0 CD2 B:HIS708 4.2 71.5 1.0 CE1 B:HIS705 4.3 59.8 1.0 OD2 B:ASP563 4.7 109.8 1.0 CG B:ASP565 4.8 88.6 1.0 CZ B:PHE625 4.8 76.4 1.0 CB B:ASP565 4.9 73.2 1.0 NH2 B:ARG626 5.0 79.1 1.0

M.Katz, R.Diskin. Structural Basis For Matriglycan Synthesis By the LARGE1 Dual Glycosyltransferase. Plos One V. 17 78713 2022.
ISSN: ESSN 1932-6203
PubMed: 36512577
DOI: 10.1371/JOURNAL.PONE.0278713