Manganese in PDB 8zwy: Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5

The structure of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5, PDB code: 8zwy was solved by J.M.Lo, C.Ma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.44 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.645, 86.7, 86.996, 90, 95.25, 90
R / Rfree (%)	20.8 / 22.7

The binding sites of Manganese atom in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 (pdb code 8zwy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5, PDB code: 8zwy:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:20.2 occ:1.00 O1B A:UDP402 1.8 25.2 1.0 O2A A:UDP402 2.2 17.7 1.0 OD2 A:ASP156 2.4 22.0 1.0 NE2 A:HIS285 2.4 11.5 1.0 OD2 A:ASP158 2.5 22.0 1.0 OD1 A:ASP158 2.6 20.0 1.0 CG A:ASP158 2.9 19.7 1.0 O A:HOH597 3.1 34.7 1.0 CD2 A:HIS285 3.2 9.6 1.0 PB A:UDP402 3.3 37.6 1.0 H5'2 A:UDP402 3.4 18.0 1.0 CE1 A:HIS285 3.5 14.3 1.0 PA A:UDP402 3.5 21.9 1.0 CG A:ASP156 3.6 27.6 1.0 O3A A:UDP402 3.7 18.7 1.0 O A:HOH504 3.8 29.5 1.0 H3' A:UDP402 3.9 17.8 1.0 O2B A:UDP402 4.2 29.1 1.0 C5' A:UDP402 4.2 14.9 1.0 CB A:ASP156 4.3 11.8 1.0 O5' A:UDP402 4.3 14.4 1.0 CB A:ASP158 4.4 11.2 1.0 CG A:HIS285 4.4 11.5 1.0 O3B A:UDP402 4.4 24.4 1.0 ND1 A:HIS285 4.5 11.1 1.0 OD1 A:ASP156 4.5 11.4 1.0 O A:HOH615 4.6 33.3 1.0 O1A A:UDP402 4.6 18.5 1.0 C3' A:UDP402 4.8 14.8 1.0 O A:HOH638 4.9 44.9 1.0 O A:HOH513 4.9 36.3 1.0 H5'1 A:UDP402 4.9 18.0 1.0 C4' A:UDP402 4.9 19.7 1.0

Manganese binding site 2 out of 2 in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:43.8 occ:1.00 NE2 B:HIS285 2.2 39.0 1.0 OD2 B:ASP158 2.5 49.1 1.0 OD1 B:ASP158 2.5 46.1 1.0 O1B B:UDP402 2.6 57.3 1.0 O2A B:UDP402 2.8 50.5 1.0 OD2 B:ASP156 2.8 49.6 1.0 CG B:ASP158 2.8 38.7 1.0 O5' B:UDP402 3.0 62.7 1.0 CE1 B:HIS285 3.1 28.5 1.0 O3A B:UDP402 3.2 46.7 1.0 PA B:UDP402 3.3 46.0 1.0 CD2 B:HIS285 3.3 31.5 1.0 PB B:UDP402 3.5 66.3 1.0 H3' B:UDP402 3.7 54.2 1.0 CG B:ASP156 3.8 45.2 1.0 CB B:ASP156 4.2 40.6 1.0 ND1 B:HIS285 4.2 28.7 1.0 CB B:ASP158 4.3 38.0 1.0 CG B:HIS285 4.3 28.7 1.0 C5' B:UDP402 4.4 45.3 1.0 O3B B:UDP402 4.5 55.1 1.0 O B:HOH530 4.5 41.5 1.0 C3' B:UDP402 4.5 45.1 1.0 O2B B:UDP402 4.5 49.1 1.0 H5'2 B:UDP402 4.7 54.4 1.0 O1A B:UDP402 4.7 57.0 1.0 C4' B:UDP402 4.8 43.0 1.0 H4' B:UDP402 4.8 51.8 1.0 CG2 B:THR217 4.9 33.1 1.0 OD1 B:ASP156 4.9 45.4 1.0

J.M.Lo, C.C.Kung, T.R.Cheng, C.H.Wong, C.Ma. Structure-Based Mechanism and Specificity of Human Galactosyltransferase Beta 3GALT5. J.Am.Chem.Soc. 2025.
ISSN: ESSN 1520-5126
PubMed: 40130308
DOI: 10.1021/JACS.4C11724