Manganese in PDB 8zx3: Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5

The structure of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5, PDB code: 8zx3 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)	26.47 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.544, 86.367, 86.888, 90, 95.26, 90
R / Rfree (%)	20.2 / 22.9

The binding sites of Manganese atom in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 (pdb code 8zx3). 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: 8zx3:
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:24.7 occ:1.00 O A:HOH514 2.4 26.7 1.0 NE2 A:HIS285 2.4 13.7 1.0 O3B A:UDP402 2.5 47.4 1.0 O2A A:UDP402 2.5 48.1 1.0 OD1 A:ASP158 2.5 17.9 1.0 OD2 A:ASP158 2.6 31.0 1.0 O A:HOH640 2.7 33.8 1.0 CG A:ASP158 2.9 22.4 1.0 CD2 A:HIS285 3.2 8.6 1.0 CE1 A:HIS285 3.4 10.5 1.0 PA A:UDP402 3.7 57.8 1.0 PB A:UDP402 3.7 71.3 1.0 O3A A:UDP402 3.8 44.2 1.0 O A:HOH622 3.9 45.1 1.0 CB A:ASP158 4.4 14.4 1.0 CG A:HIS285 4.4 12.1 1.0 ND1 A:HIS285 4.5 15.5 1.0 CB A:ASP156 4.5 22.0 1.0 O1B A:UDP402 4.6 59.1 1.0 O5' A:UDP402 4.7 58.4 1.0 C5' A:UDP402 4.7 40.6 1.0 O2B A:UDP402 4.7 62.8 1.0 O1A A:UDP402 4.7 51.7 1.0 C3' A:UDP402 4.8 47.3 1.0 O A:HOH544 4.8 31.9 1.0 OD2 A:ASP156 4.8 41.5 1.0 CG A:ASP156 4.8 25.7 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:69.7 occ:1.00 NE2 B:HIS285 2.1 43.5 1.0 OD2 B:ASP158 2.2 45.7 1.0 O3B B:UDP402 2.2 101.2 1.0 O B:HOH504 2.5 56.1 1.0 O3A B:UDP402 2.6 125.4 1.0 PB B:UDP402 2.8 126.4 1.0 CE1 B:HIS285 2.9 35.1 1.0 CG B:ASP158 3.2 44.8 1.0 O2A B:UDP402 3.2 96.3 1.0 CD2 B:HIS285 3.2 32.1 1.0 O1B B:UDP402 3.3 99.6 1.0 PA B:UDP402 3.5 121.7 1.0 OD1 B:ASP158 3.5 57.7 1.0 ND1 B:HIS285 4.0 35.4 1.0 O2B B:UDP402 4.1 104.4 1.0 CG B:HIS285 4.2 31.0 1.0 OD2 B:ASP156 4.5 46.5 1.0 CB B:ASP158 4.5 37.0 1.0 C5' B:UDP402 4.5 93.5 1.0 O1A B:UDP402 4.5 108.1 1.0 O5' B:UDP402 4.5 97.3 1.0 CE1 B:PHE286 4.8 32.7 1.0 CG2 B:THR217 5.0 35.9 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