Manganese in PDB 8zx9: Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5

The structure of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5, PDB code: 8zx9 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)	26.63 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.98, 86.337, 87.509, 90, 95.48, 90
R / Rfree (%)	18.1 / 21.2

The binding sites of Manganese atom in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 (pdb code 8zx9). 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: 8zx9:
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:26.0 occ:1.00 O3B A:UDP402 1.8 42.9 1.0 OD2 A:ASP158 2.0 33.3 1.0 NE2 A:HIS285 2.2 22.0 1.0 O A:HOH537 2.3 28.8 1.0 O2A A:UDP402 2.4 26.3 1.0 O A:HOH538 2.7 33.9 1.0 CG A:ASP158 2.9 23.0 1.0 CE1 A:HIS285 3.0 22.8 1.0 OD1 A:ASP158 3.2 23.4 1.0 PB A:UDP402 3.2 31.8 1.0 CD2 A:HIS285 3.3 22.9 1.0 PA A:UDP402 3.5 23.1 1.0 O3A A:UDP402 3.6 29.7 1.0 O1B A:UDP402 4.1 40.0 1.0 O2B A:UDP402 4.2 36.4 1.0 ND1 A:HIS285 4.2 22.0 1.0 CB A:ASP158 4.3 20.7 1.0 CG A:HIS285 4.3 17.6 1.0 C5' A:UDP402 4.4 20.0 1.0 O A:HOH591 4.5 58.4 1.0 O5' A:UDP402 4.5 28.3 1.0 O1A A:UDP402 4.6 36.6 1.0 O2 A:GAL403 4.8 51.2 1.0 OD2 A:ASP156 4.8 30.7 1.0 C3' A:UDP402 5.0 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:46.7 occ:1.00 O3B B:UDP402 2.2 51.7 1.0 NE2 B:HIS285 2.2 43.5 1.0 OD2 B:ASP158 2.3 47.7 1.0 O1A B:UDP402 2.8 46.2 1.0 OD1 B:ASP158 2.8 51.4 1.0 CG B:ASP158 2.9 45.5 1.0 CE1 B:HIS285 3.1 33.3 1.0 CD2 B:HIS285 3.3 36.0 1.0 O5' B:UDP402 3.3 61.7 1.0 PA B:UDP402 3.4 50.0 1.0 PB B:UDP402 3.5 51.3 1.0 O3A B:UDP402 3.6 40.4 1.0 OD2 B:ASP156 3.9 51.9 1.0 O B:HOH505 4.2 66.9 1.0 ND1 B:HIS285 4.3 31.1 1.0 O2B B:UDP402 4.4 62.6 1.0 CG B:HIS285 4.4 35.6 1.0 CB B:ASP158 4.4 38.8 1.0 O1B B:UDP402 4.4 51.9 1.0 CB B:ASP156 4.6 41.4 1.0 CG B:ASP156 4.6 47.6 1.0 O2 B:GAL403 4.7 75.1 1.0 O B:HOH542 4.7 47.7 1.0 C5' B:UDP402 4.7 40.7 1.0 C3' B:UDP402 4.7 48.8 1.0 O2A B:UDP402 4.9 64.5 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