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

The structure of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5, PDB code: 8zww 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)	29.06 / 1.87
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.709, 86.133, 87.614, 90, 95.68, 90
R / Rfree (%)	19.5 / 23.4

The binding sites of Manganese atom in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 (pdb code 8zww). 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: 8zww:
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:20.7 occ:1.00 O A:HOH503 2.1 18.9 1.0 O2A A:UDP402 2.2 24.0 1.0 NE2 A:HIS285 2.2 17.0 1.0 O2B A:UDP402 2.2 25.2 1.0 OD2 A:ASP158 2.2 17.5 1.0 O A:HOH518 2.5 27.9 1.0 CE1 A:HIS285 3.0 14.9 1.0 CG A:ASP158 3.1 19.5 1.0 OD1 A:ASP158 3.2 15.6 1.0 PB A:UDP402 3.2 50.4 1.0 CD2 A:HIS285 3.3 13.6 1.0 PA A:UDP402 3.4 27.0 1.0 O3A A:UDP402 3.5 26.8 1.0 H5'2 A:UDP402 3.7 26.0 1.0 O3B A:UDP402 3.7 45.2 1.0 O A:HOH507 4.0 27.8 1.0 O A:HOH508 4.0 27.7 1.0 HO2 C:GAL5 4.0 29.1 1.0 H81 C:NGA4 4.1 50.2 1.0 H3' A:UDP402 4.2 26.2 1.0 ND1 A:HIS285 4.2 16.2 1.0 O5' A:UDP402 4.3 21.1 1.0 OD2 A:ASP156 4.3 20.0 1.0 CG A:HIS285 4.4 14.4 1.0 C5' A:UDP402 4.4 21.5 1.0 CB A:ASP158 4.5 13.4 1.0 O1A A:UDP402 4.6 26.8 1.0 O1B A:UDP402 4.6 50.7 1.0 H83 C:NGA4 4.6 50.2 1.0 O2 C:GAL5 4.7 24.1 1.0 O A:HOH624 4.8 39.2 1.0 CG2 A:THR217 4.8 10.1 1.0 C8 C:NGA4 4.9 41.6 1.0 CB A:ASP156 5.0 15.6 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:49.5 occ:1.00 O2A B:UDP402 2.2 58.3 1.0 NE2 B:HIS285 2.2 37.0 1.0 OD2 B:ASP158 2.3 44.3 1.0 O3B B:UDP402 2.4 66.2 1.0 OD1 B:ASP158 2.9 40.1 1.0 CG B:ASP158 3.0 40.8 1.0 CE1 B:HIS285 3.2 30.7 1.0 PB B:UDP402 3.2 78.1 1.0 CD2 B:HIS285 3.2 28.4 1.0 O1B B:UDP402 3.3 86.2 1.0 PA B:UDP402 3.5 62.2 1.0 H5'2 B:UDP402 3.6 61.1 1.0 O3A B:UDP402 3.7 67.3 1.0 OD2 B:ASP156 3.8 48.2 1.0 H3' B:UDP402 4.3 59.4 1.0 ND1 B:HIS285 4.3 32.9 1.0 CG B:HIS285 4.4 32.2 1.0 C5' B:UDP402 4.4 50.7 1.0 O5' B:UDP402 4.4 54.6 1.0 CB B:ASP158 4.5 35.6 1.0 CB B:ASP156 4.6 41.5 1.0 CG B:ASP156 4.6 43.6 1.0 O2B B:UDP402 4.6 61.9 1.0 O1A B:UDP402 4.7 67.5 1.0 CG2 B:THR217 5.0 32.8 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