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

The structure of Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5, PDB code: 8zwp 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)	28.93 / 1.86
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.646, 86.36, 87.187, 90, 95.47, 90
R / Rfree (%)	19.9 / 23.3

The binding sites of Manganese atom in the Structure-Based Mechanism and Specificity of Human Galactosyltransferase B3GALT5 (pdb code 8zwp). 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: 8zwp:
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:30.1 occ:1.00 O3B A:UDP402 2.1 34.6 1.0 O2A A:UDP402 2.2 32.6 1.0 NE2 A:HIS285 2.3 19.6 1.0 OD1 A:ASP158 2.3 26.6 1.0 OD2 A:ASP156 2.3 32.2 1.0 OD2 A:ASP158 2.5 33.2 1.0 CG A:ASP158 2.8 31.3 1.0 CD2 A:HIS285 3.2 21.4 1.0 CE1 A:HIS285 3.3 23.6 1.0 PB A:UDP402 3.3 53.0 1.0 H5'2 A:UDP402 3.4 39.1 1.0 CG A:ASP156 3.5 33.3 1.0 PA A:UDP402 3.5 42.2 1.0 H3' A:UDP402 3.7 37.6 1.0 O3A A:UDP402 3.7 44.5 1.0 O A:HOH544 3.7 39.5 1.0 O A:HOH518 3.9 41.3 1.0 O1B A:UDP402 4.0 56.7 1.0 CB A:ASP156 4.0 21.2 1.0 C5' A:UDP402 4.2 32.5 1.0 CB A:ASP158 4.3 23.1 1.0 O5' A:UDP402 4.4 36.1 1.0 CG A:HIS285 4.4 18.6 1.0 ND1 A:HIS285 4.4 20.1 1.0 OD1 A:ASP156 4.5 24.8 1.0 C3' A:UDP402 4.5 31.3 1.0 O A:HOH613 4.6 36.7 1.0 O2B A:UDP402 4.6 43.1 1.0 O1A A:UDP402 4.7 40.7 1.0 C4' A:UDP402 4.8 33.2 1.0 O A:HOH521 4.9 45.0 1.0 H4' A:UDP402 4.9 39.8 1.0 N A:ASP158 4.9 19.3 1.0 CG2 A:THR217 5.0 19.1 1.0 H5'1 A:UDP402 5.0 39.1 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:50.0 occ:1.00 NE2 B:HIS285 2.3 40.7 1.0 OD1 B:ASP158 2.4 46.2 1.0 O3B B:UDP402 2.4 66.0 1.0 OD2 B:ASP156 2.5 52.2 1.0 OD2 B:ASP158 2.6 47.6 1.0 O2A B:UDP402 2.7 66.7 1.0 CG B:ASP158 2.8 45.2 1.0 O5' B:UDP402 3.2 71.9 1.0 CE1 B:HIS285 3.2 34.9 1.0 CD2 B:HIS285 3.2 38.2 1.0 H3' B:UDP402 3.4 75.5 1.0 PA B:UDP402 3.4 66.9 1.0 PB B:UDP402 3.5 72.5 1.0 CG B:ASP156 3.5 50.5 1.0 O3A B:UDP402 3.9 74.8 1.0 CB B:ASP156 3.9 48.5 1.0 O1B B:UDP402 3.9 71.6 1.0 O B:HOH535 4.2 52.9 1.0 C3' B:UDP402 4.3 62.9 1.0 CB B:ASP158 4.3 44.5 1.0 ND1 B:HIS285 4.3 40.2 1.0 CG B:HIS285 4.4 38.9 1.0 O B:HOH505 4.5 54.4 1.0 C5' B:UDP402 4.5 59.8 1.0 OD1 B:ASP156 4.6 42.6 1.0 O3' B:UDP402 4.8 57.1 1.0 C4' B:UDP402 4.8 61.7 1.0 H4' B:UDP402 4.8 74.0 1.0 O1A B:UDP402 4.8 75.2 1.0 N B:ASP158 4.8 42.7 1.0 O2B B:UDP402 4.8 67.4 1.0 H5'2 B:UDP402 4.9 71.8 1.0 CG2 B:THR217 4.9 39.0 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