Manganese in PDB 9h6l: Human B4GALNT1 in Complex with Udp

All present enzymatic activity of Human B4GALNT1 in Complex with Udp:
2.4.1.92;

The structure of Human B4GALNT1 in Complex with Udp, PDB code: 9h6l was solved by J.W.J.Welland, J.E.Deane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.76 / 2.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.183, 133.527, 86.922, 90, 94.83, 90
R / Rfree (%)	19.1 / 23.3

The binding sites of Manganese atom in the Human B4GALNT1 in Complex with Udp (pdb code 9h6l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human B4GALNT1 in Complex with Udp, PDB code: 9h6l:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human B4GALNT1 in Complex with Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human B4GALNT1 in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn602 b:82.9 occ:1.00 OD2 A:ASP358 1.8 77.5 1.0 O2B A:UDP601 1.8 99.1 1.0 O2A A:UDP601 1.8 84.9 1.0 NE2 A:HIS483 2.1 65.8 1.0 CG A:ASP358 2.7 68.9 1.0 CE1 A:HIS483 2.8 57.8 1.0 OD1 A:ASP358 3.0 70.9 1.0 PB A:UDP601 3.1 75.3 1.0 PA A:UDP601 3.2 78.3 1.0 CD2 A:HIS483 3.3 65.1 1.0 O3A A:UDP601 3.5 80.8 1.0 O1B A:UDP601 3.8 84.0 1.0 C5' A:UDP601 4.0 70.3 1.0 ND1 A:HIS483 4.0 58.5 1.0 O5' A:UDP601 4.0 76.2 1.0 NH1 A:ARG288 4.0 75.0 1.0 CB A:ASP358 4.1 62.8 1.0 CG A:HIS483 4.2 62.4 1.0 NH2 A:ARG288 4.3 61.1 1.0 O3B A:UDP601 4.3 75.4 1.0 O1A A:UDP601 4.4 72.9 1.0 CZ A:ARG288 4.7 66.8 1.0

Manganese binding site 2 out of 2 in the Human B4GALNT1 in Complex with Udp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human B4GALNT1 in Complex with Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn602 b:82.5 occ:1.00 O3B B:UDP601 1.8 100.6 1.0 OD2 B:ASP358 1.8 94.9 1.0 O2A B:UDP601 1.8 91.8 1.0 NE2 B:HIS483 1.9 77.5 1.0 CE1 B:HIS483 2.7 69.4 1.0 CG B:ASP358 2.7 73.5 1.0 OD1 B:ASP358 3.1 82.1 1.0 CD2 B:HIS483 3.1 67.7 1.0 PA B:UDP601 3.2 72.1 1.0 PB B:UDP601 3.2 84.0 1.0 O3A B:UDP601 3.4 74.2 1.0 ND1 B:HIS483 3.9 58.9 1.0 O1B B:UDP601 3.9 99.4 1.0 C5' B:UDP601 4.0 75.9 1.0 CG B:HIS483 4.1 63.0 1.0 CB B:ASP358 4.1 67.4 1.0 O5' B:UDP601 4.1 72.2 1.0 NH1 B:ARG288 4.2 80.8 1.0 O1A B:UDP601 4.3 77.7 1.0 O2B B:UDP601 4.3 86.2 1.0 NH2 B:ARG288 4.5 81.8 1.0 CZ B:ARG288 4.9 80.3 1.0

J.W.J.Welland, H.G.Barrow, P.J.Stansfeld, J.E.Deane. Conformational Dynamics and Membrane Insertion Mechanism of B4GALNT1 in Ganglioside Synthesis. Nat Commun V. 16 5442 2025.
ISSN: ESSN 2041-1723
PubMed: 40593514
DOI: 10.1038/S41467-025-60593-9