Magnesium in PDB 7jho: Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp

All present enzymatic activity of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp:
2.4.1.149;

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp, PDB code: 7jho was solved by Y.Hao, X.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.22 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.651, 76.511, 82.704, 90.00, 109.93, 90.00
R / Rfree (%)	16.5 / 21.1

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp (pdb code 7jho). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp, PDB code: 7jho:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:43.0 occ:1.00 OD2 A:ASP247 2.2 30.4 1.0 O A:HOH731 2.3 37.2 1.0 O2B A:UDP401 2.3 58.1 1.0 NE2 A:HIS376 2.3 24.0 1.0 O A:HOH506 2.4 23.9 1.0 O2A A:UDP401 2.4 50.1 1.0 CG A:ASP247 3.1 21.6 1.0 CD2 A:HIS376 3.1 23.9 1.0 OD1 A:ASP247 3.2 16.8 1.0 CE1 A:HIS376 3.4 27.6 1.0 PB A:UDP401 3.5 0.1 1.0 PA A:UDP401 3.7 72.4 1.0 O1B A:UDP401 3.9 80.4 1.0 O3A A:UDP401 4.0 81.5 1.0 O A:HOH561 4.0 35.2 1.0 O A:HOH583 4.3 42.1 1.0 CG A:HIS376 4.3 21.2 1.0 ND1 A:HIS376 4.4 19.1 1.0 CB A:ASP247 4.5 15.6 1.0 OD2 A:ASP245 4.6 24.1 1.0 O1A A:UDP401 4.6 75.4 1.0 O3B A:UDP401 4.7 78.4 1.0 O5' A:UDP401 4.7 71.1 1.0 O A:HOH568 4.7 36.1 1.0 CB A:SER377 4.7 17.8 1.0 C5' A:UDP401 4.9 59.9 1.0

Magnesium binding site 2 out of 2 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:36.2 occ:1.00 O2B B:UDP402 2.1 47.4 1.0 OD2 B:ASP247 2.2 25.8 1.0 O B:HOH700 2.3 31.4 1.0 O2A B:UDP402 2.3 47.9 1.0 O B:HOH508 2.3 21.2 1.0 NE2 B:HIS376 2.3 20.3 1.0 CG B:ASP247 3.1 25.0 1.0 CD2 B:HIS376 3.2 21.3 1.0 OD1 B:ASP247 3.3 20.7 1.0 PB B:UDP402 3.3 75.0 1.0 CE1 B:HIS376 3.4 22.6 1.0 PA B:UDP402 3.5 71.7 1.0 O3A B:UDP402 3.8 80.2 1.0 O1B B:UDP402 3.9 60.8 1.0 O B:HOH517 3.9 34.5 1.0 CG B:HIS376 4.4 17.8 1.0 ND1 B:HIS376 4.4 21.6 1.0 O5' B:UDP402 4.4 51.3 1.0 O3B B:UDP402 4.5 87.6 1.0 OD2 B:ASP245 4.5 29.4 1.0 CB B:ASP247 4.5 19.3 1.0 O1A B:UDP402 4.6 52.7 1.0 C5' B:UDP402 4.6 43.5 1.0 CB B:SER377 4.8 18.0 1.0

Y.Hao, A.Crequer-Grandhomme, N.Javier, A.Singh, H.Chen, P.Manzanillo, M.C.Lo, X.Huang. Structures and Mechanism of Human Glycosyltransferase Beta 1,3-N-Acetylglucosaminyltransferase 2 (B3GNT2), An Important Player in Immune Homeostasis. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33158990
DOI: 10.1074/JBC.RA120.015306