Magnesium in PDB 7jhi: Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative

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

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative, PDB code: 7jhi 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)	47.33 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.431, 81.385, 157.138, 90.00, 98.63, 90.00
R / Rfree (%)	20.2 / 24.8

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

Iodine	(I)	41 atoms
Chlorine	(Cl)	5 atoms

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

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


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 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:47.5 occ:1.00 O A:HOH501 2.0 26.4 1.0 O1A A:UDP403 2.1 64.4 1.0 OD2 A:ASP247 2.1 27.6 1.0 O3B A:UDP403 2.7 54.2 1.0 OD1 A:ASP247 2.7 22.2 1.0 CG A:ASP247 2.7 21.6 1.0 NE2 A:HIS376 2.8 24.1 1.0 CD2 A:HIS376 3.2 21.6 1.0 PA A:UDP403 3.3 61.9 1.0 C5' A:UDP403 3.3 60.5 1.0 O3A A:UDP403 3.6 67.3 1.0 PB A:UDP403 3.7 71.2 1.0 O5' A:UDP403 3.8 61.5 1.0 OD2 A:ASP245 3.8 40.3 1.0 CE1 A:HIS376 4.0 16.7 1.0 CB A:ASP247 4.2 16.2 1.0 CB A:ASP245 4.5 25.1 1.0 CG A:ASP245 4.5 30.4 1.0 O2B A:UDP403 4.5 68.5 1.0 O2A A:UDP403 4.5 49.8 1.0 CG A:HIS376 4.5 24.2 1.0 O A:HOH552 4.6 23.8 1.0 C4' A:UDP403 4.7 52.5 1.0 O1B A:UDP403 4.8 71.8 1.0 ND1 A:HIS376 4.9 24.6 1.0

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


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 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:47.0 occ:1.00 O B:HOH504 2.6 37.0 1.0 O B:HOH585 2.7 30.9 1.0 NE2 B:HIS376 2.8 44.3 1.0 OD2 B:ASP247 3.4 29.6 1.0 CD2 B:HIS376 3.7 46.9 1.0 CE1 B:HIS376 3.8 37.8 1.0 OD1 B:ASP247 4.1 18.3 1.0 CG B:ASP247 4.2 27.1 1.0 OD1 B:ASP245 4.4 30.3 1.0 ND1 B:HIS376 4.9 43.7 1.0 CG B:HIS376 4.9 42.7 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 Iodide- Derivative within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:33.6 occ:1.00 O2A C:UDP403 2.1 51.0 1.0 OD2 C:ASP247 2.2 31.9 1.0 NE2 C:HIS376 2.2 30.5 1.0 O2B C:UDP403 2.3 50.5 1.0 CE1 C:HIS376 3.1 25.0 1.0 CG C:ASP247 3.1 24.1 1.0 CD2 C:HIS376 3.2 34.1 1.0 PA C:UDP403 3.5 48.6 1.0 OD1 C:ASP247 3.5 24.0 1.0 PB C:UDP403 3.6 46.8 1.0 O3A C:UDP403 3.8 50.2 1.0 ND1 C:HIS376 4.2 38.9 1.0 CG C:HIS376 4.3 40.1 1.0 O1B C:UDP403 4.3 44.8 1.0 O5' C:UDP403 4.4 45.0 1.0 O1A C:UDP403 4.4 38.5 1.0 CB C:ASP247 4.5 20.2 1.0 CB C:SER377 4.5 30.4 1.0 OD1 C:ASP245 4.6 33.2 1.0 O3B C:UDP403 4.6 56.1 1.0 OG C:SER377 5.0 29.0 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