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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7jhi:

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

Magnesium Binding Sites:

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 7jhi

Go back to Magnesium Binding Sites List in 7jhi
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 7jhi

Go back to Magnesium Binding Sites List in 7jhi
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 7jhi

Go back to Magnesium Binding Sites List in 7jhi
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

Reference:

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
Page generated: Tue Dec 15 03:37:52 2020

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