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

Enzymatic activity of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp-N-Acetylglucosamine

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

Protein crystallography data

The structure of Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp-N-Acetylglucosamine, PDB code: 7jhl 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) 46.42 / 2.26
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.654, 76.638, 134.206, 90.00, 105.27, 90.00
R / Rfree (%) 17.5 / 22.4

Other elements in 7jhl:

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

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp-N-Acetylglucosamine (pdb code 7jhl). 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 with Udp-N-Acetylglucosamine, PDB code: 7jhl:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7jhl

Go back to Magnesium Binding Sites List in 7jhl
Magnesium binding site 1 out of 3 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp-N-Acetylglucosamine


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-N-Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:36.8
occ:1.00
 O1B A:UD1402 2.1 38.3 1.0
O A:HOH609 2.2 32.4 1.0
OD2 A:ASP247 2.2 38.1 1.0
O A:HOH501 2.2 27.8 1.0
NE2 A:HIS376 2.2 32.3 1.0
O2A A:UD1402 2.3 40.0 1.0
CG A:ASP247 3.2 32.2 1.0
CD2 A:HIS376 3.2 31.9 1.0
CE1 A:HIS376 3.3 33.5 1.0
PB A:UD1402 3.4 40.8 1.0
OD1 A:ASP247 3.4 27.3 1.0
PA A:UD1402 3.5 30.9 1.0
O3A A:UD1402 3.7 37.0 1.0
O A:HOH556 3.8 46.0 1.0
O A:HOH599 4.1 46.0 1.0
CG A:HIS376 4.3 28.6 1.0
ND1 A:HIS376 4.3 30.1 1.0
O2B A:UD1402 4.4 42.4 1.0
N2' A:UD1402 4.4 48.8 1.0
O1A A:UD1402 4.4 41.7 1.0
O1' A:UD1402 4.4 45.6 1.0
OD2 A:ASP245 4.4 39.5 1.0
C8' A:UD1402 4.5 43.5 1.0
CB A:ASP247 4.6 28.1 1.0
C5B A:UD1402 4.6 32.5 1.0
O5B A:UD1402 4.6 38.4 1.0
CB A:SER377 4.7 30.3 1.0
C7' A:UD1402 5.0 54.4 1.0

Magnesium binding site 2 out of 3 in 7jhl

Go back to Magnesium Binding Sites List in 7jhl
Magnesium binding site 2 out of 3 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp-N-Acetylglucosamine


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-N-Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:60.9
occ:1.00
 OD1 A:ASP118 3.6 52.0 1.0
OD1 A:ASP114 4.1 48.8 1.0
CB A:LYS117 4.3 33.0 1.0
CG A:ASP118 4.3 45.9 1.0
CG A:ASP114 4.3 56.5 1.0
CD A:LYS117 4.4 41.9 1.0
OD2 A:ASP118 4.5 44.1 1.0
CB A:ASP114 4.6 40.1 1.0
O A:ASP114 4.7 29.1 1.0
OD2 A:ASP114 4.8 54.9 1.0
CA A:ASP114 5.0 34.6 1.0

Magnesium binding site 3 out of 3 in 7jhl

Go back to Magnesium Binding Sites List in 7jhl
Magnesium binding site 3 out of 3 in the Structure of Human Beta 1,3-N-Acetylglucosaminyltransferase 2 with Udp-N-Acetylglucosamine


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 with Udp-N-Acetylglucosamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:28.4
occ:1.00
 OD2 B:ASP247 2.1 27.0 1.0
O B:HOH590 2.1 26.0 1.0
O2A B:UD1402 2.1 32.6 1.0
O1B B:UD1402 2.2 30.5 1.0
O B:HOH504 2.3 23.8 1.0
NE2 B:HIS376 2.3 28.8 1.0
CG B:ASP247 3.0 23.5 1.0
CD2 B:HIS376 3.2 27.7 1.0
OD1 B:ASP247 3.3 24.7 1.0
CE1 B:HIS376 3.4 22.9 1.0
PA B:UD1402 3.4 30.6 1.0
PB B:UD1402 3.5 32.9 1.0
O3A B:UD1402 3.7 37.5 1.0
O B:HOH581 4.1 42.6 1.0
O B:HOH611 4.2 44.7 1.0
C5B B:UD1402 4.4 31.9 1.0
O1A B:UD1402 4.4 32.8 1.0
N2' B:UD1402 4.4 40.9 1.0
CG B:HIS376 4.4 30.5 1.0
CB B:ASP247 4.4 23.2 1.0
OD2 B:ASP245 4.5 34.5 1.0
O1' B:UD1402 4.5 39.0 1.0
ND1 B:HIS376 4.5 33.6 1.0
O5B B:UD1402 4.5 34.4 1.0
O2B B:UD1402 4.5 39.9 1.0
C8' B:UD1402 4.6 43.0 1.0
CB B:SER377 4.7 29.2 1.0
C7' B:UD1402 5.0 43.9 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: Wed Oct 2 21:52:08 2024

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