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 / R_free (%)*	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

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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

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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

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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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