Magnesium in PDB 5ylu: Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan

Enzymatic activity of Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan

All present enzymatic activity of Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan:
3.6.3.10;

Protein crystallography data

The structure of Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan, PDB code: 5ylu was solved by K.Abe, K.Irie, H.Nakanishi, Y.Fujiyoshi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.18 / 2.80
*Space group*	P 3₁ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	104.820, 104.820, 367.080, 90.00, 90.00, 120.00
*R / R_free (%)*	23.7 / 28.8

Other elements in 5ylu:

The structure of Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan (pdb code 5ylu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan, PDB code: 5ylu:

Magnesium binding site 1 out of 1 in 5ylu

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Magnesium Binding Sites List in 5ylu

Magnesium binding site 1 out of 1 in the Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Gastric Proton Pump Complexed with Vonoprazan within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg1104 b:56.1 occ:1.00	OD2	A:ASP726	1.6	31.7	1.0
	F3	A:BFD385	1.8	32.9	1.0
	OD1	A:ASP726	1.9	35.0	1.0
	CG	A:ASP726	2.0	32.2	1.0
	OD2	A:BFD385	2.8	24.9	1.0
	O	A:THR387	2.9	30.6	1.0
	BE	A:BFD385	3.0	26.9	1.0
	F2	A:BFD385	3.1	33.1	1.0
	OD1	A:BFD385	3.3	25.8	1.0
	CG	A:BFD385	3.3	25.1	1.0
	O	A:SER225	3.4	29.1	1.0
	CB	A:ASP726	3.6	25.9	1.0
	ND2	A:ASN729	3.7	30.2	1.0
	OD1	A:ASN729	3.7	32.7	1.0
	C	A:THR387	4.0	30.0	1.0
	OD2	A:ASP730	4.1	34.9	1.0
	CG	A:ASN729	4.2	29.7	1.0
	N	A:GLY727	4.2	27.6	1.0
	F1	A:BFD385	4.3	28.7	1.0
	CB	A:THR387	4.4	25.5	1.0
	C	A:SER225	4.5	28.7	1.0
	CG	A:ASP730	4.6	25.4	1.0
	CA	A:ASP726	4.6	27.1	1.0
	O	A:THR228	4.6	30.7	1.0
	CA	A:THR387	4.6	26.8	1.0
	N	A:THR387	4.6	26.3	1.0
	OD1	A:ASP730	4.7	26.0	1.0
	N	A:ASP726	4.7	26.1	1.0
	CB	A:BFD385	4.8	23.9	1.0
	C	A:ASP726	4.9	28.6	1.0
	CG2	A:THR387	4.9	22.4	1.0
	CA	A:GLY727	5.0	30.7	1.0

Reference:

K.Abe, K.Irie, H.Nakanishi, H.Suzuki, Y.Fujiyoshi. Crystal Structures of the Gastric Proton Pump Nature V. 556 214 2018.
ISSN: ESSN 1476-4687
PubMed: 29618813
DOI: 10.1038/S41586-018-0003-8

Page generated: Wed Aug 13 01:01:46 2025

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