Magnesium in PDB 6dyy: Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol

Enzymatic activity of Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol

All present enzymatic activity of Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol:
3.2.2.9;

Protein crystallography data

The structure of Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol, PDB code: 6dyy was solved by R.K.Harijan, R.G.Ducati, J.B.Bonanno, S.C.Almo, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	88.44 / 1.61
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	72.564, 74.028, 176.887, 90.00, 90.00, 90.00
*R / R_free (%)*	17.9 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol (pdb code 6dyy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol, PDB code: 6dyy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6dyy

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Magnesium Binding Sites List in 6dyy

Magnesium binding site 1 out of 2 in the Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol

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 Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg302 b:32.0 occ:1.00	O	A:HOH418	2.0	32.7	1.0
	O	A:HOH591	2.0	35.6	1.0
	OE1	A:GLU161	4.1	34.3	1.0
	O	A:HOH492	4.2	24.9	1.0
	CD	A:GLU161	4.5	33.0	1.0
	OE2	A:GLU161	4.8	35.7	1.0
	O	A:HOH548	4.9	33.5	1.0
	CB	A:GLU161	5.0	26.1	1.0

Magnesium binding site 2 out of 2 in 6dyy

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Magnesium Binding Sites List in 6dyy

Magnesium binding site 2 out of 2 in the Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Helicobacter Pylori 5'-Methylthioadenosine/S- Adenosyl Homocysteine Nucleosidase (Mtan) Complexed with (3R,4S)-1- ((4-Amino-5H-Pyrrolo[3,2-D]Pyrimidin-7-Yl)Methyl)-4-(((3-(1-Butyl-1H- 1,2,3-Triazol-4-Yl)Propyl)Thio)Methyl)Pyrrolidin-3-Ol within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg304 b:28.8 occ:1.00	O	B:HOH401	1.9	35.9	1.0
	O	B:HOH601	2.0	32.9	1.0
	O	B:HOH453	2.0	28.6	1.0
	O	B:HOH424	2.2	32.6	1.0
	NZ	B:LYS133	3.5	40.8	1.0
	OE1	B:GLU229	3.8	39.4	1.0
	OE2	B:GLU137	4.0	26.2	1.0
	OE1	B:GLU137	4.1	24.6	1.0
	OE2	B:GLU229	4.2	33.4	1.0
	OE2	D:GLU202	4.2	31.2	1.0
	O	B:HOH582	4.3	28.4	1.0
	O	B:HOH432	4.3	47.9	1.0
	CD	B:GLU229	4.4	33.8	1.0
	CD	B:GLU137	4.5	23.9	1.0
	O	D:HOH451	4.9	36.2	1.0
	CD	D:GLU202	4.9	31.2	1.0
	CE	B:LYS133	4.9	35.4	1.0

Reference:

R.K.Harijan, O.Hoff, R.G.Ducati, R.S.Firestone, B.M.Hirsch, G.B.Evans, V.L.Schramm, P.C.Tyler. Selective Inhibitors of Helicobacter Pylori Methylthioadenosine Nucleosidase and Human Methylthioadenosine Phosphorylase. J. Med. Chem. V. 62 3286 2019.
ISSN: ISSN 1520-4804
PubMed: 30860833
DOI: 10.1021/ACS.JMEDCHEM.8B01642

Page generated: Wed Aug 13 05:34:03 2025

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