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 / Rfree (%) 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

Go back to 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

Go back to 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: Mon Dec 14 22:37:37 2020

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