Magnesium in PDB 5wwd: Crystal Structure of ATNUDX1

All present enzymatic activity of Crystal Structure of ATNUDX1:
3.6.1.22; 3.6.1.55; 3.6.1.67;

The structure of Crystal Structure of ATNUDX1, PDB code: 5wwd was solved by J.Liu, Z.Guan, L.Yan, T.Zou, P.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.12 / 1.39
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.522, 83.181, 115.224, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 17.7

The binding sites of Magnesium atom in the Crystal Structure of ATNUDX1 (pdb code 5wwd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of ATNUDX1, PDB code: 5wwd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of ATNUDX1


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 ATNUDX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:39.4 occ:1.00 MG A:MG205 2.3 45.7 1.0 O A:HOH342 2.7 63.2 1.0 ND1 A:HIS42 2.9 48.9 1.0 N A:HIS42 3.0 16.1 1.0 O A:HOH355 3.3 45.3 1.0 CA A:GLY41 3.4 17.9 1.0 O A:HOH302 3.6 68.3 1.0 CG A:HIS42 3.7 39.3 1.0 C A:GLY41 3.7 15.1 1.0 CB A:HIS42 3.8 22.3 1.0 CE1 A:HIS42 3.9 49.1 1.0 CA A:HIS42 4.0 14.6 1.0 OE2 A:GLU56 4.1 32.5 1.0 O A:HOH433 4.2 36.8 1.0 OE1 A:GLU56 4.4 27.1 1.0 NZ A:LYS110 4.6 45.6 1.0 CD A:GLU56 4.6 29.7 1.0 O A:HOH455 4.6 47.3 1.0 O A:HOH365 4.8 46.3 1.0 N A:GLY41 4.8 15.9 1.0 O A:GLY40 4.9 18.6 1.0 MG A:MG206 4.9 41.0 1.0 O A:GLY41 4.9 16.5 1.0 CD2 A:HIS42 4.9 49.0 1.0 NE2 A:HIS42 5.0 51.2 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of ATNUDX1


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 ATNUDX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:45.7 occ:1.00 O A:HOH302 2.1 68.3 1.0 MG A:MG204 2.3 39.4 1.0 O A:HOH365 2.5 46.3 1.0 O A:HOH342 2.7 63.2 1.0 OE2 A:GLU56 3.4 32.5 1.0 O A:HOH455 3.6 47.3 1.0 MG A:MG206 3.6 41.0 1.0 OE1 A:GLU56 4.0 27.1 1.0 CD A:GLU56 4.1 29.7 1.0 N A:HIS42 4.2 16.1 1.0 NH1 A:ARG55 4.5 21.0 1.0 OE1 A:GLU59 4.5 30.8 1.0 CB A:HIS42 4.6 22.3 1.0 ND1 A:HIS42 4.7 48.9 1.0 O A:HOH355 4.8 45.3 1.0 CA A:GLY41 4.8 17.9 1.0 O A:HIS42 4.9 18.4 1.0 CA A:HIS42 5.0 14.6 1.0 C A:GLY41 5.0 15.1 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of ATNUDX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:41.0 occ:1.00 O A:HOH342 2.5 63.2 1.0 OE2 A:GLU107 2.6 34.3 1.0 OE1 A:GLU59 2.6 30.8 1.0 OE1 A:GLU56 3.0 27.1 1.0 O A:HOH365 3.3 46.3 1.0 CD A:GLU107 3.4 24.8 1.0 OE1 A:GLU107 3.5 28.6 1.0 OE2 A:GLU60 3.6 25.0 1.0 MG A:MG205 3.6 45.7 1.0 CD A:GLU59 3.8 23.0 1.0 CB A:GLU59 3.8 18.4 1.0 CD A:GLU56 3.9 29.7 1.0 CG A:GLU60 4.0 16.1 1.0 NZ A:LYS110 4.1 45.6 1.0 CD A:GLU60 4.2 20.8 1.0 OE2 A:GLU56 4.3 32.5 1.0 CG A:GLU59 4.4 22.4 1.0 O A:HOH302 4.5 68.3 1.0 O A:HOH355 4.8 45.3 1.0 OE2 A:GLU59 4.8 27.9 1.0 CG A:GLU107 4.8 24.3 1.0 MG A:MG204 4.9 39.4 1.0 O A:GLU56 4.9 14.9 1.0 CA A:GLU56 5.0 14.4 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of ATNUDX1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg204 b:51.6 occ:1.00 MG B:MG205 2.3 42.6 1.0 O B:HOH363 3.1 38.3 1.0 OE2 B:GLU56 3.4 28.8 1.0 MG B:MG206 3.8 44.5 1.0 OE1 B:GLU56 3.9 29.9 1.0 ND1 B:HIS42 4.0 56.0 1.0 CD B:GLU56 4.1 28.5 1.0 N B:HIS42 4.1 16.9 1.0 NZ B:LYS110 4.5 40.1 1.0 CA B:GLY41 4.5 18.9 1.0 CB B:HIS42 4.7 19.1 1.0 CG B:HIS42 4.7 46.4 1.0 C B:GLY41 4.8 15.4 1.0 OE1 B:GLU59 4.9 30.3 1.0 CE1 B:HIS42 4.9 58.2 1.0 CA B:HIS42 5.0 15.7 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of ATNUDX1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg205 b:42.6 occ:1.00 MG B:MG204 2.3 51.6 1.0 ND1 B:HIS42 2.6 56.0 1.0 N B:HIS42 3.1 16.9 1.0 CE1 B:HIS42 3.1 58.2 1.0 CG B:HIS42 3.2 46.4 1.0 CA B:GLY41 3.6 18.9 1.0 CB B:HIS42 3.7 19.1 1.0 C B:GLY41 3.8 15.4 1.0 NE2 B:HIS42 4.0 56.5 1.0 CA B:HIS42 4.0 15.7 1.0 CD2 B:HIS42 4.0 55.3 1.0 OE2 B:GLU56 4.4 28.8 1.0 NZ B:LYS110 4.6 40.1 1.0 OE1 B:GLU56 4.8 29.9 1.0 CD B:GLU56 4.9 28.5 1.0 N B:GLY41 5.0 16.8 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of ATNUDX1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of ATNUDX1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg206 b:44.5 occ:1.00 OE2 B:GLU107 2.6 35.3 1.0 OE1 B:GLU59 2.9 30.3 1.0 OE1 B:GLU56 3.0 29.9 1.0 CD B:GLU107 3.4 26.6 1.0 OE1 B:GLU107 3.4 29.2 1.0 NZ B:LYS110 3.6 40.1 1.0 CG B:GLU60 3.7 17.4 1.0 O B:HOH363 3.8 38.3 1.0 CB B:GLU59 3.8 20.8 1.0 MG B:MG204 3.8 51.6 1.0 OE2 B:GLU60 4.0 40.6 1.0 CD B:GLU59 4.0 26.1 1.0 CD B:GLU56 4.1 28.5 1.0 CD B:GLU60 4.3 29.1 1.0 OE2 B:GLU56 4.5 28.8 1.0 CG B:GLU59 4.5 24.4 1.0 CE B:LYS110 4.7 43.4 1.0 CG B:GLU107 4.8 21.0 1.0 O B:GLU56 4.8 15.4 1.0 C B:GLU59 4.9 16.6 1.0 N B:GLU60 4.9 14.7 1.0 CA B:GLU59 5.0 17.6 1.0

J.Liu, Z.Guan, H.Liu, L.Qi, D.Zhang, T.Zou, P.Yin. Structural Insights Into the Substrate Recognition Mechanism of Arabidopsis Gpp-Bound NUDX1 For Noncanonical Monoterpene Biosynthesis. Mol Plant V. 11 218 2018.
ISSN: ESSN 1752-9867
PubMed: 29066356
DOI: 10.1016/J.MOLP.2017.10.006