Magnesium in PDB 5zcu: Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin

All present enzymatic activity of Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin:
3.1.3.16;

The structure of Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin, PDB code: 5zcu was solved by S.Han, Y.Lee, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.50 / 2.41
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	75.036, 134.577, 190.267, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25

The structure of Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin also contains other interesting chemical elements:

Bromine

(Br)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin (pdb code 5zcu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin, PDB code: 5zcu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin


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 RCAR3:PP2C Wild-Type with Pyrabactin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:34.5 occ:1.00 OD2 A:ASP118 1.9 36.3 1.0 OD2 A:ASP368 2.0 42.1 1.0 O C:HOH412 2.0 34.2 1.0 OD1 A:ASP306 2.1 36.3 1.0 O A:HOH509 2.2 30.1 1.0 O A:HOH518 2.3 29.4 1.0 CG A:ASP118 2.8 32.2 1.0 CG A:ASP368 3.1 42.6 1.0 CG A:ASP306 3.1 37.4 1.0 OD1 A:ASP118 3.1 34.0 1.0 OD2 A:ASP306 3.4 35.2 1.0 OD1 A:ASP368 3.5 43.3 1.0 O C:HOH414 3.9 23.8 1.0 MG A:MG402 3.9 38.1 1.0 O4 C:SO4302 3.9 50.8 1.0 O A:HOH512 3.9 29.6 1.0 CB A:ASP118 4.2 25.4 1.0 CB A:ASP368 4.3 40.2 1.0 N A:GLY307 4.4 42.1 1.0 CB A:ASP306 4.4 37.7 1.0 N A:ASP306 4.5 41.4 1.0 O A:HOH517 4.5 36.3 1.0 OD1 A:ASP75 4.6 33.2 1.0 O A:ASN369 4.7 32.1 1.0 CB A:SER305 4.8 42.5 1.0 C A:ASP306 4.8 42.2 1.0 CA A:ASP306 4.8 39.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin


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 RCAR3:PP2C Wild-Type with Pyrabactin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:38.1 occ:1.00 O A:HOH509 2.1 30.1 1.0 O A:GLY119 2.1 29.9 1.0 O A:HOH517 2.2 36.3 1.0 O C:HOH414 2.3 23.8 1.0 OD1 A:ASP118 2.3 34.0 1.0 C A:GLY119 3.3 29.4 1.0 CG A:ASP118 3.5 32.2 1.0 OE1 A:GLU74 3.9 52.6 1.0 MG A:MG401 3.9 34.5 1.0 O4 C:SO4302 4.0 50.8 1.0 N A:GLY119 4.0 26.6 1.0 O A:HOH506 4.0 25.5 1.0 OD2 A:ASP118 4.1 36.3 1.0 O C:HOH412 4.1 34.2 1.0 N A:HIS120 4.2 28.6 1.0 CA A:GLY119 4.2 31.8 1.0 CA A:HIS120 4.3 33.8 1.0 CB A:GLU74 4.3 35.7 1.0 O A:HOH518 4.3 29.4 1.0 OD1 A:ASP75 4.3 33.2 1.0 C A:ASP118 4.4 30.8 1.0 OD1 A:ASP368 4.4 43.3 1.0 O2 C:SO4302 4.5 53.9 1.0 CB A:HIS120 4.6 26.8 1.0 OD1 A:ASN369 4.6 41.9 1.0 OG C:SER100 4.7 34.0 1.0 CB A:ASP118 4.7 25.4 1.0 CB C:SER100 4.7 35.2 1.0 O A:ASP118 4.8 30.7 1.0 S C:SO4302 4.8 53.4 1.0 CA A:ASP118 4.8 25.9 1.0 OD2 A:ASP368 4.8 42.1 1.0 O A:GLU74 4.9 36.2 1.0 CD A:GLU74 4.9 48.6 1.0 C A:GLU74 5.0 36.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin


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 RCAR3:PP2C Wild-Type with Pyrabactin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:37.7 occ:1.00 O B:HOH517 2.1 36.4 1.0 OD2 B:ASP368 2.1 49.1 1.0 OD2 B:ASP118 2.1 33.6 1.0 OD1 B:ASP306 2.2 37.1 1.0 O B:HOH531 2.3 23.5 1.0 CG B:ASP118 3.0 31.4 1.0 CG B:ASP306 3.0 40.2 1.0 CG B:ASP368 3.1 50.3 1.0 OD1 B:ASP118 3.1 31.9 1.0 OD2 B:ASP306 3.1 38.6 1.0 OD1 B:ASP368 3.4 51.0 1.0 O B:HOH502 3.6 36.6 1.0 O4 D:SO4302 3.7 79.1 1.0 MG B:MG402 3.9 43.5 1.0 O B:HOH513 4.0 22.0 1.0 CB B:ASP368 4.4 44.2 1.0 CB B:ASP118 4.4 33.7 1.0 CB B:ASP306 4.5 38.4 1.0 N B:GLY307 4.5 38.1 1.0 N B:ASP306 4.7 38.4 1.0 OD1 B:ASP75 4.9 51.8 1.0 O B:ASN369 4.9 34.6 1.0 S D:SO4302 4.9 79.4 1.0 C B:ASP306 4.9 38.5 1.0 CA B:ASP306 4.9 35.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of RCAR3:PP2C Wild-Type with Pyrabactin


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 RCAR3:PP2C Wild-Type with Pyrabactin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:43.5 occ:1.00 OD1 B:ASP118 2.1 31.9 1.0 O B:GLY119 2.1 35.6 1.0 O B:HOH502 2.1 36.6 1.0 O B:HOH517 2.3 36.4 1.0 C B:GLY119 3.3 35.5 1.0 CG B:ASP118 3.3 31.4 1.0 OD1 B:ASP75 3.5 51.8 1.0 N B:GLY119 3.6 34.7 1.0 MG B:MG401 3.9 37.7 1.0 CB B:GLU74 3.9 45.0 1.0 CA B:GLY119 4.0 33.8 1.0 C B:ASP118 4.0 35.6 1.0 OE1 B:GLU74 4.0 54.4 1.0 OD2 B:ASP118 4.0 33.6 1.0 OD1 B:ASN369 4.0 43.8 1.0 O B:HOH531 4.0 23.5 1.0 O B:GLU74 4.3 35.8 1.0 C B:GLU74 4.3 37.5 1.0 CA B:ASP118 4.3 32.8 1.0 N B:HIS120 4.4 38.7 1.0 OD1 B:ASP368 4.4 51.0 1.0 CB B:ASP118 4.4 33.7 1.0 CG B:ASP75 4.6 49.9 1.0 N B:ASP75 4.6 34.4 1.0 O B:ASP118 4.6 37.0 1.0 CA B:GLU74 4.6 43.4 1.0 CA B:HIS120 4.7 37.9 1.0 O4 D:SO4302 4.8 79.1 1.0 CG B:ASN369 4.8 42.1 1.0 O1 D:SO4302 4.8 77.6 1.0 CB B:ASN369 4.9 38.1 1.0 CD B:GLU74 4.9 52.1 1.0 CG B:GLU74 5.0 46.6 1.0

S.Han, Y.Lee, E.J.Park, M.K.Min, Y.Lee, T.H.Kim, B.G.Kim, S.Lee. Structural Determinants For Pyrabactin Recognition in Aba Receptors in Oryza Sativa. Plant Mol.Biol. V. 100 319 2019.
ISSN: ISSN 0167-4412
PubMed: 30941543
DOI: 10.1007/S11103-019-00862-6