Magnesium in PDB 5cvc: Structure of Maize Serine Racemase

The structure of Structure of Maize Serine Racemase, PDB code: 5cvc was solved by Y.Song, L.Zou, J.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.38 / 2.09
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	50.992, 204.017, 211.847, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 22.9

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

Magnesium binding site 1 out of 3 in the Structure of Maize Serine Racemase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Maize Serine Racemase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:28.6 occ:1.00 OE2 A:GLU218 2.0 23.9 1.0 OD1 A:ASP224 2.1 21.6 1.0 O A:HOH515 2.1 24.8 1.0 O A:ALA222 2.1 21.2 1.0 O A:HOH511 2.2 27.0 1.0 O A:HOH519 2.2 33.4 1.0 CG A:ASP224 3.0 22.1 1.0 CD A:GLU218 3.0 26.3 1.0 C A:ALA222 3.3 24.4 1.0 OD2 A:ASP224 3.4 21.7 1.0 CG A:GLU218 3.5 25.0 1.0 N A:ASP224 3.7 24.3 1.0 O A:ALA249 3.9 25.1 1.0 O A:LEU247 4.0 20.4 1.0 N A:SER225 4.1 24.4 1.0 CB A:ALA222 4.1 23.9 1.0 OE1 A:GLU218 4.1 27.4 1.0 N A:ASP223 4.1 23.2 1.0 CB A:ASP224 4.2 23.1 1.0 OG A:SER225 4.2 24.4 1.0 CA A:ALA222 4.3 23.9 1.0 CA A:ASP223 4.3 24.6 1.0 C A:ASP223 4.4 24.5 1.0 CA A:ASP224 4.4 23.6 1.0 O A:ILE192 4.5 20.5 1.0 O A:SER193 4.5 28.0 1.0 C A:ASP224 4.8 25.2 1.0 CB A:SER225 4.8 25.2 1.0 CA A:SER193 4.9 22.2 1.0 CB A:GLU218 5.0 24.4 1.0

Magnesium binding site 2 out of 3 in the Structure of Maize Serine Racemase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Maize Serine Racemase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:31.4 occ:1.00 O B:HOH506 2.1 21.3 1.0 O B:HOH515 2.1 24.6 1.0 O B:HOH516 2.1 26.9 1.0 OE2 B:GLU218 2.2 25.3 1.0 OD1 B:ASP224 2.2 26.7 1.0 O B:ALA222 2.2 26.1 1.0 CG B:ASP224 3.1 26.2 1.0 CD B:GLU218 3.2 27.5 1.0 C B:ALA222 3.4 26.9 1.0 CG B:GLU218 3.5 26.8 1.0 OD2 B:ASP224 3.6 25.7 1.0 O B:ALA249 3.7 27.4 1.0 N B:ASP224 3.8 25.7 1.0 O B:LEU247 3.9 24.6 1.0 CB B:ALA222 4.0 26.8 1.0 N B:SER225 4.2 26.3 1.0 N B:ASP223 4.2 26.8 1.0 CA B:ALA222 4.3 26.6 1.0 OE1 B:GLU218 4.3 28.2 1.0 OG B:SER225 4.3 27.5 1.0 O B:ILE192 4.3 23.8 1.0 CB B:ASP224 4.4 25.3 1.0 CA B:ASP223 4.5 26.6 1.0 O B:SER193 4.5 27.8 1.0 C B:ASP223 4.5 26.4 1.0 CA B:ASP224 4.5 25.8 1.0 CA B:SER193 4.7 24.6 1.0 CB B:SER225 4.8 26.6 1.0 C B:ASP224 4.9 26.6 1.0 C B:LEU247 4.9 25.3 1.0 C B:ALA249 5.0 26.9 1.0 CB B:GLU218 5.0 25.4 1.0

Magnesium binding site 3 out of 3 in the Structure of Maize Serine Racemase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Maize Serine Racemase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:29.8 occ:1.00 OE2 C:GLU218 2.0 33.2 1.0 O C:HOH515 2.0 24.3 1.0 O C:HOH514 2.2 33.3 1.0 OD1 C:ASP224 2.2 31.2 1.0 O C:HOH507 2.2 29.1 1.0 O C:ALA222 2.3 29.6 1.0 CD C:GLU218 3.0 34.3 1.0 CG C:ASP224 3.0 32.1 1.0 OD2 C:ASP224 3.4 30.4 1.0 C C:ALA222 3.4 31.4 1.0 CG C:GLU218 3.5 32.7 1.0 N C:ASP224 3.8 34.2 1.0 O C:ALA249 3.8 35.2 1.0 N C:SER225 4.0 33.8 1.0 OG C:SER225 4.0 36.6 1.0 OE1 C:GLU218 4.1 36.7 1.0 O C:LEU247 4.1 27.6 1.0 CB C:ALA222 4.2 33.0 1.0 O C:ILE192 4.3 29.4 1.0 CB C:ASP224 4.3 32.3 1.0 N C:ASP223 4.3 32.0 1.0 CA C:ALA222 4.4 31.2 1.0 O C:SER193 4.4 30.5 1.0 CA C:ASP223 4.4 35.0 1.0 C C:ASP223 4.5 34.2 1.0 CA C:ASP224 4.5 33.3 1.0 CB C:SER225 4.6 34.3 1.0 C C:ASP224 4.8 33.1 1.0 CA C:SER193 4.8 27.1 1.0 CA C:SER225 4.9 33.1 1.0 CG2 C:ILE192 4.9 28.3 1.0 CB C:GLU218 4.9 31.0 1.0

L.Zou, Y.Song, C.Wang, J.Sun, L.Wang, B.Cheng, J.Fan. Crystal Structure of Maize Serine Racemase with Pyridoxal 5'-Phosphate. Acta Crystallogr.,Sect.F V. 72 165 2016.
ISSN: ESSN 2053-230X
PubMed: 26919519
DOI: 10.1107/S2053230X16000960