Magnesium in PDB 5x2l: Crystal Structure of Human Serine Racemase

All present enzymatic activity of Crystal Structure of Human Serine Racemase:
4.3.1.17; 4.3.1.18; 5.1.1.18;

The structure of Crystal Structure of Human Serine Racemase, PDB code: 5x2l was solved by T.Obita, K.Matsumoto, H.Mori, N.Toyooka, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.06 / 1.81
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.120, 112.590, 88.000, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 25.8

The binding sites of Magnesium atom in the Crystal Structure of Human Serine Racemase (pdb code 5x2l). 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 Human Serine Racemase, PDB code: 5x2l:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Serine Racemase


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 Human Serine Racemase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:33.6 occ:1.00 OD1 A:ASP216 2.0 34.3 1.0 O A:HOH528 2.1 32.6 1.0 O A:HOH552 2.1 29.1 1.0 O A:HOH543 2.1 26.4 1.0 OE2 A:GLU210 2.1 29.3 1.0 O A:ALA214 2.2 35.1 1.0 CG A:ASP216 3.1 34.2 1.0 CD A:GLU210 3.1 36.8 1.0 C A:ALA214 3.4 35.9 1.0 CG A:GLU210 3.5 31.9 1.0 OD2 A:ASP216 3.6 35.0 1.0 N A:ASP216 3.9 32.4 1.0 O A:SER242 4.0 34.9 1.0 O A:VAL240 4.0 34.1 1.0 CB A:ALA214 4.0 35.0 1.0 ND2 A:ASN229 4.2 39.0 1.0 N A:CYS217 4.2 27.9 1.0 O A:VAL184 4.2 26.6 1.0 OE1 A:GLU210 4.2 28.8 1.0 N A:ASP215 4.3 33.3 1.0 CB A:ASP216 4.3 32.0 1.0 CA A:ALA214 4.3 36.6 1.0 CA A:ASP215 4.4 35.0 1.0 O A:GLY185 4.4 31.9 1.0 C A:ASP215 4.5 34.6 1.0 CA A:ASP216 4.5 33.0 1.0 CB A:CYS217 4.7 29.1 1.0 OD1 A:ASN229 4.9 40.4 1.0 C A:ASP216 4.9 33.5 1.0 CA A:GLY185 5.0 30.5 1.0 CB A:GLU210 5.0 30.5 1.0 CG A:ASN229 5.0 37.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Serine Racemase


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 Human Serine Racemase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:31.2 occ:1.00 OD1 B:ASP216 2.0 34.6 1.0 O B:HOH537 2.1 28.2 1.0 O B:HOH531 2.1 30.9 1.0 OE2 B:GLU210 2.1 28.8 1.0 O B:HOH553 2.1 28.9 1.0 O B:ALA214 2.1 31.6 1.0 CD B:GLU210 3.1 34.2 1.0 CG B:ASP216 3.2 39.6 1.0 C B:ALA214 3.3 36.2 1.0 CG B:GLU210 3.5 28.2 1.0 OD2 B:ASP216 3.8 34.8 1.0 N B:ASP216 3.8 35.6 1.0 O B:VAL240 3.9 33.8 1.0 CB B:ALA214 4.0 34.9 1.0 O B:VAL184 4.0 25.5 1.0 O B:SER242 4.1 34.9 1.0 ND2 B:ASN229 4.2 39.1 1.0 N B:CYS217 4.2 32.7 1.0 OE1 B:GLU210 4.2 28.8 1.0 N B:ASP215 4.2 40.4 1.0 CA B:ALA214 4.2 41.2 1.0 CB B:ASP216 4.3 37.0 1.0 CA B:ASP215 4.4 38.3 1.0 O B:GLY185 4.4 29.4 1.0 C B:ASP215 4.5 35.2 1.0 CA B:ASP216 4.5 36.2 1.0 CB B:CYS217 4.7 30.5 1.0 OD1 B:ASN229 4.8 40.0 1.0 CA B:GLY185 4.9 34.5 1.0 C B:ASP216 4.9 34.6 1.0 CB B:GLU210 5.0 29.6 1.0 CG B:ASN229 5.0 40.6 1.0 C B:VAL184 5.0 27.9 1.0

S.Takahara, K.Nakagawa, T.Uchiyama, T.Yoshida, K.Matsumoto, Y.Kawasumi, M.Mizuguchi, T.Obita, Y.Watanabe, D.Hayakawa, H.Gouda, H.Mori, N.Toyooka. Design, Synthesis, and Evaluation of Novel Inhibitors For Wild-Type Human Serine Racemase. Bioorg. Med. Chem. Lett. 2017.
ISSN: ESSN 1464-3405
PubMed: 29277459
DOI: 10.1016/J.BMCL.2017.12.021