Manganese in PDB 3hmk: Crystal Structure of Serine Racemase

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

The structure of Crystal Structure of Serine Racemase, PDB code: 3hmk was solved by M.A.Smith, J.Barker, V.Mack, A.Ebneth, B.Felicetti, M.Woods, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.10 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.261, 102.960, 120.923, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 28.9

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

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


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Serine Racemase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn340 b:19.0 occ:0.50 O A:HOH375 2.0 19.5 1.0 OD1 A:ASP216 2.1 18.2 1.0 OE2 A:GLU210 2.1 16.9 1.0 O A:HOH395 2.1 13.1 1.0 O A:ALA214 2.2 18.3 1.0 CD A:GLU210 3.1 17.5 1.0 CG A:ASP216 3.1 17.9 1.0 C A:ALA214 3.4 18.1 1.0 CG A:GLU210 3.4 16.6 1.0 OD2 A:ASP216 3.6 18.0 1.0 N A:ASP216 3.9 17.8 1.0 O A:SER242 3.9 21.9 1.0 O A:VAL240 4.0 20.7 1.0 O A:VAL184 4.0 16.1 1.0 CB A:ALA214 4.0 17.9 1.0 OE1 A:GLU210 4.2 19.0 1.0 OD1 A:ASN229 4.2 25.1 1.0 N A:CYS217 4.3 17.8 1.0 CA A:ALA214 4.3 18.1 1.0 N A:ASP215 4.3 18.1 1.0 CB A:ASP216 4.3 17.9 1.0 O A:GLY185 4.5 16.0 1.0 CA A:ASP215 4.5 18.2 1.0 C A:ASP215 4.6 18.0 1.0 CA A:ASP216 4.6 17.7 1.0 ND2 A:ASN229 4.7 24.4 1.0 CA A:GLY185 4.9 16.0 1.0 CB A:CYS217 4.9 18.0 1.0 C A:VAL184 4.9 16.3 1.0 CB A:GLU210 4.9 16.9 1.0 CG A:ASN229 4.9 25.5 1.0 C A:ASP216 5.0 17.6 1.0 C A:SER242 5.0 22.1 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Serine Racemase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Serine Racemase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn340 b:28.0 occ:0.70 O B:HOH351 2.0 18.4 1.0 OD1 B:ASP216 2.1 27.1 1.0 OE2 B:GLU210 2.1 24.4 1.0 O B:HOH394 2.2 20.1 1.0 O B:HOH361 2.2 23.5 1.0 O B:ALA214 2.2 27.6 1.0 CG B:ASP216 3.0 26.9 1.0 CD B:GLU210 3.1 23.3 1.0 C B:ALA214 3.4 27.5 1.0 OD2 B:ASP216 3.4 26.5 1.0 CG B:GLU210 3.5 23.5 1.0 N B:ASP216 3.7 27.5 1.0 O B:VAL184 4.1 20.9 1.0 N B:CYS217 4.1 27.8 1.0 CB B:ALA214 4.2 27.6 1.0 CB B:ASP216 4.2 27.4 1.0 N B:ASP215 4.2 27.4 1.0 OE1 B:GLU210 4.3 22.1 1.0 O B:VAL240 4.3 29.4 1.0 O B:SER242 4.3 31.0 1.0 OD1 B:ASN229 4.3 40.1 1.0 CA B:ASP215 4.4 27.4 1.0 CA B:ALA214 4.4 27.6 1.0 C B:ASP215 4.4 27.5 1.0 CA B:ASP216 4.4 27.4 1.0 O B:GLY185 4.5 21.4 1.0 CB B:CYS217 4.7 27.9 1.0 C B:ASP216 4.8 27.7 1.0 ND2 B:ASN229 5.0 40.1 1.0 CB B:GLU210 5.0 23.3 1.0

M.A.Smith, V.Mack, A.Ebneth, I.Moraes, B.Felicetti, M.Wood, D.Schonfeld, O.Mather, A.Cesura, J.Barker. The Structure of Mammalian Serine Racemase: Evidence For Conformational Changes Upon Inhibitor Binding. J.Biol.Chem. V. 285 12873 2010.
ISSN: ISSN 0021-9258
PubMed: 20106978
DOI: 10.1074/JBC.M109.050062