Magnesium in PDB 2o06: Human Spermidine Synthase

All present enzymatic activity of Human Spermidine Synthase:
2.5.1.16;

The structure of Human Spermidine Synthase, PDB code: 2o06 was solved by J.Min, H.Wu, H.Zeng, P.Loppnau, J.Weigelt, M.Sundstrom, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, A.N.Plotnikov, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.81 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	119.096, 135.239, 83.321, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 21.3

The binding sites of Magnesium atom in the Human Spermidine Synthase (pdb code 2o06). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Spermidine Synthase, PDB code: 2o06:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Spermidine Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Spermidine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:38.4 occ:1.00 O A:HOH760 3.5 21.1 1.0 N A:GLN268 3.6 17.6 1.0 O A:HOH897 3.7 40.1 1.0 CB A:THR267 4.0 17.3 1.0 CA A:THR267 4.0 16.9 1.0 CB A:GLN268 4.2 19.0 1.0 C A:THR267 4.3 17.2 1.0 CA A:GLN268 4.5 18.3 1.0 CG2 A:THR267 4.5 16.9 1.0

Magnesium binding site 2 out of 3 in the Human Spermidine Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Spermidine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:31.8 occ:1.00 OD2 A:ASP200 2.6 30.5 1.0 OD1 A:ASP168 2.7 19.0 1.0 NE2 A:HIS91 2.8 21.1 1.0 CG A:ASP200 3.3 29.0 1.0 N A:GLY201 3.4 21.6 1.0 C A:ASP200 3.5 23.0 1.0 CA A:GLY201 3.5 21.1 1.0 O A:ASP200 3.6 22.6 1.0 CA A:ASP168 3.6 19.7 1.0 CE1 A:HIS91 3.6 21.2 1.0 CG A:ASP168 3.6 20.1 1.0 CB A:ASP168 3.7 20.2 1.0 CD2 A:HIS91 3.8 21.4 1.0 O A:HOH883 3.9 28.5 1.0 OD1 A:ASP200 3.9 34.4 1.0 CB A:LYS198 4.0 23.9 1.0 O A:ASP168 4.2 18.8 1.0 CA A:ASP200 4.2 24.1 1.0 CB A:ASP200 4.2 24.4 1.0 N A:ASP200 4.3 24.2 1.0 C A:ASP168 4.4 19.4 1.0 N A:ASP168 4.6 21.0 1.0 O A:PHE167 4.6 21.9 1.0 CD A:LYS198 4.6 24.9 1.0 OD2 A:ASP168 4.8 20.4 1.0 ND1 A:HIS91 4.8 22.1 1.0 CG A:LYS198 4.8 26.0 1.0 C A:LYS198 4.9 24.2 1.0 C A:GLY201 4.9 20.5 1.0 CA A:LYS198 4.9 24.2 1.0 CG A:HIS91 4.9 20.3 1.0 C A:PHE167 5.0 21.6 1.0

Magnesium binding site 3 out of 3 in the Human Spermidine Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Spermidine Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:35.0 occ:1.00 N B:GLN268 3.4 15.8 1.0 O B:HOH727 3.5 22.3 1.0 O B:HOH764 3.6 27.8 1.0 CA B:THR267 3.8 17.4 1.0 CB B:THR267 3.8 17.9 1.0 C B:THR267 4.1 17.0 1.0 CB B:GLN268 4.1 17.2 1.0 CA B:GLN268 4.3 16.5 1.0 CG2 B:THR267 4.4 17.7 1.0 O B:HOH861 4.7 51.9 1.0 O B:HOH806 4.9 31.1 1.0

H.Wu, J.Min, Y.Ikeguchi, H.Zeng, A.Dong, P.Loppnau, A.E.Pegg, A.N.Plotnikov. Structure and Mechanism of Spermidine Synthases. Biochemistry V. 46 8331 2007.
ISSN: ISSN 0006-2960
PubMed: 17585781
DOI: 10.1021/BI602498K