Magnesium in PDB 2ddt: Crystal Structure of Sphingomyelinase From Bacillus Cereus with Magnesium Ion

All present enzymatic activity of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Magnesium Ion:
3.1.4.12;

The structure of Crystal Structure of Sphingomyelinase From Bacillus Cereus with Magnesium Ion, PDB code: 2ddt was solved by H.Ago, M.Oda, H.Tsuge, N.Katunuma, M.Miyano, J.Sakurai, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.69 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.844, 50.893, 59.506, 81.87, 81.84, 79.68
R / Rfree (%)	19.3 / 23

The binding sites of Magnesium atom in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Magnesium Ion (pdb code 2ddt). 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 Sphingomyelinase From Bacillus Cereus with Magnesium Ion, PDB code: 2ddt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Magnesium Ion


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 Sphingomyelinase From Bacillus Cereus with Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg310 b:19.4 occ:1.00 O A:HOH367 2.1 19.6 1.0 OE1 A:GLU53 2.1 16.6 1.0 O A:HOH322 2.1 14.2 1.0 O A:HOH326 2.2 14.7 1.0 O A:HOH352 2.3 18.1 1.0 O A:HOH384 2.4 20.9 1.0 CD A:GLU53 3.0 16.8 1.0 OE2 A:GLU53 3.2 18.0 1.0 ND2 A:ASN16 4.0 15.3 1.0 OD1 A:ASN16 4.1 15.4 1.0 CD1 A:TYR18 4.2 21.9 1.0 OD2 A:ASP295 4.2 22.3 1.0 O A:HOH426 4.2 23.5 1.0 NE2 A:HIS296 4.3 19.1 1.0 CG A:GLU53 4.3 13.2 1.0 CD2 A:HIS296 4.4 14.7 1.0 OD1 A:ASP295 4.4 17.7 1.0 O A:HOH500 4.4 27.1 1.0 CG A:ASN16 4.4 11.4 1.0 O A:HOH777 4.5 42.2 1.0 O A:HOH382 4.5 20.2 1.0 CE1 A:TYR18 4.6 19.5 1.0 O A:HOH731 4.7 40.0 1.0 O A:HOH558 4.7 29.2 1.0 O A:HOH677 4.7 35.2 1.0 CG A:ASP295 4.7 17.3 1.0 O A:HOH336 4.9 16.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Magnesium Ion


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 Sphingomyelinase From Bacillus Cereus with Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg311 b:16.6 occ:1.00 OE1 A:GLU99 1.9 17.2 1.0 O A:PHE55 2.1 13.3 1.0 OD2 A:ASP100 2.1 19.1 1.0 O A:HOH330 2.2 15.6 1.0 O A:HOH372 2.3 20.2 1.0 OD1 A:ASN57 2.4 15.7 1.0 CD A:GLU99 3.0 17.3 1.0 CG A:ASP100 3.0 13.3 1.0 C A:PHE55 3.2 11.3 1.0 OE2 A:GLU99 3.4 20.1 1.0 CG A:ASN57 3.5 16.2 1.0 OD1 A:ASP100 3.7 15.6 1.0 NH2 A:ARG80 3.8 14.2 1.0 N A:ASP100 3.9 15.0 1.0 CA A:PHE55 3.9 12.6 1.0 CB A:ASP100 4.0 14.0 1.0 N A:ASN57 4.1 13.5 1.0 ND2 A:ASN57 4.1 16.1 1.0 NE A:ARG80 4.1 17.9 1.0 CG A:GLU99 4.3 17.4 1.0 O A:HOH636 4.3 33.9 1.0 N A:ASP56 4.3 13.3 1.0 CZ A:ARG80 4.3 18.9 1.0 O A:HOH604 4.4 31.5 1.0 C A:ASP56 4.5 13.0 1.0 CB A:PHE55 4.5 12.3 1.0 CA A:ASP56 4.5 12.8 1.0 O A:HOH493 4.5 26.8 1.0 CA A:ASP100 4.6 15.1 1.0 CB A:ASN57 4.6 16.2 1.0 CA A:ASN57 4.6 15.1 1.0 CA A:GLU99 4.8 17.7 1.0 C A:GLU99 4.8 15.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Magnesium Ion


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 Sphingomyelinase From Bacillus Cereus with Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg308 b:19.6 occ:1.00 OE1 B:GLU53 2.0 15.8 1.0 O B:HOH334 2.0 15.8 1.0 O B:HOH328 2.1 15.4 1.0 O B:HOH351 2.3 18.3 1.0 O B:HOH353 2.3 18.6 1.0 O B:HOH386 2.4 21.5 1.0 CD B:GLU53 3.0 15.7 1.0 OE2 B:GLU53 3.3 18.2 1.0 O B:HOH505 3.9 26.9 1.0 ND2 B:ASN16 4.0 12.6 1.0 OD1 B:ASN16 4.2 14.3 1.0 O B:HOH816 4.2 43.8 1.0 OD2 B:ASP295 4.2 21.9 1.0 NE2 B:HIS296 4.3 16.5 1.0 CD1 B:TYR18 4.3 22.9 1.0 O B:HOH385 4.3 19.8 1.0 CG B:GLU53 4.4 13.5 1.0 OD1 B:ASP295 4.4 18.9 1.0 CD2 B:HIS296 4.4 16.9 1.0 CG B:ASN16 4.5 11.1 1.0 O B:HOH726 4.6 38.9 1.0 CE1 B:TYR18 4.7 22.1 1.0 CG B:ASP295 4.8 18.3 1.0 O B:HOH771 4.8 41.4 1.0 O B:HOH375 4.8 20.1 1.0 O B:HOH721 4.9 37.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Sphingomyelinase From Bacillus Cereus with Magnesium Ion


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 Sphingomyelinase From Bacillus Cereus with Magnesium Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg309 b:16.9 occ:1.00 OE1 B:GLU99 1.9 17.0 1.0 O B:HOH400 2.1 21.1 1.0 O B:PHE55 2.1 15.3 1.0 O B:HOH383 2.2 20.8 1.0 OD2 B:ASP100 2.2 19.0 1.0 OD1 B:ASN57 2.3 18.6 1.0 CD B:GLU99 3.0 18.4 1.0 CG B:ASP100 3.1 14.4 1.0 C B:PHE55 3.2 13.4 1.0 OE2 B:GLU99 3.4 22.3 1.0 CG B:ASN57 3.4 17.4 1.0 OD1 B:ASP100 3.7 15.5 1.0 CA B:PHE55 3.9 13.0 1.0 N B:ASP100 3.9 14.8 1.0 NH2 B:ARG80 4.0 14.5 1.0 N B:ASN57 4.0 14.4 1.0 CB B:ASP100 4.0 16.4 1.0 ND2 B:ASN57 4.0 20.2 1.0 O B:HOH523 4.2 28.1 1.0 NE B:ARG80 4.2 22.3 1.0 CG B:GLU99 4.3 17.4 1.0 N B:ASP56 4.3 15.0 1.0 O B:HOH465 4.4 25.2 1.0 C B:ASP56 4.5 14.6 1.0 CZ B:ARG80 4.5 18.7 1.0 CA B:ASP56 4.5 15.0 1.0 CB B:PHE55 4.5 12.6 1.0 CB B:ASN57 4.6 16.8 1.0 O B:HOH487 4.6 26.2 1.0 CA B:ASP100 4.6 14.6 1.0 CA B:ASN57 4.6 15.5 1.0 CA B:GLU99 4.8 17.3 1.0 C B:GLU99 4.9 15.9 1.0

H.Ago, M.Oda, M.Takahashi, H.Tsuge, S.Ochi, N.Katunuma, M.Miyano, J.Sakurai. Structural Basis of the Sphingomyelin Phosphodiesterase Activity in Neutral Sphingomyelinase From Bacillus Cereus. J.Biol.Chem. V. 281 16157 2006.
ISSN: ISSN 0021-9258
PubMed: 16595670
DOI: 10.1074/JBC.M601089200