Magnesium in PDB 3bqp: Crystal Structure of Human Saposin D (Orthorhombic)

The structure of Crystal Structure of Human Saposin D (Orthorhombic), PDB code: 3bqp was solved by G.G.Prive, K.Popovic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.28 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.450, 61.450, 64.570, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.4

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

Magnesium binding site 1 out of 3 in the Crystal Structure of Human Saposin D (Orthorhombic)


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 Saposin D (Orthorhombic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg81 b:23.9 occ:1.00 O A:HOH642 1.8 39.5 1.0 O A:HOH673 2.0 30.2 1.0 O A:HOH654 2.0 46.7 1.0 O A:HOH630 2.0 25.3 1.0 O A:HOH600 4.0 34.8 1.0 OD1 A:ASP41 4.2 21.8 1.0 OD2 A:ASP41 4.3 26.7 1.0 NE2 A:GLN44 4.3 31.1 0.5 CG A:ASP41 4.6 18.7 1.0 O A:HOH577 4.8 30.4 1.0 NE2 A:GLN44 4.9 28.1 0.5

Magnesium binding site 2 out of 3 in the Crystal Structure of Human Saposin D (Orthorhombic)


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 Saposin D (Orthorhombic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg82 b:20.7 occ:1.00 O A:HOH674 2.0 18.4 1.0 O A:HOH675 2.0 24.4 1.0 O B:HOH632 2.1 18.8 1.0 O B:HOH633 2.1 23.8 1.0 O A:HOH606 2.1 26.7 1.0 O A:HOH585 2.1 27.6 1.0 OE2 A:GLU53 4.1 21.9 1.0 OE2 B:GLU53 4.1 22.0 1.0 O A:HOH553 4.2 21.6 1.0 OE1 A:GLU53 4.2 17.1 1.0 O B:HOH575 4.2 20.4 1.0 OE1 B:GLU53 4.3 16.8 1.0 O A:HOH603 4.3 33.5 1.0 O B:HOH620 4.5 38.1 1.0 CD A:GLU53 4.5 18.1 1.0 CE2 A:PHE4 4.6 14.4 1.0 CD B:GLU53 4.6 17.7 1.0 CE2 B:PHE4 4.7 14.0 1.0 O A:HOH529 4.8 20.5 1.0 O B:HOH526 4.9 18.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Human Saposin D (Orthorhombic)


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 Human Saposin D (Orthorhombic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg83 b:26.6 occ:1.00 O A:HOH676 1.9 33.2 1.0 O A:HOH677 1.9 40.5 1.0 O A:LEU39 4.1 17.0 1.0 OD1 A:ASP41 4.2 21.8 1.0 O A:HOH600 4.2 34.8 1.0 O A:HOH534 4.3 25.3 1.0 O A:HOH577 4.3 30.4 1.0 O A:SER37 4.7 26.1 1.0 O A:HOH630 4.7 25.3 1.0 CA A:PRO40 4.9 17.6 1.0 C A:LEU39 4.9 16.1 1.0

K.Popovic, G.G.Prive. Structures of the Human Ceramide Activator Protein Saposin D. Acta Crystallogr.,Sect.D V. 64 589 2008.
ISSN: ISSN 0907-4449
PubMed: 18453694
DOI: 10.1107/S0907444908003120