Magnesium in PDB 3vzd: Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp

All present enzymatic activity of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp:
2.7.1.91;

The structure of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp, PDB code: 3vzd was solved by X.Min, N.P.Walker, Z.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	102.202, 106.573, 226.020, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 26.9

The structure of Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp also contains other interesting chemical elements:

Chlorine

(Cl)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp (pdb code 3vzd). 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 Sphingosine Kinase 1 with Inhibitor and Adp, PDB code: 3vzd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 Sphingosine Kinase 1 with Inhibitor and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:63.6 occ:1.00 OE2 B:GLU343 2.9 31.2 0.5 O6 B:POP402 3.2 0.1 1.0 O B:ASP341 3.3 37.7 1.0 O B:POP402 3.4 0.0 1.0 C B:GLY342 3.5 37.0 1.0 O B:GLY342 3.5 36.1 1.0 N B:GLY82 3.6 28.4 1.0 CA B:GLY342 3.7 36.7 1.0 CD B:GLU343 3.8 34.1 0.5 CA B:GLY82 3.9 26.2 1.0 O3 B:POP402 3.9 0.9 1.0 P2 B:POP402 3.9 0.3 1.0 N B:GLU343 4.1 37.2 1.0 CG B:GLU343 4.2 35.5 0.5 C B:ASP341 4.3 37.3 1.0 P1 B:POP402 4.3 0.7 1.0 N B:GLY342 4.5 37.2 1.0 O B:HOH537 4.6 45.0 1.0 CA B:GLU343 4.6 38.8 0.5 C B:ASP81 4.6 29.9 1.0 OE1 B:GLU343 4.7 34.5 0.5 CB B:ASP81 4.8 30.4 1.0 O5 B:POP402 4.9 0.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 Sphingosine Kinase 1 with Inhibitor and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:52.9 occ:1.00 O1A C:ADP402 2.4 61.2 1.0 OE2 C:GLU343 2.8 13.9 0.5 O C:ASP341 3.2 29.8 1.0 CA C:GLY82 3.4 26.5 1.0 N C:GLY82 3.4 28.3 1.0 C C:GLY342 3.5 29.3 1.0 O3B C:ADP402 3.5 58.0 1.0 CA C:GLY342 3.5 28.9 1.0 O C:GLY342 3.7 29.2 1.0 CD C:GLU343 3.8 20.2 0.5 PA C:ADP402 3.9 61.8 1.0 N C:GLU343 3.9 29.1 1.0 C C:ASP341 4.1 29.2 1.0 CG C:GLU343 4.1 21.8 0.5 N C:GLY342 4.3 28.4 1.0 C C:ASP81 4.5 30.5 1.0 CA C:GLU343 4.5 28.6 0.5 PB C:ADP402 4.6 57.0 1.0 O C:HOH528 4.7 41.7 1.0 O3A C:ADP402 4.7 59.8 1.0 O5' C:ADP402 4.8 64.0 1.0 C C:GLY82 4.8 25.8 1.0 N C:ASP81 4.8 33.2 1.0 O2A C:ADP402 4.8 57.3 1.0 OE1 C:GLU343 4.9 21.1 0.5 O2B C:ADP402 4.9 56.5 1.0 CB C:GLU343 5.0 26.6 0.5 CB C:ASP81 5.0 31.8 1.0 C5' C:ADP402 5.0 63.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Sphingosine Kinase 1 with Inhibitor and Adp


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 Sphingosine Kinase 1 with Inhibitor and Adp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg403 b:49.0 occ:1.00 O2A E:ADP402 2.4 65.0 1.0 OE2 E:GLU343 2.6 27.0 0.5 O E:ASP341 3.2 29.6 1.0 O3B E:ADP402 3.3 65.3 1.0 N E:GLY82 3.4 26.6 1.0 CA E:GLY82 3.5 25.9 1.0 C E:GLY342 3.5 30.7 1.0 CA E:GLY342 3.6 30.1 1.0 CD E:GLU343 3.6 26.6 0.5 O E:GLY342 3.7 30.8 1.0 N E:GLU343 3.9 31.3 1.0 PA E:ADP402 3.9 64.0 1.0 C E:ASP341 4.1 29.8 1.0 CG E:GLU343 4.3 28.3 0.5 N E:GLY342 4.4 29.7 1.0 C E:ASP81 4.4 27.6 1.0 PB E:ADP402 4.4 66.7 1.0 OE1 E:GLU343 4.5 27.0 0.5 CA E:GLU343 4.6 31.9 0.5 O3A E:ADP402 4.6 65.7 1.0 O5' E:ADP402 4.7 66.9 1.0 O1B E:ADP402 4.7 63.5 1.0 C5' E:ADP402 4.8 66.8 1.0 CB E:ASP81 4.8 29.2 1.0 O E:HOH520 4.8 29.5 1.0 N E:ASP81 4.9 28.4 1.0 CA E:ASP81 4.9 28.9 1.0 O1A E:ADP402 5.0 58.5 1.0 C E:GLY82 5.0 26.7 1.0

Z.Wang, X.Min, S.H.Xiao, S.Johnstone, W.Romanow, D.Meininger, H.Xu, J.Liu, J.Dai, S.An, S.Thibault, N.Walker. Molecular Basis of Sphingosine Kinase 1 Substrate Recognition and Catalysis. Structure V. 21 798 2013.
ISSN: ISSN 0969-2126
PubMed: 23602659
DOI: 10.1016/J.STR.2013.02.025