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Magnesium in PDB 2f9r: Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom

Enzymatic activity of Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom

All present enzymatic activity of Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom:
3.1.4.41;

Protein crystallography data

The structure of Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom, PDB code: 2f9r was solved by M.T.Murakami, A.Gabdoulkhakov, M.F.Fernandes-Pedrosa, C.Betzel, D.V.Tambourgi, R.K.Arni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.85
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 140.587, 140.587, 113.608, 90.00, 90.00, 120.00
R / Rfree (%) 18.7 / 23.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom (pdb code 2f9r). 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 the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom, PDB code: 2f9r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2f9r

Go back to Magnesium Binding Sites List in 2f9r
Magnesium binding site 1 out of 4 in the Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom


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 the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:18.8
occ:0.60
 OD1 A:ASP34 1.7 17.2 1.0
O A:HOH719 2.3 28.4 1.0
OE2 A:GLU32 2.3 24.3 1.0
OD2 A:ASP91 2.5 25.5 1.0
CG A:ASP34 2.8 15.6 1.0
CD A:GLU32 3.1 17.0 1.0
OE1 A:GLU32 3.3 18.2 1.0
CG A:ASP91 3.3 19.5 1.0
OD2 A:ASP34 3.4 16.1 1.0
CB A:ASP91 3.5 15.5 1.0
CZ3 A:TRP230 3.5 22.7 0.6
NZ A:LYS93 3.8 27.1 1.0
CH2 A:TRP230 3.9 23.0 0.6
CB A:ASP34 4.0 13.4 1.0
CD2 A:HIS47 4.1 19.0 1.0
CE A:LYS93 4.2 21.9 1.0
CZ3 A:TRP230 4.3 20.5 0.4
NE2 A:HIS12 4.4 16.8 1.0
CG A:GLU32 4.4 11.9 1.0
OD1 A:ASP91 4.5 26.5 1.0
CA A:ASP34 4.5 14.4 1.0
CD2 A:HIS12 4.7 16.9 1.0
NE2 A:HIS47 4.7 21.4 1.0
CE3 A:TRP230 4.7 23.5 0.6
O A:HOH683 4.8 28.6 1.0
N A:ASP34 4.8 12.8 1.0
CA A:ASP91 5.0 13.8 1.0

Magnesium binding site 2 out of 4 in 2f9r

Go back to Magnesium Binding Sites List in 2f9r
Magnesium binding site 2 out of 4 in the Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom


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 the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:19.7
occ:1.00
 OD1 B:ASP34 1.8 16.5 1.0
O B:HOH734 1.9 37.5 1.0
O B:HOH733 2.0 31.0 1.0
OE2 B:GLU32 2.1 25.1 1.0
OD2 B:ASP91 2.1 24.2 1.0
CG B:ASP34 3.0 14.6 1.0
CD B:GLU32 3.0 19.2 1.0
CG B:ASP91 3.2 17.5 1.0
OE1 B:GLU32 3.3 17.5 1.0
CB B:ASP91 3.5 13.4 1.0
OD2 B:ASP34 3.5 13.3 1.0
NZ B:LYS93 3.7 28.0 1.0
CZ3 B:TRP230 4.2 26.2 0.5
CB B:ASP34 4.2 13.3 1.0
CE B:LYS93 4.2 22.6 1.0
CD2 B:HIS47 4.3 14.5 1.0
CG B:GLU32 4.3 13.8 1.0
OD1 B:ASP91 4.3 23.8 1.0
NE2 B:HIS12 4.4 14.9 1.0
CD2 B:HIS12 4.6 17.1 1.0
CA B:ASP34 4.6 12.8 1.0
O B:HOH760 4.8 29.5 1.0
NE2 B:HIS47 4.8 15.1 1.0
CH2 B:TRP230 4.8 25.5 0.5
N B:ASP34 4.9 13.0 1.0

Magnesium binding site 3 out of 4 in 2f9r

Go back to Magnesium Binding Sites List in 2f9r
Magnesium binding site 3 out of 4 in the Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom


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 the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:26.0
occ:0.60
 OD1 C:ASP34 1.8 19.1 1.0
OE2 C:GLU32 2.0 29.1 1.0
OD2 C:ASP91 2.3 27.7 1.0
CG C:ASP34 2.9 17.1 1.0
CD C:GLU32 3.0 23.2 1.0
CG C:ASP91 3.3 22.8 1.0
OE1 C:GLU32 3.4 23.5 1.0
CB C:ASP91 3.5 19.8 1.0
OD2 C:ASP34 3.5 15.5 1.0
NZ C:LYS93 3.9 27.6 1.0
CB C:ASP34 4.2 17.2 1.0
CE C:LYS93 4.2 22.8 1.0
CD2 C:HIS47 4.3 18.6 1.0
CG C:GLU32 4.3 20.0 1.0
NE2 C:HIS12 4.3 15.8 1.0
OD1 C:ASP91 4.4 28.9 1.0
CZ3 C:TRP230 4.5 34.5 0.5
CA C:ASP34 4.6 16.9 1.0
CD2 C:HIS12 4.6 15.2 1.0
CH2 C:TRP230 4.7 34.6 0.5
N C:ASP34 4.8 16.8 1.0
NE2 C:HIS47 4.9 21.0 1.0
CA C:ASP91 5.0 19.0 1.0

Magnesium binding site 4 out of 4 in 2f9r

Go back to Magnesium Binding Sites List in 2f9r
Magnesium binding site 4 out of 4 in the Crystal Structure of the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom


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 the Inactive State of the Smase I, A Sphingomyelinase D From Loxosceles Laeta Venom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:19.1
occ:0.80
 OD1 D:ASP34 1.7 17.9 1.0
OE2 D:GLU32 2.1 24.4 1.0
OD2 D:ASP91 2.2 28.3 1.0
O D:HOH767 2.4 31.5 1.0
CG D:ASP34 2.9 17.7 1.0
CD D:GLU32 3.0 20.1 1.0
CG D:ASP91 3.1 23.3 1.0
CB D:ASP91 3.3 19.2 1.0
OE1 D:GLU32 3.3 20.8 1.0
OD2 D:ASP34 3.5 17.1 1.0
CZ3 D:TRP230 3.5 31.8 0.5
CZ3 D:TRP230 3.6 33.4 0.5
CH2 D:TRP230 3.6 33.5 0.5
NZ D:LYS93 3.8 30.9 1.0
CB D:ASP34 4.0 16.1 1.0
CE D:LYS93 4.1 27.9 1.0
CH2 D:TRP230 4.1 31.5 0.5
CG D:GLU32 4.2 16.3 1.0
OD1 D:ASP91 4.3 27.6 1.0
CD2 D:HIS47 4.3 18.9 1.0
CA D:ASP34 4.5 15.4 1.0
CE3 D:TRP230 4.6 31.6 0.5
NE2 D:HIS12 4.6 16.1 1.0
N D:ASP34 4.8 14.9 1.0
CD2 D:HIS12 4.8 16.6 1.0
CA D:ASP91 4.8 19.5 1.0
CZ2 D:TRP230 4.8 33.6 0.5
CE3 D:TRP230 4.9 33.1 0.5
NE2 D:HIS47 4.9 19.8 1.0

Reference:

M.T.Murakami, A.Gabdoulkhakov, M.F.Fernandes-Pedrosa, D.V.Tambourgi, R.K.Arni. Structural Basis For Metal Ion Coordination and the Catalytic Mechanism of Sphingomyelinases D. J.Biol.Chem. V. 280 13658 2005.
ISSN: ISSN 0021-9258
PubMed: 15654080
DOI: 10.1074/JBC.M412437200
Page generated: Mon Dec 14 07:22:43 2020

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