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Magnesium in PDB 1xx1: Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D

Enzymatic activity of Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D

All present enzymatic activity of Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D:
3.1.4.41;

Protein crystallography data

The structure of Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D, PDB code: 1xx1 was solved by M.T.Murakami, 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) 30.00 / 1.75
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 139.818, 139.818, 113.461, 90.00, 90.00, 120.00
R / Rfree (%) 18.6 / 22.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D (pdb code 1xx1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D, PDB code: 1xx1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1xx1

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Magnesium binding site 1 out of 4 in the Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg9001

b:7.3
occ:1.00
 O A:HOH9251 1.9 21.7 1.0
OD1 A:ASP34 1.9 14.4 1.0
OE2 A:GLU32 1.9 19.4 1.0
OD2 A:ASP91 2.0 20.6 1.0
O A:HOH9252 2.0 27.2 1.0
O A:HOH9245 2.0 16.7 1.0
CD A:GLU32 2.9 17.4 1.0
CG A:ASP34 3.0 12.7 1.0
CG A:ASP91 3.0 17.5 1.0
OE1 A:GLU32 3.3 12.8 1.0
OD2 A:ASP34 3.3 10.6 1.0
CB A:ASP91 3.4 12.4 1.0
O2 A:SO43001 3.6 35.6 1.0
NZ A:LYS93 3.9 20.5 1.0
OD1 A:ASP91 4.1 21.5 1.0
CB A:ASP34 4.2 13.0 1.0
CG A:GLU32 4.3 13.0 1.0
O3 A:SO43001 4.3 35.7 1.0
CE A:LYS93 4.3 18.8 1.0
CD2 A:HIS47 4.4 19.0 1.0
O A:HOH9221 4.4 39.7 1.0
CA A:ASP34 4.6 11.6 1.0
S A:SO43001 4.6 39.6 1.0
NE2 A:HIS12 4.6 15.2 1.0
CD2 A:HIS12 4.8 16.4 1.0
N A:ASP34 4.9 12.5 1.0
CA A:ASP91 4.9 11.7 1.0
NE2 A:HIS47 5.0 17.6 1.0

Magnesium binding site 2 out of 4 in 1xx1

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Magnesium binding site 2 out of 4 in the Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg9002

b:6.8
occ:1.00
 OD1 B:ASP34 1.8 14.4 1.0
OD2 B:ASP91 1.9 18.6 1.0
O B:HOH9259 2.0 26.5 1.0
OE2 B:GLU32 2.0 15.4 1.0
O B:HOH9256 2.0 25.0 1.0
O B:HOH9274 2.1 17.6 1.0
CG B:ASP34 2.9 15.3 1.0
CD B:GLU32 3.0 15.7 1.0
CG B:ASP91 3.0 18.1 1.0
OE1 B:GLU32 3.3 13.1 1.0
OD2 B:ASP34 3.4 13.9 1.0
CB B:ASP91 3.4 12.4 1.0
O1 B:SO43002 3.7 29.6 1.0
NZ B:LYS93 3.9 26.4 1.0
O3 B:SO43002 4.1 34.3 1.0
OD1 B:ASP91 4.1 20.7 1.0
CB B:ASP34 4.2 12.2 1.0
CE B:LYS93 4.2 24.2 1.0
CG B:GLU32 4.3 12.8 1.0
CD2 B:HIS47 4.4 18.9 1.0
S B:SO43002 4.5 36.5 1.0
O B:HOH9067 4.6 34.6 1.0
NE2 B:HIS12 4.6 16.9 1.0
CA B:ASP34 4.6 11.7 1.0
CD2 B:HIS12 4.9 16.4 1.0
CA B:ASP91 4.9 12.5 1.0
N B:ASP34 4.9 10.8 1.0

Magnesium binding site 3 out of 4 in 1xx1

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Magnesium binding site 3 out of 4 in the Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg9003

b:7.6
occ:1.00
 OD1 C:ASP34 1.9 15.4 1.0
OE2 C:GLU32 1.9 17.0 1.0
OD2 C:ASP91 1.9 20.2 1.0
O C:HOH9230 2.0 26.7 1.0
O C:HOH9016 2.1 20.1 1.0
O C:HOH9195 2.1 29.8 1.0
CG C:ASP34 2.9 14.3 1.0
CD C:GLU32 2.9 15.5 1.0
CG C:ASP91 3.0 16.7 1.0
OE1 C:GLU32 3.3 13.1 1.0
OD2 C:ASP34 3.3 12.1 1.0
CB C:ASP91 3.4 13.1 1.0
O4 C:SO43003 3.8 30.4 1.0
NZ C:LYS93 3.9 24.1 1.0
OD1 C:ASP91 4.1 20.2 1.0
O3 C:SO43003 4.1 31.8 1.0
CB C:ASP34 4.2 13.5 1.0
CE C:LYS93 4.2 21.4 1.0
CG C:GLU32 4.2 14.8 1.0
CD2 C:HIS47 4.4 19.1 1.0
O C:HOH9086 4.4 39.0 1.0
O C:HOH9246 4.5 37.4 1.0
CA C:ASP34 4.6 12.9 1.0
O C:HOH9074 4.6 29.1 1.0
S C:SO43003 4.7 32.0 1.0
N C:ASP34 4.8 12.5 1.0
NE2 C:HIS12 4.8 14.5 1.0
CA C:ASP91 4.9 14.2 1.0
CD2 C:HIS12 5.0 16.9 1.0
C C:ALA33 5.0 12.7 1.0

Magnesium binding site 4 out of 4 in 1xx1

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Magnesium binding site 4 out of 4 in the Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structural Basis For Ion-Coordination and the Catalytic Mechanism of Sphingomyelinases D within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg9004

b:8.2
occ:1.00
 OD1 D:ASP34 1.9 16.2 1.0
OE2 D:GLU32 1.9 18.4 1.0
O D:HOH9110 2.0 23.4 1.0
O D:HOH9198 2.0 21.3 1.0
OD2 D:ASP91 2.0 21.3 1.0
O D:HOH9179 2.0 19.5 1.0
CD D:GLU32 2.9 17.1 1.0
CG D:ASP34 3.0 12.5 1.0
CG D:ASP91 3.0 17.8 1.0
OE1 D:GLU32 3.3 15.1 1.0
CB D:ASP91 3.4 13.6 1.0
OD2 D:ASP34 3.4 12.7 1.0
O2 D:SO43004 3.7 28.8 1.0
NZ D:LYS93 4.0 22.4 1.0
O D:HOH9157 4.1 42.9 1.0
OD1 D:ASP91 4.2 20.0 1.0
O4 D:SO43004 4.2 28.8 1.0
CB D:ASP34 4.2 13.2 1.0
CG D:GLU32 4.2 14.1 1.0
CE D:LYS93 4.3 25.2 1.0
O D:HOH9075 4.4 27.4 1.0
O D:HOH9183 4.4 35.6 1.0
CD2 D:HIS47 4.4 17.7 1.0
NE2 D:HIS12 4.5 18.2 1.0
S D:SO43004 4.6 28.7 1.0
CA D:ASP34 4.6 13.4 1.0
CD2 D:HIS12 4.8 16.2 1.0
N D:ASP34 4.9 13.2 1.0
CA D:ASP91 4.9 13.7 1.0

Reference:

M.T.Murakami, 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: Tue Aug 13 18:25:19 2024

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