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Sodium in PDB 5tcd: Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine

Enzymatic activity of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine

All present enzymatic activity of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine:
3.1.4.12;

Protein crystallography data

The structure of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine, PDB code: 5tcd was solved by A.Gorelik, F.Liu, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.44 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.223, 104.223, 113.893, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.8

Other elements in 5tcd:

The structure of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Iodine (I) 37 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine (pdb code 5tcd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine, PDB code: 5tcd:

Sodium binding site 1 out of 1 in 5tcd

Go back to Sodium Binding Sites List in 5tcd
Sodium binding site 1 out of 1 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na514

b:36.5
occ:1.00
 O A:ASP46 2.3 37.6 1.0
O A:VAL49 2.3 28.6 1.0
O A:HOH614 2.4 35.7 1.0
O A:HOH775 2.4 28.0 1.0
O A:HOH765 2.7 27.8 1.0
OG1 A:THR51 2.7 34.1 1.0
HG1 A:THR51 3.0 40.9 1.0
H A:THR51 3.0 42.5 1.0
C A:ASP46 3.5 35.1 1.0
HB2 A:ASP46 3.5 41.5 1.0
HG23 A:THR51 3.6 38.0 1.0
C A:VAL49 3.6 29.9 1.0
N A:THR51 3.6 35.4 1.0
HA A:ASP50 3.7 58.4 1.0
H A:VAL49 3.7 33.3 1.0
CB A:THR51 3.8 32.7 1.0
HA A:GLN47 4.0 47.1 1.0
CG2 A:THR51 4.1 31.6 1.0
OD2 A:ASP55 4.1 37.5 1.0
HA A:ASP46 4.1 40.9 1.0
HG21 A:THR51 4.2 38.0 1.0
CA A:ASP46 4.2 34.1 1.0
OD1 A:ASP55 4.2 40.0 1.0
CB A:ASP46 4.3 34.6 1.0
CA A:THR51 4.3 33.2 1.0
CA A:ASP50 4.3 48.7 1.0
C A:ASP50 4.4 48.4 1.0
N A:ASP50 4.4 48.3 1.0
N A:VAL49 4.4 27.8 1.0
N A:GLN47 4.5 36.7 1.0
CA A:GLN47 4.6 39.3 1.0
CA A:VAL49 4.6 28.1 1.0
HB A:THR51 4.6 39.3 1.0
CG A:ASP55 4.6 40.2 1.0
HB A:VAL49 4.6 31.5 1.0
C A:GLN47 4.7 40.2 1.0
O A:GLN47 4.7 42.6 1.0
O A:THR51 4.9 34.2 1.0
C A:THR51 4.9 33.1 1.0
CG A:ASP46 5.0 36.8 1.0
HG22 A:THR51 5.0 38.0 1.0

Reference:

A.Gorelik, F.Liu, K.Illes, B.Nagar. Crystal Structure of the Human Alkaline Sphingomyelinase Provides Insights Into Substrate Recognition. J. Biol. Chem. V. 292 7087 2017.
ISSN: ESSN 1083-351X
PubMed: 28292932
DOI: 10.1074/JBC.M116.769273
Page generated: Tue Oct 8 00:07:44 2024

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