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Calcium in PDB 5uvg: Crystal Structure of the Human Neutral Sphingomyelinase 2 (NSMASE2) Catalytic Domain with Insertion Deleted and Calcium Bound

Enzymatic activity of Crystal Structure of the Human Neutral Sphingomyelinase 2 (NSMASE2) Catalytic Domain with Insertion Deleted and Calcium Bound

All present enzymatic activity of Crystal Structure of the Human Neutral Sphingomyelinase 2 (NSMASE2) Catalytic Domain with Insertion Deleted and Calcium Bound:
3.1.4.12;

Protein crystallography data

The structure of Crystal Structure of the Human Neutral Sphingomyelinase 2 (NSMASE2) Catalytic Domain with Insertion Deleted and Calcium Bound, PDB code: 5uvg was solved by M.V.Airola, K.E.Guja, M.Garcia-Diaz, Y.A.Hannun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.85 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.610, 91.050, 50.030, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Human Neutral Sphingomyelinase 2 (NSMASE2) Catalytic Domain with Insertion Deleted and Calcium Bound (pdb code 5uvg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of the Human Neutral Sphingomyelinase 2 (NSMASE2) Catalytic Domain with Insertion Deleted and Calcium Bound, PDB code: 5uvg:

Calcium binding site 1 out of 1 in 5uvg

Go back to Calcium Binding Sites List in 5uvg
Calcium binding site 1 out of 1 in the Crystal Structure of the Human Neutral Sphingomyelinase 2 (NSMASE2) Catalytic Domain with Insertion Deleted and Calcium Bound


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Human Neutral Sphingomyelinase 2 (NSMASE2) Catalytic Domain with Insertion Deleted and Calcium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:30.0
occ:1.00
 O A:HOH873 2.3 30.0 1.0
O A:HOH869 2.3 30.0 1.0
O A:HOH906 2.5 30.0 1.0
OE1 A:GLU364 2.5 16.8 1.0
HD22 A:ASN130 3.5 10.2 1.0
CD A:GLU364 3.5 34.0 1.0
HE2 A:HIS639 3.7 15.2 1.0
OE2 A:GLU364 3.8 33.4 1.0
OD2 A:ASP638 4.2 26.0 1.0
ND2 A:ASN130 4.3 9.2 1.0
OD1 A:ASP638 4.3 16.4 1.0
HB2 A:CYS132 4.4 20.9 1.0
OD1 A:ASN130 4.5 12.3 1.0
NE2 A:HIS639 4.5 13.0 1.0
HD2 A:HIS639 4.6 14.2 1.0
SG A:CYS132 4.7 27.0 1.0
CG A:ASP638 4.7 19.1 1.0
O A:HOH807 4.7 14.9 1.0
CG A:ASN130 4.8 14.0 1.0
CG A:GLU364 4.8 13.1 1.0
HA A:CYS132 4.8 13.6 1.0
HG3 A:GLU364 4.9 11.5 1.0
HD21 A:ASN130 4.9 10.2 1.0
CD2 A:HIS639 4.9 13.3 1.0
HD11 A:LEU134 5.0 19.4 1.0

Reference:

M.V.Airola, P.Shanbhogue, A.A.Shamseddine, K.E.Guja, C.E.Senkal, R.Maini, N.Bartke, B.X.Wu, L.M.Obeid, M.Garcia-Diaz, Y.A.Hannun. Structure of Human NSMASE2 Reveals An Interdomain Allosteric Activation Mechanism For Ceramide Generation. Proc. Natl. Acad. Sci. V. 114 E5549 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28652336
DOI: 10.1073/PNAS.1705134114
Page generated: Wed Jul 9 10:37:07 2025

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