Calcium in PDB 6g7o: Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution

Protein crystallography data

The structure of Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution, PDB code: 6g7o was solved by C.Leyrat, I.Vasiliauskaite-Brooks, R.D.Healey, R.Sounier, C.Grison, F.Hoh, S.Basu, S.Granier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.60 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.880, 68.830, 257.520, 90.00, 90.00, 90.00
R / Rfree (%) 24.8 / 27

Other elements in 6g7o:

The structure of Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Zinc (Zn) 1 atom
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution (pdb code 6g7o). 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 Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution, PDB code: 6g7o:

Calcium binding site 1 out of 1 in 6g7o

Go back to Calcium Binding Sites List in 6g7o
Calcium binding site 1 out of 1 in the Crystal Structure of Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution


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 Human Alkaline Ceramidase 3 (ACER3) at 2.7 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca412

b:97.4
occ:1.00
O A:TRP20 2.2 0.8 1.0
O A:GLU22 2.3 0.8 1.0
OD1 A:ASN24 2.5 0.5 1.0
OD1 A:ASP19 2.7 0.2 1.0
OE2 A:GLU33 2.7 0.1 1.0
OD2 A:ASP19 2.9 0.7 1.0
CG A:ASP19 3.0 0.8 1.0
C A:TRP20 3.3 0.4 1.0
C A:GLU22 3.4 0.1 1.0
CD A:GLU33 3.7 0.1 1.0
CG A:ASN24 3.7 0.8 1.0
N A:TRP20 3.8 0.5 1.0
NE A:ARG7 3.9 0.2 1.0
CG A:GLU33 3.9 0.6 1.0
N A:GLU22 3.9 0.0 1.0
CD A:ARG7 4.0 0.2 1.0
CA A:TRP20 4.1 0.0 1.0
C A:CYS21 4.1 0.2 1.0
CA A:GLU22 4.2 0.6 1.0
C A:ASP19 4.3 0.2 1.0
N A:CYS21 4.3 0.2 1.0
ND2 A:ASN24 4.3 0.9 1.0
CB A:ASP19 4.4 0.3 1.0
N A:ASN24 4.4 0.1 1.0
N A:GLU23 4.4 0.3 1.0
O A:CYS21 4.5 0.4 1.0
CZ A:ARG7 4.6 0.8 1.0
CA A:CYS21 4.6 0.5 1.0
C A:GLU23 4.7 0.1 1.0
CA A:GLU23 4.7 0.1 1.0
CB A:TRP20 4.7 96.8 1.0
CA A:ASP19 4.7 0.8 1.0
O A:ASP19 4.8 0.6 1.0
OE1 A:GLU33 4.8 0.0 1.0
CB A:GLU22 4.9 0.9 1.0
CB A:ASN24 4.9 0.7 1.0
CA A:ASN24 4.9 1.0 1.0
NH2 A:ARG7 5.0 0.3 1.0

Reference:

I.Vasiliauskaite-Brooks, R.D.Healey, P.Rochaix, J.Saint-Paul, R.Sounier, C.Grison, T.Waltrich-Augusto, M.Fortier, F.Hoh, E.M.Saied, C.Arenz, S.Basu, C.Leyrat, S.Granier. Structure of A Human Intramembrane Ceramidase Explains Enzymatic Dysfunction Found in Leukodystrophy. Nat Commun V. 9 5437 2018.
ISSN: ESSN 2041-1723
PubMed: 30575723
DOI: 10.1038/S41467-018-07864-W
Page generated: Sat Dec 12 06:08:02 2020

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