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Calcium in PDB 6yxh: Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect

Enzymatic activity of Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect

All present enzymatic activity of Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect:
3.5.1.23;

Protein crystallography data

The structure of Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect, PDB code: 6yxh was solved by R.D.Healey, S.Basu, A.S.Humm, C.Leyrat, F.Dupeux, A.Pica, S.Granier, J.A.Marquez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.18 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 61.47, 69.97, 259.49, 90, 90, 90
R / Rfree (%) 23.2 / 28

Other elements in 6yxh:

The structure of Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect (pdb code 6yxh). 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 Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect, PDB code: 6yxh:

Calcium binding site 1 out of 1 in 6yxh

Go back to Calcium Binding Sites List in 6yxh
Calcium binding site 1 out of 1 in the Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:116.6
occ:1.00
 OD1 A:ASP19 2.2 111.9 1.0
O A:TRP20 2.3 107.0 1.0
O A:GLU22 2.3 111.2 1.0
OD1 A:ASN24 2.6 117.3 1.0
OE2 A:GLU33 2.7 124.2 1.0
CG A:ASP19 3.1 111.3 1.0
C A:TRP20 3.4 106.8 1.0
OD2 A:ASP19 3.4 112.1 1.0
C A:GLU22 3.5 111.1 1.0
CD A:GLU33 3.5 121.7 1.0
CG A:ASN24 3.5 115.5 1.0
CG A:GLU33 3.6 115.4 1.0
N A:TRP20 3.6 105.9 1.0
N A:GLU22 3.7 109.3 1.0
O A:HOH533 3.9 101.1 1.0
ND2 A:ASN24 3.9 116.0 1.0
CA A:TRP20 4.0 105.7 1.0
NE A:ARG7 4.0 132.3 1.0
CA A:GLU22 4.1 110.1 1.0
C A:ASP19 4.2 106.9 1.0
N A:ASN24 4.3 111.7 1.0
CB A:ASP19 4.4 108.8 1.0
N A:CYS21 4.5 107.6 1.0
N A:GLU23 4.5 111.6 1.0
CD A:ARG7 4.6 129.8 1.0
C A:CYS21 4.6 109.4 1.0
CZ A:ARG7 4.6 133.8 1.0
CA A:ASP19 4.6 108.0 1.0
OE1 A:GLU33 4.7 123.2 1.0
CB A:ASN24 4.7 111.8 1.0
CB A:TRP20 4.7 104.7 1.0
C A:GLU23 4.7 112.7 1.0
CA A:ASN24 4.7 111.0 1.0
CD1 A:LEU84 4.7 106.5 1.0
CB A:GLU22 4.7 111.4 1.0
NH2 A:ARG7 4.7 134.0 1.0
CA A:CYS21 4.8 108.8 1.0
CA A:GLU23 4.9 112.4 1.0
O A:ASP19 5.0 107.0 1.0

Reference:

R.D.Healey, S.Basu, A.S.Humm, C.Leyrat, F.Dupeux, A.Pica, S.Granier, J.A.Marquez. Rapid, Automated Serial Crystallography Analysis of Membrane Proteins Through Crystaldirect To Be Published.
Page generated: Wed Jul 9 20:28:11 2025

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