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Sodium 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:

Calcium (Ca) 1 atom
Magnesium (Mg) 2 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Cryogenic Human Alkaline Ceramidase 3 (ACER3) at 2.6 A Resolution Determined By Serial Crystallography (Ssx) Using Crystaldirect, PDB code: 6yxh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6yxh

Go back to Sodium Binding Sites List in 6yxh
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na408

b:66.9
occ:1.00
 OD2 A:ASP246 2.5 67.4 1.0
O A:HOH541 2.7 63.2 1.0
CG A:ASP246 3.4 62.6 1.0
OD1 A:ASP246 3.5 64.0 1.0
OE1 A:GLU248 4.0 90.9 1.0
CB A:GLU248 4.3 61.5 1.0
CD A:GLU248 4.5 87.1 1.0
CB A:ASP246 4.8 56.8 1.0
OD1 A:ASP249 4.8 65.9 1.0
O A:HOH548 4.9 58.8 1.0

Sodium binding site 2 out of 2 in 6yxh

Go back to Sodium Binding Sites List in 6yxh
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na binding site number 2 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:Na409

b:102.8
occ:1.00
 OD2 A:ASP19 2.5 112.1 1.0
ND2 A:ASN24 3.4 116.0 1.0
CG A:ASP19 3.6 111.3 1.0
CB A:ASP19 4.3 108.8 1.0
OD1 A:ASP19 4.6 111.9 1.0
O A:HOH533 4.6 101.1 1.0
CG A:ARG7 4.6 126.8 1.0
CG A:ASN24 4.7 115.5 1.0
NE A:ARG7 4.8 132.3 1.0
OG1 A:THR14 4.9 122.0 1.0
CD A:ARG7 5.0 129.8 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: Mon Aug 18 08:36:26 2025

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