Atomistry » Sodium » PDB 6ytt-6z6u » 6yxh
Atomistry »
  Sodium »
    PDB 6ytt-6z6u »
      6yxh »

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: Tue Oct 8 15:16:47 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy