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Sodium in PDB 6yod: Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging

Enzymatic activity of Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging

All present enzymatic activity of Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging:
3.2.1.17;

Protein crystallography data

The structure of Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging, PDB code: 6yod was solved by C.-Y.Huang, I.Martiel, P.Villanueva-Perez, E.Panepucci, M.Caffrey, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.50 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.990, 78.990, 38.190, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.1

Other elements in 6yod:

The structure of Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging also contains other interesting chemical elements:

Bromine (Br) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging (pdb code 6yod). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging, PDB code: 6yod:

Sodium binding site 1 out of 1 in 6yod

Go back to Sodium Binding Sites List in 6yod
Sodium binding site 1 out of 1 in the Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Lysozyme From Sin Imisx Setup Collected By Rotation Serial Crystallography on Crystals Prelocated By 2D X-Ray Phase- Contrast Imaging within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:26.9
occ:1.00
 O A:CYS64 2.3 28.4 1.0
O A:SER60 2.4 25.6 1.0
OG A:SER72 2.5 35.0 1.0
O A:HOH367 2.6 33.3 1.0
O A:ARG73 2.6 31.7 1.0
O A:HOH360 2.8 33.6 1.0
CB A:SER72 3.3 32.5 1.0
C A:CYS64 3.4 22.5 1.0
C A:SER60 3.5 24.1 1.0
C A:ARG73 3.6 31.8 1.0
CA A:ASN65 3.9 26.9 1.0
CA A:SER60 4.1 21.8 1.0
N A:ASN65 4.1 25.9 1.0
N A:ARG73 4.1 32.5 1.0
C A:SER72 4.2 40.1 1.0
CB A:SER60 4.2 24.6 1.0
N A:CYS64 4.3 26.4 1.0
CA A:SER72 4.4 38.5 1.0
N A:ASN74 4.4 32.6 1.0
CA A:ARG73 4.4 30.9 1.0
O A:HOH342 4.5 35.9 0.7
CA A:CYS64 4.5 23.6 1.0
CA A:ASN74 4.6 28.4 1.0
O A:ARG61 4.6 29.0 1.0
C A:ARG61 4.6 31.1 1.0
N A:ARG61 4.6 26.9 1.0
CB A:THR69 4.7 29.1 1.0
CB A:ASN74 4.7 25.7 1.0
N A:ASP66 4.7 26.6 1.0
O A:SER72 4.7 38.4 1.0
ND2 A:ASN65 4.8 31.9 1.0
O A:HOH350 4.8 44.4 0.8
CB A:ASN65 4.9 27.6 1.0
CA A:ARG61 4.9 29.1 1.0
C A:ASN65 4.9 24.8 1.0
N A:TRP62 4.9 26.6 1.0
BR A:BR204 4.9 38.3 0.5
N A:TRP63 5.0 26.7 1.0

Reference:

I.Martiel, C.Y.Huang, P.Villanueva-Perez, E.Panepucci, S.Basu, M.Caffrey, B.Pedrini, O.Bunk, M.Stampanoni, M.Wang. Low-Dose in Situ Prelocation of Protein Microcrystals By 2D X-Ray Phase-Contrast Imaging For Serial Crystallography. Iucrj V. 7 1131 2020.
ISSN: ESSN 2052-2525
PubMed: 33209324
DOI: 10.1107/S2052252520013238
Page generated: Tue Oct 8 15:11:25 2024

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