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Sodium in PDB 8dyz: Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset

Enzymatic activity of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset

All present enzymatic activity of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset:
3.2.1.17;

Protein crystallography data

The structure of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset, PDB code: 8dyz was solved by S.P.Meisburger, N.Ando, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.82 / 1.27
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.632, 79.632, 38.296, 90, 90, 90
R / Rfree (%) 11.5 / 13.3

Other elements in 8dyz:

The structure of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset (pdb code 8dyz). 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 Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset, PDB code: 8dyz:

Sodium binding site 1 out of 1 in 8dyz

Go back to Sodium Binding Sites List in 8dyz
Sodium binding site 1 out of 1 in the Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Lysozyme in Tetragonal Space Group at Ambient Temperature - Diffuse Scattering Dataset within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:20.3
occ:1.00
 HG A:SER72 2.2 24.8 0.0
O A:SER60 2.3 18.3 1.0
O A:CYS64 2.4 16.4 1.0
O A:HOH360 2.5 26.8 1.0
O A:ARG73 2.5 23.4 1.0
OG A:SER72 2.5 24.9 1.0
O A:HOH341 2.5 20.6 1.0
HB2 A:SER72 3.0 24.1 1.0
HA A:ASN65 3.1 16.9 1.0
CB A:SER72 3.3 24.4 1.0
C A:CYS64 3.5 14.6 1.0
C A:SER60 3.5 15.6 1.0
C A:ARG73 3.5 22.3 1.0
HB2 A:SER60 3.7 15.1 1.0
H A:CYS64 3.8 15.2 1.0
HB A:THR69 3.9 17.1 1.0
HA A:SER60 3.9 14.6 1.0
CA A:ASN65 4.0 16.6 1.0
HB3 A:SER72 4.0 24.2 1.0
N A:ARG73 4.0 24.9 1.0
H A:ARG73 4.0 25.7 1.0
HB2 A:ASN74 4.0 21.2 1.0
H A:ASP66 4.1 15.0 1.0
HA A:ASN74 4.1 20.7 1.0
N A:ASN65 4.1 15.2 1.0
C A:SER72 4.2 25.9 1.0
CA A:SER60 4.2 14.6 1.0
CA A:SER72 4.3 25.6 1.0
HA A:ARG61 4.4 19.0 1.0
CB A:SER60 4.4 14.8 1.0
N A:ASN74 4.4 22.2 1.0
CA A:ARG73 4.4 26.7 1.0
N A:CYS64 4.4 15.4 1.0
C A:ARG61 4.5 18.9 1.0
O A:ARG61 4.5 23.0 1.0
N A:ARG61 4.5 16.4 1.0
CA A:CYS64 4.6 15.1 1.0
CA A:ASN74 4.6 20.1 1.0
HB2 A:ASN65 4.6 19.6 1.0
CA A:ARG61 4.7 19.1 1.0
O A:SER72 4.7 31.5 1.0
OD1 A:ASN65 4.8 28.9 1.0
H A:TRP63 4.8 16.3 1.0
N A:ASP66 4.8 15.1 1.0
CB A:ASN74 4.8 21.7 1.0
O A:HOH369 4.8 19.7 1.0
CB A:THR69 4.8 16.9 1.0
HA A:ARG73 4.8 25.8 1.0
N A:TRP62 4.8 18.6 1.0
CB A:ASN65 4.9 19.9 1.0
HG1 A:THR69 4.9 16.9 0.0
HG22 A:THR69 4.9 19.0 1.0
C A:ASN65 4.9 14.5 1.0
HA A:SER72 4.9 25.9 1.0
H A:ASN65 5.0 15.1 1.0

Reference:

S.P.Meisburger, D.A.Case, N.Ando. Robust Total X-Ray Scattering Workflow to Study Correlated Motion of Proteins in Crystals Biorxiv 2022.
DOI: 10.1101/2022.08.22.504832
Page generated: Wed Oct 9 11:37:14 2024

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