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Sodium in PDB 1vau: Xenon Derivative of Hen Egg-White Lysozyme

Enzymatic activity of Xenon Derivative of Hen Egg-White Lysozyme

All present enzymatic activity of Xenon Derivative of Hen Egg-White Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Xenon Derivative of Hen Egg-White Lysozyme, PDB code: 1vau was solved by K.Takeda, H.Miyatake, S.Y.Park, M.Kawamoto, N.Kamiya, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.330, 78.330, 36.940, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 20.3

Other elements in 1vau:

The structure of Xenon Derivative of Hen Egg-White Lysozyme also contains other interesting chemical elements:

Xenon (Xe) 3 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Xenon Derivative of Hen Egg-White Lysozyme (pdb code 1vau). 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 Xenon Derivative of Hen Egg-White Lysozyme, PDB code: 1vau:

Sodium binding site 1 out of 1 in 1vau

Go back to Sodium Binding Sites List in 1vau
Sodium binding site 1 out of 1 in the Xenon Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xenon Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:11.8
occ:1.00
O A:SER60 2.3 11.8 1.0
O A:HOH315 2.4 11.7 1.0
O A:HOH319 2.4 14.9 1.0
O A:CYS64 2.4 9.9 1.0
O A:ARG73 2.5 14.3 1.0
OG A:SER72 2.6 14.3 1.0
CB A:SER72 3.2 15.0 1.0
C A:SER60 3.4 11.8 1.0
C A:ARG73 3.5 14.3 1.0
C A:CYS64 3.5 9.9 1.0
N A:ARG73 3.8 14.8 1.0
CA A:ASN65 3.9 9.9 1.0
CA A:SER60 4.1 11.4 1.0
N A:ASN65 4.1 9.9 1.0
C A:SER72 4.2 15.0 1.0
CB A:SER60 4.2 10.9 1.0
CA A:ARG73 4.3 14.5 1.0
CA A:SER72 4.4 15.1 1.0
N A:ASN74 4.4 14.0 1.0
N A:ARG61 4.5 12.0 1.0
N A:CYS64 4.5 10.3 1.0
C A:ARG61 4.6 12.2 1.0
CA A:ASN74 4.6 13.8 1.0
O A:ARG61 4.6 12.2 1.0
CA A:CYS64 4.6 10.1 1.0
ND2 A:ASN65 4.6 10.2 1.0
CB A:THR69 4.6 11.9 1.0
N A:ASP66 4.7 10.0 1.0
CL A:CL302 4.7 16.7 1.0
CB A:ASN65 4.7 10.2 1.0
CB A:ASN74 4.8 12.8 1.0
CA A:ARG61 4.8 12.3 1.0
C A:ASN65 4.8 9.9 1.0
O A:SER72 4.8 15.2 1.0
N A:TRP62 4.9 12.1 1.0
O A:HOH424 4.9 37.0 1.0
O A:THR69 5.0 13.4 1.0

Reference:

K.Takeda, H.Miyatake, S.Y.Park, M.Kawamoto, N.Kamiya, K.Miki. Multi-Wavelength Anomalous Diffraction Method For I and Xe Atoms Using Ultra-High-Energy X-Rays From Spring-8 J.Appl.Crystallogr. V. 37 925 2004.
ISSN: ISSN 0021-8898
Page generated: Tue Dec 15 05:37:31 2020

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