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Xenon 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:

Chlorine (Cl) 2 atoms
Sodium (Na) 1 atom

Xenon Binding Sites:

The binding sites of Xenon atom in the Xenon Derivative of Hen Egg-White Lysozyme (pdb code 1vau). This binding sites where shown within 5.0 Angstroms radius around Xenon atom.
In total 3 binding sites of Xenon where determined in the Xenon Derivative of Hen Egg-White Lysozyme, PDB code: 1vau:
Jump to Xenon binding site number: 1; 2; 3;

Xenon binding site 1 out of 3 in 1vau

Go back to Xenon Binding Sites List in 1vau
Xenon binding site 1 out of 3 in the Xenon Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 1 of Xenon Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe201

b:18.9
occ:0.22
CD1 A:ILE55 2.5 18.3 0.8
CG1 A:ILE55 3.4 13.6 0.8
CD1 A:ILE55 3.6 17.6 0.2
CG2 A:VAL92 3.7 11.9 1.0
CD1 A:LEU56 3.7 10.2 1.0
CE A:MET12 3.7 11.3 1.0
CG1 A:ILE55 3.7 13.7 0.2
CB A:SER91 3.9 10.3 1.0
CG A:LEU56 4.1 8.3 1.0
N A:VAL92 4.2 10.4 1.0
CD1 A:ILE88 4.2 13.9 1.0
CB A:ILE88 4.3 11.4 1.0
C A:SER91 4.4 10.4 1.0
CA A:VAL92 4.5 10.5 1.0
CB A:ILE55 4.6 11.2 0.2
O A:ILE88 4.6 11.3 1.0
CB A:ILE55 4.7 11.7 0.8
CG A:MET12 4.7 11.4 1.0
CD1 A:LEU17 4.7 12.9 1.0
CB A:VAL92 4.7 10.9 1.0
CG1 A:ILE88 4.7 12.8 1.0
O A:SER91 4.8 10.3 1.0
CG2 A:ILE88 4.8 12.4 1.0
CA A:SER91 4.8 10.3 1.0
OG A:SER91 4.9 10.0 1.0

Xenon binding site 2 out of 3 in 1vau

Go back to Xenon Binding Sites List in 1vau
Xenon binding site 2 out of 3 in the Xenon Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 2 of Xenon Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe202

b:11.4
occ:0.23
OG1 A:THR43 3.4 12.3 1.0
N A:ARG45 3.7 13.0 1.0
N A:ASN44 3.7 11.3 1.0
CB A:THR43 3.8 10.3 1.0
CA A:ASN44 3.9 11.9 1.0
C A:ASN44 3.9 12.4 1.0
C A:THR43 3.9 11.0 1.0
O A:THR43 4.2 11.1 1.0
CB A:ARG45 4.2 14.2 1.0
NH2 A:ARG45 4.2 18.0 1.0
CG2 A:THR51 4.3 10.5 1.0
O A:HOH372 4.3 29.3 1.0
CA A:ARG45 4.4 13.8 1.0
CZ A:ARG45 4.6 18.5 1.0
CA A:THR43 4.6 10.5 1.0
O A:ASN44 4.6 12.2 1.0
NE A:ARG45 4.8 18.2 1.0

Xenon binding site 3 out of 3 in 1vau

Go back to Xenon Binding Sites List in 1vau
Xenon binding site 3 out of 3 in the Xenon Derivative of Hen Egg-White Lysozyme


Mono view


Stereo pair view

A full contact list of Xenon with other atoms in the Xe binding site number 3 of Xenon Derivative of Hen Egg-White Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Xe203

b:31.8
occ:0.32
O A:LEU129 3.7 22.7 1.0
C A:LEU129 4.1 22.6 1.0
CA A:LEU129 4.1 22.4 1.0
CB A:ALA10 4.2 11.2 1.0
O A:ARG128 4.4 22.1 1.0
CA A:ALA10 4.6 11.3 1.0
O A:ALA10 4.8 11.5 1.0
CD2 A:LEU129 4.9 24.1 1.0
OXT A:LEU129 5.0 23.9 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: Wed Dec 16 02:39:27 2020

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