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Sodium in PDB 5fek: Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel

Enzymatic activity of Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel

All present enzymatic activity of Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel, PDB code: 5fek was solved by S.Tsujino, T.Tomizaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.30 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.600, 78.600, 37.400, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22.8

Other elements in 5fek:

The structure of Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel (pdb code 5fek). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel, PDB code: 5fek:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5fek

Go back to Sodium Binding Sites List in 5fek
Sodium binding site 1 out of 2 in the Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:37.5
occ:1.00
 OG A:SER91 2.7 31.8 1.0
O A:TYR53 2.8 26.4 1.0
N A:LEU56 3.0 28.9 1.0
N A:ILE55 3.3 25.6 1.0
C A:GLY54 3.5 24.7 1.0
CB A:SER91 3.5 31.9 1.0
CA A:GLY54 3.5 24.7 1.0
N A:GLN57 3.6 28.2 1.0
CA A:LEU56 3.6 30.3 1.0
C A:LEU56 3.7 32.2 1.0
CD1 A:ILE58 3.8 34.2 1.0
CB A:LEU56 3.8 29.9 1.0
C A:TYR53 3.9 27.5 1.0
CG1 A:ILE58 4.0 32.5 1.0
C A:ILE55 4.0 31.6 1.0
O A:GLY54 4.1 25.5 1.0
CA A:ILE55 4.1 28.4 1.0
O A:LEU83 4.1 35.7 1.0
N A:ILE58 4.1 29.4 1.0
CG2 A:ILE55 4.1 37.1 1.0
N A:GLY54 4.2 25.4 1.0
CB A:LEU83 4.2 31.3 1.0
CA A:SER91 4.3 27.8 1.0
CB A:ILE58 4.3 30.6 1.0
CD2 A:LEU83 4.5 36.0 1.0
CA A:GLN57 4.6 26.6 1.0
O A:LEU56 4.6 28.3 1.0
CB A:ILE55 4.7 32.8 1.0
CG A:LEU83 4.7 30.8 1.0
CD1 A:LEU83 4.8 33.1 1.0
CG A:LEU56 4.8 31.6 1.0
C A:GLN57 4.9 27.9 1.0
CA A:ILE58 4.9 29.7 1.0
CA A:LEU83 5.0 30.3 1.0
C A:LEU83 5.0 31.2 1.0

Sodium binding site 2 out of 2 in 5fek

Go back to Sodium Binding Sites List in 5fek
Sodium binding site 2 out of 2 in the Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hen Egg Lysozyme at Room Temperature Solved From 3600 Diffraction Images Acquired By Ultrasonic Acoustic Levitation Method and Processed By Crystfel within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:41.3
occ:1.00
 O A:SER60 2.2 35.3 1.0
O A:CYS64 2.5 30.0 1.0
O A:HOH321 2.5 38.7 1.0
O A:HOH314 2.5 30.7 1.0
OG A:SER72 2.5 35.9 1.0
O A:ARG73 2.5 39.3 1.0
CB A:SER72 3.2 40.6 1.0
C A:SER60 3.4 33.4 1.0
C A:CYS64 3.5 27.4 1.0
C A:ARG73 3.6 38.1 1.0
CA A:ASN65 3.9 33.3 1.0
N A:ARG73 3.9 38.4 1.0
C A:SER72 4.0 47.8 1.0
N A:ASN65 4.1 33.8 1.0
CA A:SER60 4.1 30.4 1.0
CA A:SER72 4.2 43.1 1.0
N A:ASN74 4.4 37.0 1.0
CB A:SER60 4.4 29.6 1.0
O A:ARG61 4.4 36.4 1.0
CA A:ARG73 4.4 39.3 1.0
N A:CYS64 4.4 25.3 1.0
C A:ARG61 4.4 38.3 1.0
N A:ARG61 4.5 33.5 1.0
O A:SER72 4.5 44.5 1.0
CA A:ASN74 4.5 36.3 1.0
CA A:CYS64 4.6 29.7 1.0
CB A:THR69 4.6 33.6 1.0
CA A:ARG61 4.7 39.9 1.0
CL A:CL202 4.7 54.1 1.0
N A:ASP66 4.7 30.5 1.0
OD1 A:ASN65 4.7 45.5 1.0
CB A:ASN74 4.8 35.0 1.0
N A:TRP62 4.8 35.1 1.0
C A:ASN65 4.8 29.0 1.0
O A:THR69 4.9 38.4 1.0
CB A:ASN65 4.9 35.1 1.0

Reference:

S.Tsujino, T.Tomizaki. Ultrasonic Acoustic Levitation For Fast Frame Rate X-Ray Protein Crystallography at Room Temperature. Sci Rep V. 6 25558 2016.
ISSN: ESSN 2045-2322
PubMed: 27150272
DOI: 10.1038/SREP25558
Page generated: Tue Dec 15 10:58:50 2020

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