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Sodium in PDB 5myy: Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate

Enzymatic activity of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate

All present enzymatic activity of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate, PDB code: 5myy was solved by S.Panneerselvam, A.Burkhardt, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.68 / 1.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.740, 78.740, 37.010, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 14.3

Other elements in 5myy:

The structure of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate also contains other interesting chemical elements:

Cadmium (Cd) 10 atoms
Chlorine (Cl) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate (pdb code 5myy). 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 Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate, PDB code: 5myy:

Sodium binding site 1 out of 1 in 5myy

Go back to Sodium Binding Sites List in 5myy
Sodium binding site 1 out of 1 in the Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg-White Lysozyme (Hewl) Cocrystallized in the Presence of Cadmium Sulphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na221

b:12.4
occ:1.00
 O A:SER60 2.3 12.1 1.0
O A:CYS64 2.4 11.2 1.0
O A:ARG73 2.4 14.3 1.0
O A:HOH380 2.4 15.4 1.0
OG A:SER72 2.5 15.2 1.0
O A:HOH361 2.5 13.1 1.0
CB A:SER72 3.2 15.0 1.0
C A:ARG73 3.5 14.0 1.0
C A:SER60 3.5 10.7 1.0
C A:CYS64 3.5 10.7 1.0
N A:ARG73 3.9 14.8 1.0
CA A:ASN65 3.9 10.9 1.0
CD A:CD204 4.0 19.4 0.1
CA A:SER60 4.1 10.3 1.0
N A:ASN65 4.1 11.0 1.0
C A:SER72 4.2 15.4 1.0
CB A:SER60 4.2 10.3 1.0
CA A:ARG73 4.3 14.8 1.0
CA A:SER72 4.3 15.4 1.0
N A:ASN74 4.4 14.2 1.0
N A:CYS64 4.4 11.2 1.0
O A:HOH373 4.5 39.5 1.0
C A:ARG61 4.5 13.0 1.0
O A:ARG61 4.6 15.4 1.0
N A:ARG61 4.6 11.8 1.0
CA A:ASN74 4.6 13.4 1.0
CA A:CYS64 4.6 10.8 1.0
N A:ASP66 4.7 10.3 1.0
CB A:THR69 4.7 11.9 1.0
CL A:CL212 4.7 16.3 1.0
OD1 A:ASN65 4.7 14.5 1.0
CB A:ASN74 4.7 14.1 1.0
O A:SER72 4.8 18.8 1.0
CA A:ARG61 4.8 12.9 1.0
C A:ASN65 4.9 10.1 1.0
N A:TRP62 4.9 12.0 1.0
CB A:ASN65 4.9 12.1 1.0

Reference:

S.Panneerselvam, E.P.Kumpula, I.Kursula, A.Burkhardt, A.Meents. Rapid Cadmium Sad Phasing at the Standard Wavelength (1 Angstrom ). Acta Crystallogr D Struct V. 73 581 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28695858
DOI: 10.1107/S2059798317006970
Page generated: Mon Oct 7 22:49:00 2024

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