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Sodium in PDB 5oer: Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns

Enzymatic activity of Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns

All present enzymatic activity of Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns, PDB code: 5oer was solved by A.Gorel, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.93 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.100, 79.100, 39.200, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.4

Other elements in 5oer:

The structure of Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns also contains other interesting chemical elements:

Gadolinium (Gd) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns (pdb code 5oer). 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 Refined Against 5000 9 Kev Diffraction Patterns, PDB code: 5oer:

Sodium binding site 1 out of 1 in 5oer

Go back to Sodium Binding Sites List in 5oer
Sodium binding site 1 out of 1 in the Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns


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 Refined Against 5000 9 Kev Diffraction Patterns within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:27.7
occ:1.00
 O A:GLY104 2.7 12.7 1.0
OD1 A:ASP101 2.7 19.2 1.0
O A:ILE98 2.8 13.7 1.0
O A:HOH314 3.4 25.9 1.0
N A:GLY104 3.5 14.5 1.0
CG A:ASP101 3.5 19.1 1.0
CB A:ALA107 3.5 12.9 1.0
C A:ILE98 3.7 14.2 1.0
C A:GLY104 3.7 13.2 1.0
OD2 A:ASP101 3.7 19.6 1.0
C A:ASN103 3.7 16.0 1.0
CB A:ASN103 3.8 18.8 1.0
CG2 A:ILE98 3.9 14.4 1.0
N A:ASN103 4.0 17.9 1.0
CA A:ASN103 4.0 17.6 1.0
CA A:VAL99 4.0 14.6 1.0
CA A:GLY104 4.0 13.8 1.0
N A:VAL99 4.2 14.4 1.0
O A:ASN103 4.3 15.7 1.0
N A:ALA107 4.4 12.6 1.0
C A:VAL99 4.4 15.3 1.0
CA A:ALA107 4.5 12.8 1.0
O A:VAL99 4.5 15.3 1.0
N A:ASP101 4.7 17.8 1.0
CB A:ASP101 4.7 18.8 1.0
CA A:ILE98 4.7 14.3 1.0
N A:GLY102 4.9 18.7 1.0
N A:MET105 4.9 12.7 1.0
CG A:ASN103 4.9 20.3 1.0
CB A:ILE98 4.9 14.2 1.0

Reference:

A.Gorel, K.Motomura, H.Fukuzawa, R.B.Doak, M.L.Grunbein, M.Hilpert, I.Inoue, M.Kloos, G.Kovacsova, E.Nango, K.Nass, C.M.Roome, R.L.Shoeman, R.Tanaka, K.Tono, Y.Joti, M.Yabashi, S.Iwata, L.Foucar, K.Ueda, T.R.M.Barends, I.Schlichting. Multi-Wavelength Anomalous Diffraction De Novo Phasing Using A Two-Colour X-Ray Free-Electron Laser with Wide Tunability. Nat Commun V. 8 1170 2017.
ISSN: ESSN 2041-1723
PubMed: 29079797
DOI: 10.1038/S41467-017-00754-7
Page generated: Mon Aug 18 01:31:00 2025

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