Gadolinium in PDB 5oer: 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;

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

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

Sodium

(Na)

1 atom

The binding sites of Gadolinium 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 Gadolinium atom.
In total 2 binding sites of Gadolinium where determined in the Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns, PDB code: 5oer:
Jump to Gadolinium binding site number: 1; 2;

Gadolinium binding site 1 out of 2 in the Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd 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:Gd203 b:14.8 occ:0.81 O7 A:DO3201 2.3 18.4 0.8 O5 A:DO3201 2.3 18.9 0.8 O1 A:DO3201 2.3 21.9 0.8 O3 A:DO3201 2.4 17.3 0.8 O A:HOH306 2.4 15.8 1.0 N4 A:DO3201 2.7 19.2 0.8 C4 A:DO3201 3.0 19.6 0.8 C1 A:DO3201 3.1 19.7 0.8 C9 A:DO3201 3.2 21.5 0.8 C13 A:DO3201 3.3 19.6 0.8 N1 A:DO3201 3.3 20.1 0.8 C10 A:DO3201 3.4 20.6 0.8 C11 A:DO3201 3.4 18.4 0.8 C15 A:DO3201 3.4 18.8 0.8 C3 A:DO3201 3.4 19.4 0.8 C16 A:DO3201 3.4 19.0 0.8 C7 A:DO3201 3.5 19.4 0.8 N3 A:DO3201 3.5 19.6 0.8 N2 A:DO3201 3.5 19.4 0.8 C8 A:DO3201 3.6 19.8 0.8 C2 A:DO3201 3.6 19.6 0.8 C6 A:DO3201 3.6 19.4 0.8 C14 A:DO3201 3.7 19.4 0.8 C5 A:DO3201 3.7 19.4 0.8 C12 A:DO3201 3.8 18.6 0.8 O A:HOH318 4.2 18.8 1.0 O2 A:DO3201 4.3 22.1 0.8 O A:HOH303 4.3 20.0 1.0 O6 A:DO3201 4.4 19.9 0.8 O1 A:DO3202 4.4 16.3 0.7 C17 A:DO3201 4.5 18.7 0.8 O4 A:DO3201 4.5 18.0 0.8 O2 A:DO3202 4.6 16.4 0.7 C9 A:DO3202 4.9 17.2 0.7

Gadolinium binding site 2 out of 2 in the Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Hen Egg-White Lysozyme Refined Against 5000 9 Kev Diffraction Patterns within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd204 b:14.7 occ:0.73 O5 A:DO3202 2.3 18.9 0.7 O3 A:DO3202 2.4 20.1 0.7 O1 A:DO3202 2.4 16.3 0.7 O7 A:DO3202 2.5 18.2 0.7 O A:HOH318 2.6 18.8 1.0 N4 A:DO3202 2.7 18.6 0.7 C4 A:DO3202 2.8 20.1 0.7 C13 A:DO3202 3.1 19.4 0.7 N3 A:DO3202 3.1 19.8 0.7 C11 A:DO3202 3.2 20.3 0.7 C12 A:DO3202 3.2 20.5 0.7 C9 A:DO3202 3.3 17.2 0.7 C3 A:DO3202 3.3 20.2 0.7 N2 A:DO3202 3.4 20.2 0.7 C10 A:DO3202 3.4 17.6 0.7 C14 A:DO3202 3.4 19.5 0.7 C5 A:DO3202 3.4 19.5 0.7 C6 A:DO3202 3.5 19.4 0.7 N1 A:DO3202 3.5 18.4 0.7 C7 A:DO3202 3.5 18.4 0.7 C16 A:DO3202 3.5 18.6 0.7 C15 A:DO3202 3.5 18.5 0.7 C8 A:DO3202 3.5 18.4 0.7 C1 A:DO3202 3.7 19.0 0.7 C2 A:DO3202 3.7 19.7 0.7 O6 A:DO3202 4.3 19.3 0.7 O A:HOH303 4.3 20.0 1.0 O A:HOH306 4.3 15.8 1.0 O4 A:DO3202 4.4 20.7 0.7 C17 A:DO3202 4.5 18.6 0.7 O2 A:DO3202 4.5 16.4 0.7 O4 A:DO3201 4.5 18.0 0.8 O3 A:DO3201 4.5 17.3 0.8 C11 A:DO3201 5.0 18.4 0.8

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