Gadolinium in PDB 4n5r: Hen Egg-White Lysozyme Phased Using Free-Electron Laser Data

All present enzymatic activity of Hen Egg-White Lysozyme Phased Using Free-Electron Laser Data:
3.2.1.17;

The structure of Hen Egg-White Lysozyme Phased Using Free-Electron Laser Data, PDB code: 4n5r was solved by T.R.M.Barends, L.Foucar, S.Botha, R.B.Doak, R.L.Shoeman, K.Nass, J.E.Koglin, G.J.Williams, S.Boutet, M.Messerschmidt, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.55 / 2.10
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 (%)	23.1 / 25.6

The binding sites of Gadolinium atom in the Hen Egg-White Lysozyme Phased Using Free-Electron Laser Data (pdb code 4n5r). 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 Phased Using Free-Electron Laser Data, PDB code: 4n5r:
Jump to Gadolinium binding site number: 1; 2;

Gadolinium binding site 1 out of 2 in the Hen Egg-White Lysozyme Phased Using Free-Electron Laser Data


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 Phased Using Free-Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd201 b:32.5 occ:0.53 O3 A:DO3204 2.2 36.0 0.8 O1 A:DO3204 2.5 42.6 0.8 N2 A:DO3204 2.5 40.2 0.8 O5 A:DO3204 2.5 42.1 0.8 N3 A:DO3204 2.5 43.7 0.8 O7 A:DO3204 2.7 48.0 0.8 N1 A:DO3204 2.7 39.8 0.8 N4 A:DO3204 2.7 48.5 0.8 C11 A:DO3204 3.0 39.3 0.8 C13 A:DO3204 3.2 45.5 0.8 C12 A:DO3204 3.2 38.9 0.8 C14 A:DO3204 3.2 44.1 0.8 C9 A:DO3204 3.3 42.7 0.8 C3 A:DO3204 3.3 42.9 0.8 C6 A:DO3204 3.3 47.5 0.8 C4 A:DO3204 3.4 43.6 0.8 C10 A:DO3204 3.4 42.0 0.8 C2 A:DO3204 3.4 42.0 0.8 C1 A:DO3204 3.4 41.8 0.8 C5 A:DO3204 3.4 45.2 0.8 C16 A:DO3204 3.6 50.2 0.8 C7 A:DO3204 3.6 46.3 0.8 C15 A:DO3204 3.6 47.6 0.8 C8 A:DO3204 3.7 44.1 0.8 O4 A:DO3204 4.2 38.6 0.8 O6 A:DO3204 4.3 47.2 0.8 O3 A:DO3203 4.4 33.6 0.8 O2 A:DO3204 4.5 44.4 0.8 O4 A:DO3203 4.7 39.4 0.8 C17 A:DO3204 4.9 46.3 0.8 C11 A:DO3203 4.9 37.3 0.8

Gadolinium binding site 2 out of 2 in the Hen Egg-White Lysozyme Phased Using Free-Electron Laser Data


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 Phased Using Free-Electron Laser Data within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd202 b:31.2 occ:0.65 O1 A:DO3203 2.0 48.3 0.8 O5 A:DO3203 2.2 37.1 0.8 O7 A:DO3203 2.4 35.3 0.8 O3 A:DO3203 2.5 33.6 0.8 N2 A:DO3203 2.7 37.9 0.8 N4 A:DO3203 2.7 36.8 0.8 N3 A:DO3203 2.8 38.1 0.8 N1 A:DO3203 2.8 41.4 0.8 C9 A:DO3203 3.0 45.8 0.8 C13 A:DO3203 3.2 38.3 0.8 C16 A:DO3203 3.3 36.5 0.8 C11 A:DO3203 3.3 37.3 0.8 C12 A:DO3203 3.4 36.0 0.8 C15 A:DO3203 3.4 35.6 0.8 C10 A:DO3203 3.4 43.6 0.8 C14 A:DO3203 3.4 36.6 0.8 C5 A:DO3203 3.6 38.3 0.8 C3 A:DO3203 3.6 36.6 0.8 C6 A:DO3203 3.6 39.0 0.8 C2 A:DO3203 3.6 39.1 0.8 C7 A:DO3203 3.6 38.1 0.8 C1 A:DO3203 3.6 39.9 0.8 C4 A:DO3203 3.7 37.5 0.8 C8 A:DO3203 3.7 39.4 0.8 O2 A:DO3203 4.2 47.0 0.8 O7 A:DO3204 4.2 48.0 0.8 O6 A:DO3203 4.3 37.6 0.8 O4 A:DO3203 4.5 39.4 0.8 C17 A:DO3203 4.5 36.0 0.8 C17 A:DO3204 4.6 46.3 0.8 C15 A:DO3204 4.9 47.6 0.8

T.R.Barends, L.Foucar, S.Botha, R.B.Doak, R.L.Shoeman, K.Nass, J.E.Koglin, G.J.Williams, S.Boutet, M.Messerschmidt, I.Schlichting. De Novo Protein Crystal Structure Determination From X-Ray Free-Electron Laser Data. Nature V. 505 244 2014.
ISSN: ISSN 0028-0836
PubMed: 24270807
DOI: 10.1038/NATURE12773