Gadolinium in PDB 6sr4: X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay

All present enzymatic activity of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay:
3.2.1.17;

The structure of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay, PDB code: 6sr4 was solved by M.Kloos, A.Gorel, K.Nass, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.81 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	79.000, 79.000, 39.500, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 27.8

The structure of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Gadolinium atom in the X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay (pdb code 6sr4). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 2 binding sites of Gadolinium where determined in the X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay, PDB code: 6sr4:
Jump to Gadolinium binding site number: 1; 2;

Gadolinium binding site 1 out of 2 in the X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd201 b:45.0 occ:1.00 O3 A:DO3204 1.9 43.4 1.0 N1 A:DO3204 2.3 25.7 1.0 N2 A:DO3204 2.7 43.8 1.0 N3 A:DO3204 2.9 58.1 1.0 O1 A:DO3204 2.9 30.9 1.0 C11 A:DO3204 2.9 42.0 1.0 C10 A:DO3204 2.9 29.8 1.0 N4 A:DO3204 3.0 52.1 1.0 O5 A:DO3204 3.0 50.8 1.0 C1 A:DO3204 3.1 40.9 1.0 O7 A:DO3204 3.1 39.0 1.0 C12 A:DO3204 3.3 41.9 1.0 C2 A:DO3204 3.3 41.8 1.0 C9 A:DO3204 3.3 36.6 1.0 C8 A:DO3204 3.4 40.6 1.0 C7 A:DO3204 3.4 47.3 1.0 C3 A:DO3204 3.5 49.8 1.0 C6 A:DO3204 3.5 55.0 1.0 C13 A:DO3204 3.5 57.3 1.0 C14 A:DO3204 3.6 57.0 1.0 C4 A:DO3204 3.6 54.4 1.0 C5 A:DO3204 3.7 56.0 1.0 O4 A:DO3204 3.9 43.8 1.0 C16 A:DO3204 4.0 50.4 1.0 C15 A:DO3204 4.0 48.2 1.0 O4 A:DO3203 4.1 65.2 1.0 O A:HOH303 4.2 40.6 1.0 O3 A:DO3203 4.3 53.5 1.0 O6 A:DO3204 4.5 59.7 1.0 O2 A:DO3204 4.5 41.9 1.0 C11 A:DO3203 4.6 55.1 1.0

Gadolinium binding site 2 out of 2 in the X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 112 Fs Time Delay within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd202 b:33.0 occ:1.00 O7 A:DO3203 1.8 41.8 1.0 O5 A:DO3203 2.3 64.6 1.0 O1 A:DO3203 2.3 65.1 1.0 O3 A:DO3203 2.3 53.5 1.0 N2 A:DO3203 2.8 57.0 1.0 N4 A:DO3203 2.8 44.0 1.0 N3 A:DO3203 2.8 55.6 1.0 N1 A:DO3203 2.9 54.3 1.0 O A:HOH303 2.9 40.6 1.0 C15 A:DO3203 3.0 39.9 1.0 C16 A:DO3203 3.3 41.6 1.0 C11 A:DO3203 3.3 55.1 1.0 C13 A:DO3203 3.3 61.5 1.0 C12 A:DO3203 3.4 56.8 1.0 C9 A:DO3203 3.4 64.7 1.0 C14 A:DO3203 3.5 56.1 1.0 C7 A:DO3203 3.5 46.7 1.0 C5 A:DO3203 3.5 51.6 1.0 C3 A:DO3203 3.6 56.8 1.0 C6 A:DO3203 3.6 46.2 1.0 C8 A:DO3203 3.6 49.7 1.0 C4 A:DO3203 3.6 58.2 1.0 C10 A:DO3203 3.7 62.2 1.0 C2 A:DO3203 3.7 57.6 1.0 C1 A:DO3203 3.7 55.1 1.0 C17 A:DO3203 4.1 40.8 1.0 O7 A:DO3204 4.2 39.0 1.0 O4 A:DO3203 4.4 65.2 1.0 O2 A:DO3203 4.4 70.5 1.0 O6 A:DO3203 4.5 62.1 1.0

K.Nass, A.Gorel, M.M.Abdullah, A.V Martin, M.Kloos, A.Marinelli, A.Aquila, T.R.M.Barends, F.J.Decker, R.Bruce Doak, L.Foucar, E.Hartmann, M.Hilpert, M.S.Hunter, Z.Jurek, J.E.Koglin, A.Kozlov, A.A.Lutman, G.N.Kovacs, C.M.Roome, R.L.Shoeman, R.Santra, H.M.Quiney, B.Ziaja, S.Boutet, I.Schlichting. Structural Dynamics in Proteins Induced By and Probed with X-Ray Free-Electron Laser Pulses. Nat Commun V. 11 1814 2020.
ISSN: ESSN 2041-1723
PubMed: 32286284
DOI: 10.1038/S41467-020-15610-4