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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 6sr4:

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

Gadolinium Binding Sites:

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 6sr4

Go back to Gadolinium Binding Sites List in 6sr4
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 6sr4

Go back to Gadolinium Binding Sites List in 6sr4
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

Reference:

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
Page generated: Fri Aug 8 08:42:10 2025

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