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Sodium in PDB 6sr3: X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay

Enzymatic activity of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay

All present enzymatic activity of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay, PDB code: 6sr3 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 (%) 21.9 / 28.6

Other elements in 6sr3:

The structure of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay also contains other interesting chemical elements:

Gadolinium (Gd) 2 atoms
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay (pdb code 6sr3). 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 X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay, PDB code: 6sr3:

Sodium binding site 1 out of 1 in 6sr3

Go back to Sodium Binding Sites List in 6sr3
Sodium binding site 1 out of 1 in the X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 62 Fs Time Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:31.3
occ:1.00
 O A:HOH325 2.3 24.0 1.0
OG A:SER72 2.5 46.2 1.0
O A:CYS64 2.6 25.2 1.0
O A:SER60 2.6 27.5 1.0
O A:HOH322 2.6 36.1 1.0
O A:ARG73 2.9 39.7 1.0
CB A:SER72 3.5 45.6 1.0
C A:CYS64 3.6 25.4 1.0
C A:ARG73 3.7 38.8 1.0
C A:SER60 3.8 27.1 1.0
C A:SER72 4.0 40.5 1.0
N A:ARG73 4.0 38.6 1.0
CA A:ASN65 4.0 24.1 1.0
N A:ASN65 4.2 24.2 1.0
O A:ARG61 4.2 30.6 1.0
O A:SER72 4.3 37.9 1.0
CA A:SER72 4.3 41.1 1.0
N A:ASN74 4.4 37.6 1.0
CA A:ARG73 4.4 40.0 1.0
C A:ARG61 4.6 31.0 1.0
CA A:SER60 4.6 26.4 1.0
CA A:ASN74 4.6 36.5 1.0
ND2 A:ASN65 4.6 24.0 1.0
N A:CYS64 4.7 25.6 1.0
CA A:CYS64 4.7 25.0 1.0
CB A:ASN74 4.7 35.9 1.0
CB A:THR69 4.7 30.6 1.0
CB A:ASN65 4.7 25.4 1.0
CB A:SER60 4.8 25.5 1.0
N A:ARG61 4.8 29.7 1.0
O A:THR69 4.8 32.3 1.0
CL A:CL208 4.9 49.6 1.0
CA A:ARG61 4.9 32.2 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: Tue Oct 8 13:30:49 2024

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