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Sodium 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:

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: 112 Fs Time Delay (pdb code 6sr4). 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: 112 Fs Time Delay, PDB code: 6sr4:

Sodium binding site 1 out of 1 in 6sr4

Go back to Sodium Binding Sites List in 6sr4
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na205

b:39.9
occ:1.00
 O A:CYS64 2.5 30.7 1.0
O A:SER60 2.5 34.0 1.0
O A:HOH312 2.6 40.0 1.0
OG A:SER72 2.7 48.4 1.0
O A:ARG73 2.7 44.2 1.0
O A:HOH323 2.7 48.2 1.0
C A:CYS64 3.5 30.0 1.0
CB A:SER72 3.5 49.5 1.0
C A:ARG73 3.6 43.5 1.0
C A:SER60 3.7 34.7 1.0
CA A:ASN65 4.0 29.2 1.0
N A:ARG73 4.0 43.0 1.0
N A:ASN65 4.1 29.7 1.0
C A:SER72 4.1 43.6 1.0
O A:ARG61 4.2 39.2 1.0
N A:ASN74 4.4 40.9 1.0
CA A:SER60 4.4 34.2 1.0
CA A:SER72 4.4 44.4 1.0
N A:CYS64 4.4 31.8 1.0
CA A:ARG73 4.5 44.3 1.0
C A:ARG61 4.5 39.2 1.0
CA A:CYS64 4.5 29.8 1.0
CA A:ASN74 4.5 38.7 1.0
O A:SER72 4.6 41.4 1.0
CB A:SER60 4.6 34.2 1.0
CB A:ASN74 4.7 37.8 1.0
ND2 A:ASN65 4.7 30.1 1.0
N A:ARG61 4.7 36.2 1.0
CB A:ASN65 4.8 31.2 1.0
CB A:THR69 4.8 38.6 1.0
CA A:ARG61 4.9 40.1 1.0
N A:TRP62 5.0 35.5 1.0
O A:THR69 5.0 43.2 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 13:31:18 2024

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