Atomistry » Sodium » PDB 6sfo-6sxg » 6sr5
Atomistry »
  Sodium »
    PDB 6sfo-6sxg »
      6sr5 »

Sodium in PDB 6sr5: X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 102 Fs Time Delay

Enzymatic activity of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 102 Fs Time Delay

All present enzymatic activity of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 102 Fs Time Delay:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 102 Fs Time Delay, PDB code: 6sr5 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 (%) 18.5 / 24.2

Other elements in 6sr5:

The structure of X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 102 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: 102 Fs Time Delay (pdb code 6sr5). 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: 102 Fs Time Delay, PDB code: 6sr5:

Sodium binding site 1 out of 1 in 6sr5

Go back to Sodium Binding Sites List in 6sr5
Sodium binding site 1 out of 1 in the X-Ray Pump X-Ray Probe on Lysozyme.Gd Nanocrystals: 102 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: 102 Fs Time Delay within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:39.0
occ:1.00
 O A:SER60 2.5 27.3 1.0
O A:HOH326 2.6 31.9 1.0
O A:CYS64 2.6 29.2 1.0
OG A:SER72 2.6 44.4 1.0
O A:HOH315 2.7 52.4 1.0
O A:ARG73 2.8 37.4 1.0
CB A:SER72 3.4 44.4 1.0
C A:CYS64 3.5 26.2 1.0
C A:ARG73 3.7 37.1 1.0
C A:SER60 3.7 28.2 1.0
CA A:ASN65 4.0 25.8 1.0
N A:ARG73 4.0 37.4 1.0
N A:ASN65 4.1 25.8 1.0
C A:SER72 4.1 38.9 1.0
O A:ARG61 4.3 29.5 1.0
CA A:SER60 4.3 28.0 1.0
CA A:SER72 4.4 40.5 1.0
N A:ASN74 4.4 35.2 1.0
N A:CYS64 4.5 26.9 1.0
CA A:ARG73 4.5 38.5 1.0
O A:SER72 4.5 35.5 1.0
CA A:CYS64 4.5 25.8 1.0
CB A:SER60 4.6 27.3 1.0
C A:ARG61 4.6 32.4 1.0
CA A:ASN74 4.6 33.9 1.0
CB A:ASN74 4.7 33.4 1.0
N A:ARG61 4.7 30.9 1.0
CB A:ASN65 4.7 29.0 1.0
ND2 A:ASN65 4.8 25.8 1.0
CB A:THR69 4.9 34.8 1.0
CL A:CL208 5.0 59.9 1.0
CA A:ARG61 5.0 34.5 1.0
N A:ASP66 5.0 25.8 1.0
O A:THR69 5.0 36.8 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 13:31:20 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy