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Sodium in PDB 5dm9: Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla

Enzymatic activity of Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla

All present enzymatic activity of Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla:
3.2.1.17;

Protein crystallography data

The structure of Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla, PDB code: 5dm9 was solved by J.Kobayashi, E.Nango, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.60 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.200, 79.200, 38.000, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 21.2

Other elements in 5dm9:

The structure of Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla (pdb code 5dm9). 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 Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla, PDB code: 5dm9:

Sodium binding site 1 out of 1 in 5dm9

Go back to Sodium Binding Sites List in 5dm9
Sodium binding site 1 out of 1 in the Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xfel Structure of Hen Egg-White Lysozyme Solved Using A Droplet Injector at Sacla within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:34.3
occ:1.00
 O A:SER60 2.4 33.1 1.0
O A:CYS64 2.5 30.0 1.0
O A:HOH340 2.5 32.5 1.0
OG A:SER72 2.5 37.9 1.0
O A:HOH323 2.5 31.8 1.0
O A:ARG73 2.6 34.7 1.0
CB A:SER72 3.2 39.7 1.0
C A:CYS64 3.5 29.6 1.0
C A:ARG73 3.5 36.2 1.0
C A:SER60 3.6 32.7 1.0
N A:ARG73 3.8 38.0 1.0
C A:SER72 3.8 39.7 1.0
CA A:ASN65 3.9 29.7 1.0
N A:ASN65 4.1 28.2 1.0
CA A:SER72 4.1 41.2 1.0
CA A:ARG73 4.2 38.3 1.0
O A:SER72 4.2 39.2 1.0
CA A:SER60 4.4 30.9 1.0
N A:ASN74 4.4 34.5 1.0
C A:ARG61 4.5 36.6 1.0
N A:CYS64 4.5 29.3 1.0
O A:ARG61 4.5 38.1 1.0
CA A:CYS64 4.6 29.5 1.0
N A:ARG61 4.6 33.8 1.0
CB A:SER60 4.6 30.5 1.0
CA A:ASN74 4.6 33.8 1.0
CB A:ASN65 4.7 29.7 1.0
OD1 A:ASN65 4.7 30.4 1.0
O A:HOH347 4.7 31.6 1.0
CB A:THR69 4.8 34.5 1.0
O A:THR69 4.8 38.1 1.0
N A:TRP62 4.8 35.1 1.0
CA A:ARG61 4.8 37.2 1.0
CB A:ASN74 4.9 31.9 1.0
N A:ASP66 4.9 28.3 1.0
C A:ASN65 5.0 27.3 1.0

Reference:

F.Mafune, K.Miyajima, K.Tono, Y.Takeda, J.Y.Kohno, N.Miyauchi, J.Kobayashi, Y.Joti, E.Nango, S.Iwata, M.Yabashi. Microcrystal Delivery By Pulsed Liquid Droplet For Serial Femtosecond Crystallography. Acta Crystallogr D Struct V. 72 520 2016BIOL.
ISSN: ISSN 2059-7983
PubMed: 27050131
DOI: 10.1107/S2059798316001480
Page generated: Tue Dec 15 10:50:51 2020

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