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Sodium in PDB 5ne0: Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes

Enzymatic activity of Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes

All present enzymatic activity of Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes:
3.2.1.17;

Protein crystallography data

The structure of Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes, PDB code: 5ne0 was solved by I.Martiel, N.Opara, S.A.Arnold, T.Braun, H.Stahlberg, M.Makita, C.David, C.Padeste, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.75 / 1.57
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.500, 79.500, 37.810, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 18.4

Other elements in 5ne0:

The structure of Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes (pdb code 5ne0). 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 Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes, PDB code: 5ne0:

Sodium binding site 1 out of 1 in 5ne0

Go back to Sodium Binding Sites List in 5ne0
Sodium binding site 1 out of 1 in the Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Room Temperature in-Situ Structure of Hen Egg-White Lysozyme From Crystals Enclosed Between Ultrathin Silicon Nitride Membranes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:51.6
occ:1.00
 OG A:SER72 2.4 56.8 1.0
O A:SER60 2.5 28.8 1.0
O A:CYS64 2.5 23.5 1.0
O A:ARG73 2.5 35.0 0.4
CB A:SER72 2.6 49.8 1.0
O A:HOH333 2.7 32.0 1.0
C A:CYS64 3.4 22.3 1.0
C A:ARG73 3.4 33.3 0.4
N A:ASN74 3.6 29.7 0.6
C A:SER60 3.6 24.1 1.0
N A:ARG73 3.6 35.3 0.6
C A:SER72 3.7 39.7 1.0
CA A:SER72 3.7 45.5 1.0
N A:ARG73 3.8 35.1 0.4
CA A:ASN65 3.9 27.4 1.0
N A:ASN65 4.0 23.5 1.0
CA A:ASN74 4.1 25.6 0.6
N A:ASN74 4.2 29.4 0.4
O A:ARG61 4.2 30.4 1.0
N A:CYS64 4.2 23.2 1.0
CB A:ASN74 4.3 27.4 0.6
CA A:ARG73 4.3 35.7 0.4
C A:ARG61 4.3 27.4 1.0
O A:SER72 4.3 39.1 1.0
CA A:ASN74 4.3 27.6 0.4
CA A:SER60 4.3 21.2 1.0
CA A:CYS64 4.5 21.9 1.0
C A:ARG73 4.5 34.1 0.6
N A:ARG61 4.6 23.5 1.0
CA A:ARG61 4.6 29.4 1.0
CB A:ASN65 4.6 28.1 1.0
CA A:ARG73 4.6 35.5 0.6
N A:TRP62 4.7 25.7 1.0
CB A:SER60 4.7 21.8 1.0
CB A:ASN74 4.8 28.1 0.4
N A:TRP63 4.8 24.9 1.0
OD1 A:ASN65 4.8 41.8 1.0
C A:TRP62 4.8 24.5 1.0
N A:SER72 4.8 43.5 1.0
O A:HOH338 4.9 35.6 1.0
N A:ASP66 5.0 21.2 1.0
C A:ASN65 5.0 23.6 1.0

Reference:

N.Opara, I.Martiel, S.A.Arnold, T.Braun, H.Stahlberg, M.Makita, C.David, C.Padeste. Direct Protein Crystallization on Ultrathin Membranes For Diffraction Measurements at X-Ray Free-Electron Lasers. J.Appl.Crystallogr. V. 50 909 2017.
ISSN: ISSN 0021-8898
DOI: 10.1107/S1600576717005799
Page generated: Mon Oct 7 22:55:51 2024

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