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Sodium in PDB 6jzi: Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure

Enzymatic activity of Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure

All present enzymatic activity of Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure:
3.2.1.17;

Protein crystallography data

The structure of Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure, PDB code: 6jzi was solved by E.Nango, M.Sugahara, T.Nakane, T.Tanaka, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.27 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.110, 79.110, 38.020, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.2

Other elements in 6jzi:

The structure of Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure (pdb code 6jzi). 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 Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure, PDB code: 6jzi:

Sodium binding site 1 out of 1 in 6jzi

Go back to Sodium Binding Sites List in 6jzi
Sodium binding site 1 out of 1 in the Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Hen Egg-White Lysozyme Obtained From Sfx Experiments Under Atmospheric Pressure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:27.7
occ:1.00
 O A:SER60 2.4 26.4 1.0
O A:CYS64 2.4 22.6 1.0
O A:HOH319 2.5 32.0 1.0
O A:HOH316 2.5 25.5 1.0
OG A:SER72 2.5 30.1 1.0
O A:ARG73 2.6 28.6 1.0
CB A:SER72 3.2 28.7 1.0
C A:CYS64 3.5 21.1 1.0
C A:SER60 3.5 22.4 1.0
C A:ARG73 3.6 31.6 1.0
CA A:ASN65 4.0 26.0 1.0
N A:ARG73 4.0 26.7 1.0
C A:SER72 4.1 37.2 1.0
CA A:SER60 4.2 20.2 1.0
N A:ASN65 4.2 24.7 1.0
CA A:SER72 4.3 34.9 1.0
CB A:SER60 4.4 20.9 1.0
N A:CYS64 4.4 20.0 1.0
CA A:ARG73 4.4 26.6 1.0
N A:ASN74 4.5 28.1 1.0
C A:ARG61 4.5 28.0 1.0
O A:ARG61 4.5 26.3 1.0
N A:ARG61 4.6 21.1 1.0
CA A:ASN74 4.6 26.4 1.0
O A:SER72 4.6 30.2 1.0
CA A:CYS64 4.6 19.6 1.0
CB A:THR69 4.7 25.8 1.0
O A:HOH302 4.7 23.9 1.0
N A:ASP66 4.8 21.6 1.0
CB A:ASN74 4.8 23.3 1.0
CA A:ARG61 4.8 29.9 0.5
CA A:ARG61 4.8 29.8 0.5
OD1 A:ASN65 4.8 31.4 1.0
N A:TRP62 4.8 23.8 1.0
CB A:ASN65 4.8 21.9 1.0
O A:THR69 4.9 34.5 1.0
C A:ASN65 4.9 19.3 1.0

Reference:

Y.Shimazu, K.Tono, T.Tanaka, Y.Yamanaka, T.Nakane, C.Mori, K.T.Kimura, T.Fujiwara, M.Sugahara, R.Tanaka, R.B.Doak, T.Shimamura, S.Iwata, E.Nango, M.Yabashi. High-Viscosity Sample-Injection Device For Serial Femtosecond Crystallography at Atmospheric Pressure J.Appl.Crystallogr. V. 52 2019.
ISSN: ESSN 1600-5767
DOI: 10.1107/S1600576719012846
Page generated: Mon Aug 18 05:39:37 2025

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