Atomistry » Sodium » PDB 8xxi-8zj7 » 8ybg
Atomistry »
  Sodium »
    PDB 8xxi-8zj7 »
      8ybg »

Sodium in PDB 8ybg: Crystal Structure of Lysozyme By Serial Synchrotron Crystallography

Enzymatic activity of Crystal Structure of Lysozyme By Serial Synchrotron Crystallography

All present enzymatic activity of Crystal Structure of Lysozyme By Serial Synchrotron Crystallography:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Lysozyme By Serial Synchrotron Crystallography, PDB code: 8ybg was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.51 / 1.55
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.5, 78.5, 38.3, 90, 90, 90
R / Rfree (%) 18.2 / 22

Other elements in 8ybg:

The structure of Crystal Structure of Lysozyme By Serial Synchrotron Crystallography also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Lysozyme By Serial Synchrotron Crystallography (pdb code 8ybg). 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 Crystal Structure of Lysozyme By Serial Synchrotron Crystallography, PDB code: 8ybg:

Sodium binding site 1 out of 1 in 8ybg

Go back to Sodium Binding Sites List in 8ybg
Sodium binding site 1 out of 1 in the Crystal Structure of Lysozyme By Serial Synchrotron Crystallography


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Lysozyme By Serial Synchrotron Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:33.4
occ:1.00
 O A:SER78 2.3 28.4 1.0
OG A:SER90 2.3 35.8 1.0
O A:CYS82 2.5 24.2 1.0
O A:ARG91 2.5 36.7 1.0
O A:HOH350 2.6 28.6 1.0
O A:HOH351 2.6 35.5 1.0
CB A:SER90 3.1 37.4 1.0
C A:SER78 3.5 24.2 1.0
C A:CYS82 3.5 23.4 1.0
C A:ARG91 3.5 33.4 1.0
CA A:ASN83 3.9 26.7 1.0
C A:SER90 3.9 40.2 1.0
N A:ARG91 4.0 33.5 1.0
N A:ASN83 4.1 24.5 1.0
CA A:SER90 4.1 38.3 1.0
CA A:SER78 4.2 24.9 1.0
O A:ARG79 4.3 31.8 1.0
C A:ARG79 4.4 32.8 1.0
N A:ASN92 4.4 31.0 1.0
CA A:ARG91 4.4 35.0 1.0
N A:CYS82 4.4 24.0 1.0
O A:SER90 4.4 35.8 1.0
CB A:SER78 4.4 24.1 1.0
N A:ARG79 4.5 25.8 1.0
CA A:ASN92 4.5 28.4 1.0
CA A:CYS82 4.6 25.1 1.0
CA A:ARG79 4.6 30.6 1.0
CB A:ASN92 4.7 28.3 1.0
O A:HOH371 4.7 33.4 1.0
OD1 A:ASN83 4.7 35.6 1.0
CB A:THR87 4.7 28.1 1.0
N A:TRP80 4.7 29.1 1.0
CB A:ASN83 4.7 28.6 1.0
N A:ASP84 4.8 24.0 1.0
C A:ASN83 4.9 24.9 1.0
O A:THR87 4.9 35.7 1.0
N A:TRP81 5.0 24.1 1.0
C A:TRP80 5.0 28.3 1.0

Reference:

K.H.Nam, K.H.Nam. N/A N/A.
Page generated: Mon Aug 18 16:28:19 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy