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Sodium in PDB 8h8v: Room-Temperature Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge)

Enzymatic activity of Room-Temperature Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge)

All present enzymatic activity of Room-Temperature Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge):
3.2.1.17;

Protein crystallography data

The structure of Room-Temperature Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge), PDB code: 8h8v was solved by Y.Kim, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.78 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.88, 78.88, 38.05, 90, 90, 90
R / Rfree (%) 22.6 / 25.6

Other elements in 8h8v:

The structure of Room-Temperature Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Room-Temperature Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge) (pdb code 8h8v). 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 Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge), PDB code: 8h8v:

Sodium binding site 1 out of 1 in 8h8v

Go back to Sodium Binding Sites List in 8h8v
Sodium binding site 1 out of 1 in the Room-Temperature Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Room-Temperature Structure of Lysozyme By Pink-Beam Serial Crystallography (100 Ms, Edge) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:19.6
occ:1.00
 O A:CYS82 2.3 14.4 1.0
O A:SER78 2.4 15.5 1.0
O A:HOH350 2.4 17.5 0.9
OG A:SER90 2.5 22.4 1.0
O A:ARG91 2.5 26.8 1.0
O A:HOH352 2.5 25.0 1.0
CB A:SER90 3.1 15.9 1.0
C A:CYS82 3.4 12.0 1.0
C A:ARG91 3.5 21.6 1.0
C A:SER78 3.5 10.6 1.0
N A:ARG91 3.9 24.8 1.0
CA A:ASN83 3.9 20.5 1.0
N A:ASN83 4.1 14.7 1.0
C A:SER90 4.1 31.5 1.0
CA A:SER78 4.2 13.9 1.0
CA A:ARG91 4.2 17.6 1.0
CA A:SER90 4.2 24.4 1.0
CB A:SER78 4.3 13.5 1.0
N A:ASN92 4.4 18.5 1.0
N A:CYS82 4.4 13.2 1.0
CA A:CYS82 4.5 13.4 1.0
C A:ARG79 4.6 24.0 1.0
O A:ARG79 4.6 17.7 1.0
CA A:ASN92 4.6 16.8 1.0
N A:ARG79 4.6 13.7 1.0
O A:SER90 4.7 27.4 1.0
O A:HOH381 4.7 38.1 1.0
CB A:THR87 4.7 16.8 1.0
OD1 A:ASN83 4.7 29.8 1.0
CB A:ASN83 4.7 16.1 1.0
O A:HOH376 4.7 18.9 1.0
N A:ASP84 4.8 13.2 1.0
CB A:ASN92 4.8 15.9 1.0
CA A:ARG79 4.9 22.2 1.0
N A:TRP80 4.9 18.6 1.0
C A:ASN83 4.9 10.2 1.0
O A:THR87 4.9 22.1 1.0
OG1 A:THR87 5.0 17.4 1.0

Reference:

Y.Kim, K.H.Nam. Pink-Beam Serial Synchrotron Crystallography at Pohang Light Source II Crystals V. 12 2022.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST12111637
Page generated: Wed Oct 9 12:13:03 2024

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