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Sodium in PDB 6kcd: Room Temperature Structure of Lysozyme Delivered in Shortening B By Serial Millisecond Crystallography

Enzymatic activity of Room Temperature Structure of Lysozyme Delivered in Shortening B By Serial Millisecond Crystallography

All present enzymatic activity of Room Temperature Structure of Lysozyme Delivered in Shortening B By Serial Millisecond Crystallography:
3.2.1.17;

Protein crystallography data

The structure of Room Temperature Structure of Lysozyme Delivered in Shortening B By Serial Millisecond Crystallography, PDB code: 6kcd 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) 55.99 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.450, 79.450, 38.470, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 20.7

Other elements in 6kcd:

The structure of Room Temperature Structure of Lysozyme Delivered in Shortening B By Serial Millisecond Crystallography 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 Delivered in Shortening B By Serial Millisecond Crystallography (pdb code 6kcd). 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 Delivered in Shortening B By Serial Millisecond Crystallography, PDB code: 6kcd:

Sodium binding site 1 out of 1 in 6kcd

Go back to Sodium Binding Sites List in 6kcd
Sodium binding site 1 out of 1 in the Room Temperature Structure of Lysozyme Delivered in Shortening B By Serial Millisecond Crystallography


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 Delivered in Shortening B By Serial Millisecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:42.0
occ:1.00
 O A:SER78 2.3 39.1 1.0
O A:CYS82 2.4 35.1 1.0
O A:HOH346 2.5 44.7 1.0
O A:HOH337 2.5 41.2 1.0
OG A:SER90 2.5 48.5 1.0
O A:ARG91 2.5 46.6 1.0
CB A:SER90 3.2 46.7 1.0
C A:CYS82 3.5 34.5 1.0
C A:SER78 3.5 35.6 1.0
C A:ARG91 3.6 46.1 1.0
CA A:ASN83 3.9 37.3 1.0
N A:ARG91 4.0 47.2 1.0
C A:SER90 4.1 50.8 1.0
N A:ASN83 4.1 34.4 1.0
CA A:SER78 4.2 34.0 1.0
CA A:SER90 4.3 49.5 1.0
CA A:ARG91 4.4 45.3 1.0
CB A:SER78 4.4 32.6 1.0
N A:CYS82 4.4 34.4 1.0
N A:ASN92 4.4 43.2 1.0
C A:ARG79 4.5 42.5 1.0
N A:ARG79 4.5 37.7 1.0
O A:SER90 4.6 50.2 1.0
O A:ARG79 4.6 43.7 1.0
CA A:ASN92 4.6 41.1 1.0
CA A:CYS82 4.6 35.0 1.0
CA A:ARG79 4.6 40.9 1.0
O A:HOH342 4.7 41.6 1.0
CB A:ASN92 4.7 39.2 1.0
CB A:THR87 4.7 40.0 1.0
CB A:ASN83 4.7 37.4 1.0
N A:ASP84 4.8 33.8 1.0
OD1 A:ASN83 4.8 43.7 1.0
N A:TRP80 4.8 38.8 1.0
C A:ASN83 4.9 34.5 1.0
O A:THR87 4.9 45.9 1.0

Reference:

K.H.Nam, K.H.Nam. N/A N/A.
ISSN: ESSN 2045-2322
PubMed: 31919476
DOI: 10.1038/S41598-019-56135-1
Page generated: Tue Oct 8 11:33:00 2024

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