Sodium in PDB 8d7d: Crystal Structure of Hen Egg White Lysozyme at 225 Kelvin (Triplicate)

Enzymatic activity of Crystal Structure of Hen Egg White Lysozyme at 225 Kelvin (Triplicate)

All present enzymatic activity of Crystal Structure of Hen Egg White Lysozyme at 225 Kelvin (Triplicate):
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg White Lysozyme at 225 Kelvin (Triplicate), PDB code: 8d7d was solved by F.S.Ribeiro, L.M.T.R.Lima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.50 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.487, 79.487, 37.495, 90, 90, 90
R / Rfree (%) 17.1 / 20.7

Other elements in 8d7d:

The structure of Crystal Structure of Hen Egg White Lysozyme at 225 Kelvin (Triplicate) also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Hen Egg White Lysozyme at 225 Kelvin (Triplicate) (pdb code 8d7d). 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 Hen Egg White Lysozyme at 225 Kelvin (Triplicate), PDB code: 8d7d:

Sodium binding site 1 out of 1 in 8d7d

Go back to Sodium Binding Sites List in 8d7d
Sodium binding site 1 out of 1 in the Crystal Structure of Hen Egg White Lysozyme at 225 Kelvin (Triplicate)


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 Hen Egg White Lysozyme at 225 Kelvin (Triplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:12.9
occ:1.00
 O A:SER60 2.4 12.3 1.0
O A:CYS64 2.4 10.2 1.0
O A:HOH362 2.4 15.5 1.0
O A:ARG73 2.4 15.7 1.0
O A:HOH337 2.5 11.5 1.0
OG A:SER72 2.5 14.3 1.0
CB A:SER72 3.3 14.2 1.0
C A:CYS64 3.5 8.9 1.0
C A:ARG73 3.5 16.9 1.0
C A:SER60 3.5 11.0 1.0
CA A:ASN65 3.9 10.2 1.0
N A:ARG73 4.0 15.4 1.0
CA A:SER60 4.1 10.3 1.0
N A:ASN65 4.1 10.0 1.0
C A:SER72 4.2 16.3 1.0
CB A:SER60 4.3 10.8 1.0
CA A:SER72 4.3 16.1 1.0
N A:ASN74 4.4 13.7 1.0
CA A:ARG73 4.4 16.7 1.0
N A:CYS64 4.5 9.5 1.0
C A:ARG61 4.6 14.2 1.0
CA A:ASN74 4.6 12.6 1.0
CA A:CYS64 4.6 9.3 1.0
N A:ARG61 4.6 13.2 1.0
O A:ARG61 4.6 16.1 1.0
N A:ASP66 4.6 9.5 1.0
ND2 A:ASN65 4.7 11.9 1.0
CB A:THR69 4.7 11.7 1.0
CL A:CL203 4.7 17.9 1.0
O A:SER72 4.7 17.6 1.0
CB A:ASN74 4.8 13.1 1.0
C A:ASN65 4.8 10.4 1.0
CB A:ASN65 4.8 10.6 1.0
CA A:ARG61 4.9 14.7 1.0
N A:TRP62 4.9 13.2 1.0

Reference:

F.De Sa Ribeiro, L.M.T.Lima. Linking B-Factor and Temperature-Induced Conformational Transition Biophys.Chem. 07027 2023.
ISSN: ISSN 0301-4622
DOI: 10.1016/J.BPC.2023.107027
Page generated: Wed Oct 9 11:26:13 2024

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