Sodium in PDB 8d5z: Crystal Structure of Hen Egg White Lysozyme at 125 Kelvin (Triplicate)

Enzymatic activity of Crystal Structure of Hen Egg White Lysozyme at 125 Kelvin (Triplicate)

All present enzymatic activity of Crystal Structure of Hen Egg White Lysozyme at 125 Kelvin (Triplicate):
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Hen Egg White Lysozyme at 125 Kelvin (Triplicate), PDB code: 8d5z 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) 22.27 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.704, 78.704, 37.098, 90, 90, 90
R / Rfree (%) 18.7 / 21.7

Other elements in 8d5z:

The structure of Crystal Structure of Hen Egg White Lysozyme at 125 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 125 Kelvin (Triplicate) (pdb code 8d5z). 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 125 Kelvin (Triplicate), PDB code: 8d5z:

Sodium binding site 1 out of 1 in 8d5z

Go back to Sodium Binding Sites List in 8d5z
Sodium binding site 1 out of 1 in the Crystal Structure of Hen Egg White Lysozyme at 125 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 125 Kelvin (Triplicate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:14.2
occ:1.00
 O A:SER60 2.3 11.3 1.0
O A:HOH380 2.3 13.1 1.0
O A:ARG73 2.3 16.3 1.0
O A:HOH357 2.4 9.9 1.0
OG A:SER72 2.5 16.1 1.0
O A:CYS64 2.5 7.8 1.0
CB A:SER72 3.2 16.7 1.0
C A:SER60 3.4 10.6 1.0
C A:ARG73 3.5 15.0 1.0
C A:CYS64 3.5 7.0 1.0
CA A:ASN65 4.0 8.5 1.0
N A:ARG73 4.0 17.8 1.0
CA A:SER60 4.0 9.5 1.0
C A:SER72 4.1 20.5 1.0
N A:ASN65 4.2 8.0 1.0
CB A:SER60 4.2 8.8 1.0
CA A:SER72 4.3 18.0 1.0
CA A:ARG73 4.3 15.9 1.0
N A:ASN74 4.3 13.8 1.0
N A:CYS64 4.5 8.8 1.0
N A:ARG61 4.5 12.6 1.0
C A:ARG61 4.6 13.4 1.0
CA A:ASN74 4.6 11.2 1.0
O A:ARG61 4.6 13.9 1.0
CB A:THR69 4.6 10.2 1.0
CL A:CL203 4.6 15.8 1.0
N A:ASP66 4.6 7.7 1.0
CA A:CYS64 4.7 7.9 1.0
ND2 A:ASN65 4.7 9.9 1.0
O A:SER72 4.7 22.6 1.0
CB A:ASN74 4.8 11.1 1.0
N A:TRP62 4.8 12.0 1.0
CB A:ASN65 4.9 9.1 1.0
C A:ASN65 4.9 7.5 1.0
CA A:ARG61 4.9 14.2 1.0
O A:THR69 4.9 12.7 1.0
OG A:SER60 5.0 8.2 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: Fri Jul 28 03:16:57 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy