Atomistry » Sodium » PDB 6syc-6tbn » 6syd
Atomistry »
  Sodium »
    PDB 6syc-6tbn »
      6syd »

Sodium in PDB 6syd: Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 5.5

Enzymatic activity of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 5.5

All present enzymatic activity of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 5.5:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 5.5, PDB code: 6syd was solved by A.Camara-Artigas, M.Plaza-Garrido, M.C.Salinas-Garcia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.04 / 1.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.498, 78.498, 37.341, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 23.2

Other elements in 6syd:

The structure of Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 5.5 also contains other interesting chemical elements:

Bromine (Br) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 5.5 (pdb code 6syd). 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 the Lysozyme in Presence of Bromophenol Blue at pH 5.5, PDB code: 6syd:

Sodium binding site 1 out of 1 in 6syd

Go back to Sodium Binding Sites List in 6syd
Sodium binding site 1 out of 1 in the Crystal Structure of the Lysozyme in Presence of Bromophenol Blue at pH 5.5


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 the Lysozyme in Presence of Bromophenol Blue at pH 5.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:19.2
occ:1.00
O A:SER60 2.3 18.7 1.0
O A:CYS64 2.3 15.2 1.0
O A:HOH384 2.4 23.2 1.0
O A:HOH365 2.4 17.1 1.0
O A:ARG73 2.5 24.8 1.0
OG A:SER72 2.6 26.0 1.0
HB2 A:SER72 2.8 32.0 1.0
HA A:ASN65 2.9 18.3 1.0
CB A:SER72 3.2 26.7 1.0
C A:CYS64 3.4 14.8 1.0
C A:SER60 3.5 17.9 1.0
C A:ARG73 3.5 24.7 1.0
HB2 A:SER60 3.7 17.5 1.0
HB A:THR69 3.8 23.5 1.0
HB3 A:SER72 3.8 32.0 1.0
CA A:ASN65 3.8 15.2 1.0
H A:CYS64 3.9 20.2 1.0
HA A:SER60 3.9 18.7 1.0
N A:ARG73 4.0 27.9 1.0
H A:ASP66 4.0 17.2 1.0
HB2 A:ASN74 4.0 26.1 1.0
H A:ARG73 4.0 33.5 1.0
HA A:ASN74 4.0 27.3 1.0
N A:ASN65 4.1 14.9 1.0
C A:SER72 4.1 28.3 1.0
CA A:SER60 4.2 15.6 1.0
CA A:SER72 4.3 27.7 1.0
HA A:ARG61 4.3 25.4 1.0
CA A:ARG73 4.4 27.8 1.0
CB A:SER60 4.4 14.6 1.0
N A:ASN74 4.4 23.9 1.0
N A:CYS64 4.4 16.9 1.0
HB2 A:ASN65 4.4 20.6 1.0
C A:ARG61 4.5 22.2 1.0
CA A:CYS64 4.6 15.3 1.0
CA A:ASN74 4.6 22.8 1.0
N A:ARG61 4.6 18.2 1.0
O A:ARG61 4.6 22.5 1.0
O A:HOH413 4.6 15.4 1.0
N A:ASP66 4.7 14.3 1.0
O A:SER72 4.7 28.7 1.0
CB A:THR69 4.7 19.6 1.0
CB A:ASN65 4.7 17.1 1.0
CA A:ARG61 4.7 21.2 1.0
OD1 A:ASN65 4.7 18.8 1.0
HG21 A:THR69 4.7 23.9 1.0
HA A:ARG73 4.7 33.3 1.0
CB A:ASN74 4.7 21.7 1.0
H A:TRP63 4.8 23.0 1.0
C A:ASN65 4.8 14.7 1.0
N A:TRP62 4.8 22.4 1.0
HA A:SER72 4.9 33.2 1.0
H A:ASN65 4.9 17.9 1.0
O A:THR69 5.0 23.0 1.0
H A:TRP62 5.0 26.9 1.0

Reference:

M.Plaza-Garrido, M.C.Salinas-Garcia, D.Alba-Elena, J.C.Martinez, A.Camara-Artigas. Lysozyme Crystals Dyed with Bromophenol Blue: Where Has the Dye Gone? Acta Crystallogr D Struct V. 76 845 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32876060
DOI: 10.1107/S2059798320008803
Page generated: Tue Oct 8 13:34:40 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy