Atomistry » Sodium » PDB 8oyw-8pkv » 8pfw
Atomistry »
  Sodium »
    PDB 8oyw-8pkv »
      8pfw »

Sodium in PDB 8pfw: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A, PDB code: 8pfw was solved by A.Teran, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.02 / 1.12
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.81, 77.81, 37.39, 90, 90, 90
R / Rfree (%) 20.1 / 23.9

Other elements in 8pfw:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A also contains other interesting chemical elements:

Ruthenium (Ru) 6 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A (pdb code 8pfw). 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 X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A, PDB code: 8pfw:

Sodium binding site 1 out of 1 in 8pfw

Go back to Sodium Binding Sites List in 8pfw
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:19.9
occ:1.00
 O A:HOH375 2.3 23.1 1.0
O A:SER60 2.3 18.9 1.0
O A:ARG73 2.4 25.3 1.0
O A:CYS64 2.5 15.8 1.0
OG A:SER72 2.6 23.6 1.0
O A:HOH374 2.7 23.9 1.0
C A:ARG73 3.4 22.6 1.0
C A:CYS64 3.5 14.5 1.0
C A:SER60 3.5 16.7 1.0
CB A:SER72 3.5 24.8 1.0
N A:ARG73 3.8 25.5 1.0
CA A:ASN65 4.1 16.2 1.0
CA A:SER60 4.1 16.0 1.0
C A:SER72 4.1 28.6 1.0
N A:ASN65 4.2 16.5 1.0
CA A:ARG73 4.2 25.7 1.0
N A:ASN74 4.2 22.1 1.0
N A:CYS64 4.3 16.1 1.0
CB A:SER60 4.3 15.4 1.0
CA A:SER72 4.4 28.0 1.0
CA A:ASN74 4.4 21.3 1.0
C A:ARG61 4.5 20.3 1.0
O A:ARG61 4.5 22.2 1.0
CA A:CYS64 4.5 15.8 1.0
N A:ARG61 4.6 16.8 1.0
CB A:ASN74 4.6 19.2 1.0
O A:SER72 4.7 30.0 1.0
CB A:THR69 4.7 16.6 1.0
N A:TRP62 4.7 18.7 1.0
O A:HOH335 4.8 26.2 1.0
CA A:ARG61 4.8 20.1 1.0
CB A:ASN65 4.9 19.8 1.0
N A:TRP63 4.9 16.6 1.0
C A:TRP62 4.9 18.4 1.0
O A:THR69 4.9 21.5 1.0
N A:ASP66 4.9 14.7 1.0

Reference:

S.Herrero Dominguez, A.Teran, G.Ferraro, A.E.Sanchez-Pelaez, A.Merlino. Charge Effect in Protein Metalation Reactions By Diruthenium Complexes Inorg Chem Front 2023.
DOI: 10.1039/D3QI01192E
Page generated: Mon Aug 18 15:00:50 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy