Atomistry » Sodium » PDB 8oyg-8pha » 8pfx
Atomistry »
  Sodium »
    PDB 8oyg-8pha »
      8pfx »

Sodium in PDB 8pfx: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition B

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

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

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition B, PDB code: 8pfx 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) 38.36 / 1.03
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.72, 76.72, 38.39, 90, 90, 90
R / Rfree (%) 19.2 / 21.4

Other elements in 8pfx:

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

Ruthenium (Ru) 6 atoms
Fluorine (F) 2 atoms

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(D-P-Fphf)(CO3)3] in Condition B (pdb code 8pfx). 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(D-P-Fphf)(CO3)3] in Condition B, PDB code: 8pfx:

Sodium binding site 1 out of 1 in 8pfx

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


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(D-P-Fphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:12.7
occ:1.00
 O A:SER60 2.3 11.5 1.0
O A:ARG73 2.4 15.5 1.0
O A:CYS64 2.4 10.9 1.0
O A:HOH406 2.4 16.6 1.0
O A:HOH389 2.5 14.0 1.0
OG A:SER72 2.5 17.0 1.0
CB A:SER72 3.3 17.1 1.0
C A:CYS64 3.4 10.3 1.0
C A:ARG73 3.4 15.2 1.0
C A:SER60 3.5 10.2 1.0
CA A:ASN65 3.9 10.3 1.0
N A:ARG73 4.0 17.1 1.0
N A:ASN65 4.1 10.3 1.0
CA A:SER60 4.1 9.2 1.0
C A:SER72 4.2 18.2 1.0
N A:ASN74 4.3 15.4 1.0
CB A:SER60 4.3 9.1 1.0
CA A:ARG73 4.3 17.7 1.0
CA A:SER72 4.4 17.9 1.0
N A:CYS64 4.4 10.7 1.0
C A:ARG61 4.5 12.3 1.0
CA A:ASN74 4.5 14.4 1.0
O A:HOH371 4.5 17.6 1.0
N A:ARG61 4.5 10.7 1.0
CA A:CYS64 4.6 10.5 1.0
O A:HOH422 4.6 31.8 1.0
O A:ARG61 4.6 14.8 1.0
CB A:ASN74 4.6 14.9 1.0
O A:SER72 4.7 21.8 1.0
N A:ASP66 4.7 9.8 1.0
OD1 A:ASN65 4.7 17.6 1.0
CA A:ARG61 4.7 13.5 1.0
CB A:THR69 4.8 12.7 1.0
N A:TRP62 4.8 11.8 1.0
CB A:ASN65 4.8 11.7 1.0
C A:ASN65 4.9 9.5 1.0
O A:THR69 5.0 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: Wed Oct 9 12:55:55 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