Atomistry » Ruthenium » PDB 8p6b-8s90 » 8pft
Atomistry »
  Ruthenium »
    PDB 8p6b-8s90 »
      8pft »

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

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

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 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(D-P-Fphf)(CO3)3] in Condition A, PDB code: 8pft 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) 54.98 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.75, 77.75, 37.34, 90, 90, 90
R / Rfree (%) 20.3 / 24.6

Other elements in 8pft:

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

Sodium (Na) 1 atom
Fluorine (F) 4 atoms
Chlorine (Cl) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A (pdb code 8pft). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 4 binding sites of Ruthenium where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A, PDB code: 8pft:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in 8pft

Go back to Ruthenium Binding Sites List in 8pft
Ruthenium binding site 1 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru 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 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru203

b:37.7
occ:0.35
 RU1 A:YJT203 0.0 37.7 0.3
N1 A:YJT203 2.0 39.5 0.3
O3 A:YJT203 2.0 35.3 0.3
O1 A:YJT203 2.0 36.2 0.3
OD2 A:ASP101 2.0 36.4 0.5
RU2 A:YJT203 2.3 33.2 0.3
C7 A:YJT203 2.8 50.7 0.3
C2 A:YJT203 2.9 46.8 0.3
C14 A:YJT203 2.9 36.7 0.3
C1 A:YJT203 2.9 37.2 0.3
O4 A:YJT203 3.0 30.8 0.3
CG A:ASP101 3.1 34.3 0.5
OD2 A:ASP101 3.1 35.5 0.5
N2 A:YJT203 3.1 36.3 0.3
O2 A:YJT203 3.1 34.9 0.3
OD1 A:ASP101 3.6 38.2 0.5
CG A:ASP101 3.7 33.3 0.5
O7 A:YJT203 4.1 35.5 0.3
C6 A:YJT203 4.1 52.0 0.3
C3 A:YJT203 4.2 49.4 0.3
CB A:ASP101 4.3 33.5 0.5
O A:ASP101 4.3 37.2 0.5
OD1 A:ASP101 4.3 29.5 0.5
CB A:ASP101 4.4 30.5 0.5
C8 A:YJT203 4.5 42.0 0.3
O A:ASP101 4.9 31.5 0.5

Ruthenium binding site 2 out of 4 in 8pft

Go back to Ruthenium Binding Sites List in 8pft
Ruthenium binding site 2 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru203

b:33.2
occ:0.35
 RU2 A:YJT203 0.0 33.2 0.3
N2 A:YJT203 2.0 36.3 0.3
O4 A:YJT203 2.0 30.8 0.3
O2 A:YJT203 2.0 34.9 0.3
RU1 A:YJT203 2.3 37.7 0.3
OD1 A:ASP101 2.4 38.2 0.5
OD2 A:ASP101 2.7 36.4 0.5
CG A:ASP101 2.9 34.3 0.5
C14 A:YJT203 2.9 36.7 0.3
C1 A:YJT203 2.9 37.2 0.3
O3 A:YJT203 2.9 35.3 0.3
C8 A:YJT203 2.9 42.0 0.3
N1 A:YJT203 3.0 39.5 0.3
O1 A:YJT203 3.0 36.2 0.3
C13 A:YJT203 3.4 42.3 0.3
O A:ASP101 3.8 37.2 0.5
C9 A:YJT203 3.9 45.5 0.3
O A:ASP101 4.1 31.5 0.5
O7 A:YJT203 4.1 35.5 0.3
OD2 A:ASP101 4.2 35.5 0.5
CB A:ASP101 4.2 30.5 0.5
C2 A:YJT203 4.3 46.8 0.3
CG A:ASP101 4.3 33.3 0.5
CB A:ASP101 4.4 33.5 0.5
C12 A:YJT203 4.7 45.2 0.3
C7 A:YJT203 4.8 50.7 0.3
C A:ASP101 4.8 32.5 0.5
C A:ASP101 4.9 32.0 0.5

Ruthenium binding site 3 out of 4 in 8pft

Go back to Ruthenium Binding Sites List in 8pft
Ruthenium binding site 3 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru204

b:29.4
occ:0.35
 RU1 A:YJT204 0.0 29.4 0.3
N1 A:YJT204 2.0 29.4 0.3
O3 A:YJT204 2.0 23.5 0.3
O1 A:YJT204 2.0 31.6 0.3
OD1 A:ASP119 2.1 29.8 0.5
RU2 A:YJT204 2.3 27.5 0.3
C1 A:YJT204 2.9 32.3 0.3
CG A:ASP119 2.9 27.8 0.5
C14 A:YJT204 3.0 32.8 0.3
C2 A:YJT204 3.0 30.1 0.3
OD2 A:ASP119 3.1 29.0 0.5
O4 A:YJT204 3.1 29.7 0.3
N2 A:YJT204 3.1 31.6 0.3
O2 A:YJT204 3.2 31.5 0.3
C7 A:YJT204 3.5 24.3 0.3
C3 A:YJT204 4.1 29.4 0.3
O7 A:YJT204 4.1 41.7 0.3
CB A:ASP119 4.4 27.4 0.5
CB A:ASP119 4.4 32.8 0.5
C8 A:YJT204 4.5 35.8 0.3
CG A:ASP119 4.7 34.8 0.5
C6 A:YJT204 4.8 28.8 0.3
CA A:ASP119 4.9 28.9 0.5
CA A:ASP119 4.9 25.7 0.5
C9 A:YJT204 5.0 37.2 0.3

Ruthenium binding site 4 out of 4 in 8pft

Go back to Ruthenium Binding Sites List in 8pft
Ruthenium binding site 4 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru204

b:27.5
occ:0.35
 RU2 A:YJT204 0.0 27.5 0.3
N2 A:YJT204 2.0 31.6 0.3
O4 A:YJT204 2.0 29.7 0.3
O2 A:YJT204 2.1 31.5 0.3
OD2 A:ASP119 2.1 29.0 0.5
RU1 A:YJT204 2.3 29.4 0.3
C1 A:YJT204 2.8 32.3 0.3
C14 A:YJT204 2.8 32.8 0.3
CG A:ASP119 2.9 27.8 0.5
O1 A:YJT204 2.9 31.6 0.3
N1 A:YJT204 3.0 29.4 0.3
OD1 A:ASP119 3.0 29.8 0.5
C8 A:YJT204 3.1 35.8 0.3
O3 A:YJT204 3.2 23.5 0.3
C9 A:YJT204 3.9 37.2 0.3
C13 A:YJT204 4.0 37.8 0.3
O7 A:YJT204 4.0 41.7 0.3
CB A:ASP119 4.4 27.4 0.5
C2 A:YJT204 4.4 30.1 0.3
CB A:ASP119 4.5 32.8 0.5
O A:HOH359 4.9 41.4 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: Thu Oct 10 13:14:08 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy