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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

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