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Ruthenium 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:

Sodium (Na) 1 atom
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(Danif)(CO3)3] in Condition A (pdb code 8pfw). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 6 binding sites of Ruthenium where 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:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6;

Ruthenium binding site 1 out of 6 in 8pfw

Go back to Ruthenium Binding Sites List in 8pfw
Ruthenium binding site 1 out of 6 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 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(Danif)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru205

b:9.9
occ:0.45
 RU1 A:YWR205 0.0 9.9 0.5
O5 A:YWR205 2.0 10.3 0.5
N1 A:YWR205 2.0 10.1 0.5
O1 A:YWR205 2.1 10.8 0.5
O3 A:YWR205 2.1 10.0 0.5
RU2 A:YWR205 2.3 10.9 0.5
O A:HOH348 2.3 10.0 0.5
C1 A:YWR205 2.8 13.2 0.5
C5 A:YWR205 2.9 11.9 0.5
C7 A:YWR205 2.9 9.8 0.5
C3 A:YWR205 2.9 10.9 0.5
O2 A:YWR205 3.0 10.7 0.5
N2 A:YWR205 3.0 10.0 0.5
O6 A:YWR205 3.0 10.6 0.5
O4 A:YWR205 3.1 12.1 0.5
C8 A:YWR205 3.1 10.2 0.5
C13 A:YWR205 3.6 9.9 0.5
C9 A:YWR205 4.1 11.2 0.5
O9 A:YWR205 4.2 15.8 0.5
O11 A:YWR205 4.3 18.1 0.5
O10 A:YWR205 4.3 14.8 0.5
O A:HOH329 4.4 15.7 1.0
N A:ASP119 4.4 14.9 1.0
C15 A:YWR205 4.4 9.6 0.5
CB A:THR118 4.5 15.9 1.0
CB A:ASP119 4.5 15.2 1.0
O A:ASP119 4.8 16.0 1.0
C12 A:YWR205 4.9 11.1 0.5
CA A:ASP119 4.9 14.7 1.0
CG2 A:THR118 5.0 15.4 1.0

Ruthenium binding site 2 out of 6 in 8pfw

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Ruthenium binding site 2 out of 6 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 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(Danif)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru205

b:10.9
occ:0.45
 RU2 A:YWR205 0.0 10.9 0.5
N2 A:YWR205 2.0 10.0 0.5
O4 A:YWR205 2.0 12.1 0.5
O6 A:YWR205 2.1 10.6 0.5
O2 A:YWR205 2.1 10.7 0.5
RU1 A:YWR205 2.3 9.9 0.5
C5 A:YWR205 2.9 11.9 0.5
C3 A:YWR205 2.9 10.9 0.5
C1 A:YWR205 2.9 13.2 0.5
C7 A:YWR205 2.9 9.8 0.5
C15 A:YWR205 2.9 9.6 0.5
O5 A:YWR205 3.0 10.3 0.5
O3 A:YWR205 3.0 10.0 0.5
N1 A:YWR205 3.1 10.1 0.5
O1 A:YWR205 3.1 10.8 0.5
C16 A:YWR205 3.6 10.1 0.5
C20 A:YWR205 3.8 11.2 0.5
O10 A:YWR205 4.2 14.8 0.5
O11 A:YWR205 4.3 18.1 0.5
O9 A:YWR205 4.3 15.8 0.5
C17 A:YWR206 4.5 16.4 0.5
C8 A:YWR205 4.5 10.2 0.5
O A:HOH348 4.6 10.0 0.5
C16 A:YWR206 4.6 15.2 0.5
C17 A:YWR205 4.8 10.1 0.5

Ruthenium binding site 3 out of 6 in 8pfw

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Ruthenium binding site 3 out of 6 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 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(Danif)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru206

b:12.1
occ:0.50
 RU1 A:YWR206 0.0 12.1 0.5
N1 A:YWR206 2.0 12.5 0.5
O3 A:YWR206 2.0 13.0 0.5
O5 A:YWR206 2.1 13.3 0.5
OD1 A:ASP119 2.1 17.7 1.0
RU2 A:YWR206 2.3 12.0 0.5
O A:HOH352 2.4 20.4 0.5
C5 A:YWR206 2.9 13.7 0.5
CG A:ASP119 2.9 16.2 1.0
C3 A:YWR206 2.9 12.9 0.5
C7 A:YWR206 2.9 13.7 0.5
OD2 A:ASP119 3.0 18.4 1.0
O4 A:YWR206 3.0 12.3 0.5
O6 A:YWR206 3.0 13.5 0.5
C8 A:YWR206 3.0 13.2 0.5
N2 A:YWR206 3.1 13.0 0.5
C9 A:YWR206 3.6 14.2 0.5
C13 A:YWR206 4.1 14.7 0.5
O10 A:YWR206 4.3 17.9 0.5
CB A:ASP119 4.3 15.2 1.0
O11 A:YWR206 4.3 17.3 0.5
C15 A:YWR206 4.5 14.1 0.5
C10 A:YWR206 4.9 14.4 0.5
CA A:ASP119 4.9 14.7 1.0

Ruthenium binding site 4 out of 6 in 8pfw

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Ruthenium binding site 4 out of 6 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 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(Danif)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru206

b:12.0
occ:0.50
 RU2 A:YWR206 0.0 12.0 0.5
O4 A:YWR206 2.0 12.3 0.5
OD2 A:ASP119 2.0 18.4 1.0
N2 A:YWR206 2.0 13.0 0.5
O6 A:YWR206 2.0 13.5 0.5
RU1 A:YWR206 2.3 12.1 0.5
C3 A:YWR206 2.9 12.9 0.5
C5 A:YWR206 2.9 13.7 0.5
CG A:ASP119 2.9 16.2 1.0
C7 A:YWR206 2.9 13.7 0.5
N1 A:YWR206 3.0 12.5 0.5
O3 A:YWR206 3.0 13.0 0.5
C15 A:YWR206 3.0 14.1 0.5
O5 A:YWR206 3.1 13.3 0.5
OD1 A:ASP119 3.1 17.7 1.0
C16 A:YWR206 3.4 15.2 0.5
C20 A:YWR206 4.2 15.0 0.5
O10 A:YWR206 4.3 17.9 0.5
O11 A:YWR206 4.3 17.3 0.5
CB A:ASP119 4.3 15.2 1.0
C8 A:YWR206 4.4 13.2 0.5
O9 A:YWR205 4.5 15.8 0.5
O A:HOH352 4.6 20.4 0.5
C17 A:YWR206 4.7 16.4 0.5
C1 A:YWR205 5.0 13.2 0.5

Ruthenium binding site 5 out of 6 in 8pfw

Go back to Ruthenium Binding Sites List in 8pfw
Ruthenium binding site 5 out of 6 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 Ruthenium with other atoms in the Ru binding site number 5 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:Ru207

b:12.3
occ:0.35
 RU1 A:YWR207 0.0 12.3 0.3
N1 A:YWR207 2.0 12.3 0.3
O5 A:YWR207 2.0 12.6 0.3
O1 A:YWR207 2.0 13.5 0.3
O3 A:YWR207 2.1 14.3 0.3
O A:HOH308 2.3 11.8 0.3
RU2 A:YWR207 2.3 12.7 0.3
C3 A:YWR207 2.9 15.3 0.3
C1 A:YWR207 2.9 13.4 0.3
C7 A:YWR207 2.9 13.1 0.3
C5 A:YWR207 2.9 14.5 0.3
C8 A:YWR207 3.0 14.0 0.3
O4 A:YWR207 3.0 14.5 0.3
O2 A:YWR207 3.0 12.3 0.3
N2 A:YWR207 3.1 11.7 0.3
O6 A:YWR207 3.1 14.8 0.3
C13 A:YWR207 3.6 15.0 0.3
C9 A:YWR207 3.8 14.1 0.3
O A:ASP101 4.2 18.4 1.0
O10 A:YWR207 4.3 18.2 0.3
O9 A:YWR207 4.3 16.3 0.3
O11 A:YWR207 4.3 18.9 0.3
CA A:ASP101 4.4 19.5 1.0
C15 A:YWR207 4.5 13.7 0.3
CB A:ASP101 4.5 20.4 1.0
O A:HOH364 4.7 15.0 0.3
C A:ASP101 4.7 17.6 1.0
C12 A:YWR207 4.8 15.0 0.3
C10 A:YWR207 5.0 15.1 0.3

Ruthenium binding site 6 out of 6 in 8pfw

Go back to Ruthenium Binding Sites List in 8pfw
Ruthenium binding site 6 out of 6 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 Ruthenium with other atoms in the Ru binding site number 6 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:Ru207

b:12.7
occ:0.35
 RU2 A:YWR207 0.0 12.7 0.3
O6 A:YWR207 2.0 14.8 0.3
N2 A:YWR207 2.0 11.7 0.3
O2 A:YWR207 2.0 12.3 0.3
O4 A:YWR207 2.1 14.5 0.3
RU1 A:YWR207 2.3 12.3 0.3
O A:HOH364 2.4 15.0 0.3
C5 A:YWR207 2.9 14.5 0.3
C1 A:YWR207 2.9 13.4 0.3
C3 A:YWR207 2.9 15.3 0.3
C7 A:YWR207 2.9 13.1 0.3
O5 A:YWR207 3.0 12.6 0.3
O1 A:YWR207 3.0 13.5 0.3
O3 A:YWR207 3.1 14.3 0.3
C15 A:YWR207 3.1 13.7 0.3
N1 A:YWR207 3.1 12.3 0.3
C16 A:YWR207 3.4 15.1 0.3
O9 A:YWR207 4.3 16.3 0.3
C20 A:YWR207 4.3 14.9 0.3
O11 A:YWR207 4.3 18.9 0.3
O10 A:YWR207 4.3 18.2 0.3
C8 A:YWR207 4.5 14.0 0.3
O A:HOH308 4.5 11.8 0.3
C17 A:YWR207 4.7 17.4 0.3
O3 A:NO3208 5.0 47.0 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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