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Ruthenium 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:

Fluorine (F) 2 atoms
Sodium (Na) 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 B (pdb code 8pfx). 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(D-P-Fphf)(CO3)3] in Condition B, PDB code: 8pfx:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6;

Ruthenium binding site 1 out of 6 in 8pfx

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

b:14.4
occ:0.35
 RU1 A:YJT205 0.0 14.4 0.3
N1 A:YJT205 2.0 16.9 0.3
O3 A:YJT205 2.0 13.4 0.3
O1 A:YJT205 2.0 15.4 0.3
OD2 A:ASP101 2.1 21.8 1.0
O A:HOH378 2.2 19.0 0.3
RU2 A:YJT205 2.3 15.4 0.3
C1 A:YJT205 2.9 17.0 0.3
C2 A:YJT205 3.0 18.7 0.3
C14 A:YJT205 3.0 15.3 0.3
CG A:ASP101 3.0 20.3 1.0
N2 A:YJT205 3.1 17.6 0.3
O4 A:YJT205 3.1 16.8 0.3
OD1 A:ASP101 3.1 21.7 1.0
O2 A:YJT205 3.2 16.8 0.3
C3 A:YJT205 3.5 19.2 0.3
O A:HOH311 3.7 35.5 1.0
C7 A:YJT205 3.9 18.6 0.3
O7 A:YJT205 4.1 17.8 0.3
O A:HOH387 4.2 21.8 1.0
CB A:ASP101 4.4 19.1 1.0
C8 A:YJT205 4.5 19.4 0.3
O A:HOH359 4.6 24.9 0.3
O A:ASP101 4.7 21.1 1.0
C4 A:YJT205 4.8 20.1 0.3
RU2 A:YJT206 5.0 14.5 0.2

Ruthenium binding site 2 out of 6 in 8pfx

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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(D-P-Fphf)(CO3)3] in Condition B


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru205

b:15.4
occ:0.35
 RU2 A:YJT205 0.0 15.4 0.3
N2 A:YJT205 2.0 17.6 0.3
O4 A:YJT205 2.0 16.8 0.3
O2 A:YJT205 2.0 16.8 0.3
OD1 A:ASP101 2.1 21.7 1.0
RU1 A:YJT205 2.3 14.4 0.3
O A:HOH359 2.3 24.9 0.3
C14 A:YJT205 2.8 15.3 0.3
C1 A:YJT205 2.9 17.0 0.3
CG A:ASP101 2.9 20.3 1.0
O1 A:YJT205 2.9 15.4 0.3
OD2 A:ASP101 3.0 21.8 1.0
N1 A:YJT205 3.1 16.9 0.3
O3 A:YJT205 3.1 13.4 0.3
C8 A:YJT205 3.1 19.4 0.3
C9 A:YJT205 3.5 20.8 0.3
O7 A:YJT205 4.0 17.8 0.3
C13 A:YJT205 4.2 20.8 0.3
CB A:ASP101 4.4 19.1 1.0
O A:HOH426 4.5 51.7 1.0
C2 A:YJT205 4.5 18.7 0.3
O A:HOH378 4.5 19.0 0.3
O A:ASP101 4.6 21.1 1.0
C10 A:YJT205 4.8 20.7 0.3
CH2 A:TRP63 4.9 15.1 1.0

Ruthenium binding site 3 out of 6 in 8pfx

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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(D-P-Fphf)(CO3)3] in Condition B


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru206

b:15.5
occ:0.20
 RU1 A:YJT206 0.0 15.5 0.2
RU2 A:YJT206 2.3 14.5 0.2
O A:HOH334 3.5 26.0 1.0
C4 A:YJT205 4.0 20.1 0.3
F1 A:YJT205 4.1 19.6 0.3
C5 A:YJT205 4.3 20.6 0.3
O A:HOH413 4.3 37.9 1.0
C3 A:YJT205 4.8 19.2 0.3
O A:HOH378 4.8 19.0 0.3

Ruthenium binding site 4 out of 6 in 8pfx

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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(D-P-Fphf)(CO3)3] in Condition B


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 B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru206

b:14.5
occ:0.20
 RU2 A:YJT206 0.0 14.5 0.2
RU1 A:YJT206 2.3 15.5 0.2
O A:HOH378 3.0 19.0 0.3
O A:HOH387 3.7 21.8 1.0
O A:HOH334 3.8 26.0 1.0
O A:HOH386 4.2 31.6 1.0
C4 A:YJT205 4.3 20.1 0.3
C3 A:YJT205 4.4 19.2 0.3
ND2 A:ASN103 4.4 28.0 1.0
O A:HOH413 4.6 37.9 1.0
O3 A:YJT205 4.7 13.4 0.3
C5 A:YJT205 4.8 20.6 0.3
CA A:ALA107 4.8 9.0 1.0
CB A:ALA107 5.0 10.7 1.0
RU1 A:YJT205 5.0 14.4 0.3

Ruthenium binding site 5 out of 6 in 8pfx

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Ruthenium binding site 5 out of 6 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 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(D-P-Fphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:16.1
occ:0.20
 RU1 A:YJT207 0.0 16.1 0.2
RU2 A:YJT207 2.3 17.9 0.2
O A:HOH390 4.0 11.1 0.5
OD1 A:ASN44 4.2 23.5 0.5
O A:ARG45 4.5 10.8 0.5
ND2 A:ASN44 4.7 17.1 0.5
O A:ARG45 4.7 9.1 0.5
CG A:ASN44 4.8 16.9 0.5

Ruthenium binding site 6 out of 6 in 8pfx

Go back to Ruthenium Binding Sites List in 8pfx
Ruthenium binding site 6 out of 6 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 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(D-P-Fphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:17.9
occ:0.20
 RU2 A:YJT207 0.0 17.9 0.2
RU1 A:YJT207 2.3 16.1 0.2
O A:HOH390 4.2 11.1 0.5

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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