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Ruthenium in PDB 8ph6: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(CO3)3] in Condition B

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

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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(Dphf)(CO3)3] in Condition B, PDB code: 8ph6 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) 54.36 / 1.07
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.88, 76.88, 38.61, 90, 90, 90
R / Rfree (%) 17 / 19.3

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(Dphf)(CO3)3] in Condition B (pdb code 8ph6). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 10 binding sites of Ruthenium where determined in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(CO3)3] in Condition B, PDB code: 8ph6:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Ruthenium binding site 1 out of 10 in 8ph6

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Ruthenium binding site 1 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru202

b:9.0
occ:0.30
 RU1 A:ZWL202 0.0 9.0 0.3
OD1 A:ASP101 2.0 20.9 1.0
O1 A:ZWL202 2.0 8.7 0.3
N1 A:ZWL202 2.0 11.2 0.3
O3 A:ZWL202 2.1 10.5 0.3
RU2 A:ZWL202 2.3 9.5 0.3
C1 A:ZWL202 2.8 10.3 0.3
RU2 A:ZWL202 2.8 24.2 0.2
CG A:ASP101 2.9 22.7 1.0
C7 A:ZWL202 2.9 10.3 0.3
C3 A:ZWL202 3.0 11.2 0.3
O2 A:ZWL202 3.1 9.5 0.3
C8 A:ZWL202 3.1 12.7 0.3
OD2 A:ASP101 3.1 23.0 1.0
O4 A:ZWL202 3.1 11.1 0.3
N2 A:ZWL202 3.1 10.5 0.3
C9 A:ZWL202 3.8 12.6 0.3
C13 A:ZWL202 3.9 13.4 0.3
O8 A:ZWL202 4.2 11.2 0.3
CB A:ASP101 4.3 24.9 1.0
C15 A:ZWL202 4.5 11.2 0.3
O A:HOH354 4.6 15.7 0.3
O A:ASP101 4.7 30.2 1.0
CA A:ASP101 4.8 22.1 1.0
RU1 A:ZWL202 4.8 17.9 0.2

Ruthenium binding site 2 out of 10 in 8ph6

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Ruthenium binding site 2 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru202

b:17.9
occ:0.20
 RU1 A:ZWL202 0.0 17.9 0.2
RU2 A:ZWL202 2.3 24.2 0.2
C20 A:ZWL202 2.3 12.7 0.3
C7 A:ZWL202 2.5 10.3 0.3
N2 A:ZWL202 2.7 10.5 0.3
C15 A:ZWL202 3.0 11.2 0.3
N1 A:ZWL202 3.4 11.2 0.3
C19 A:ZWL202 3.5 13.0 0.3
OD2 A:ASP101 3.9 23.0 1.0
C8 A:ZWL202 4.0 12.7 0.3
CG A:ASP101 4.1 22.7 1.0
C9 A:ZWL202 4.1 12.6 0.3
RU2 A:ZWL202 4.3 9.5 0.3
O A:ASP101 4.3 30.2 1.0
C16 A:ZWL202 4.3 11.8 0.3
OD1 A:ASP101 4.4 20.9 1.0
CB A:ASP101 4.5 24.9 1.0
C18 A:ZWL202 4.7 13.5 0.3
RU1 A:ZWL202 4.8 9.0 0.3

Ruthenium binding site 3 out of 10 in 8ph6

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Ruthenium binding site 3 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru202

b:9.5
occ:0.30
 RU2 A:ZWL202 0.0 9.5 0.3
O2 A:ZWL202 2.0 9.5 0.3
N2 A:ZWL202 2.0 10.5 0.3
O4 A:ZWL202 2.1 11.1 0.3
OD2 A:ASP101 2.1 23.0 1.0
RU1 A:ZWL202 2.3 9.0 0.3
O A:HOH354 2.3 15.7 0.3
C1 A:ZWL202 2.8 10.3 0.3
C7 A:ZWL202 2.9 10.3 0.3
CG A:ASP101 2.9 22.7 1.0
C3 A:ZWL202 2.9 11.2 0.3
OD1 A:ASP101 3.0 20.9 1.0
N1 A:ZWL202 3.0 11.2 0.3
O3 A:ZWL202 3.0 10.5 0.3
O1 A:ZWL202 3.1 8.7 0.3
C15 A:ZWL202 3.1 11.2 0.3
RU2 A:ZWL202 3.4 24.2 0.2
C16 A:ZWL202 3.5 11.8 0.3
O8 A:ZWL202 4.2 11.2 0.3
C20 A:ZWL202 4.2 12.7 0.3
CE A:LYS97 4.2 23.9 0.5
NZ A:LYS97 4.3 24.2 0.5
RU1 A:ZWL202 4.3 17.9 0.2
CB A:ASP101 4.4 24.9 1.0
C8 A:ZWL202 4.5 12.7 0.3
C17 A:ZWL202 4.9 12.5 0.3

Ruthenium binding site 4 out of 10 in 8ph6

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Ruthenium binding site 4 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru202

b:24.2
occ:0.20
 RU2 A:ZWL202 0.0 24.2 0.2
N1 A:ZWL202 1.2 11.2 0.3
C7 A:ZWL202 1.4 10.3 0.3
C8 A:ZWL202 1.9 12.7 0.3
C9 A:ZWL202 2.3 12.6 0.3
RU1 A:ZWL202 2.3 17.9 0.2
N2 A:ZWL202 2.4 10.5 0.3
RU1 A:ZWL202 2.8 9.0 0.3
OD1 A:ASP101 3.0 20.9 1.0
C13 A:ZWL202 3.1 13.4 0.3
CG A:ASP101 3.3 22.7 1.0
RU2 A:ZWL202 3.4 9.5 0.3
C15 A:ZWL202 3.5 11.2 0.3
OD2 A:ASP101 3.5 23.0 1.0
O A:ASP101 3.5 30.2 1.0
C10 A:ZWL202 3.6 14.1 0.3
C20 A:ZWL202 3.7 12.7 0.3
O1 A:ZWL202 4.0 8.7 0.3
C12 A:ZWL202 4.2 13.9 0.3
CB A:ASP101 4.2 24.9 1.0
C11 A:ZWL202 4.4 14.0 0.3
C A:ASP101 4.5 25.2 1.0
C1 A:ZWL202 4.5 10.3 0.3
O2 A:ZWL202 4.6 9.5 0.3
C16 A:ZWL202 4.7 11.8 0.3
CA A:ASP101 4.8 22.1 1.0
O3 A:ZWL202 4.8 10.5 0.3

Ruthenium binding site 5 out of 10 in 8ph6

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Ruthenium binding site 5 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru203

b:10.6
occ:0.30
 RU1 A:YWV203 0.0 10.6 0.3
NH2 A:ARG125 1.9 15.7 0.5
OD1 A:ASP119 2.0 22.7 1.0
N1 A:YWV203 2.0 10.5 0.3
O1 A:YWV203 2.1 11.6 0.3
RU2 A:YWV203 2.3 10.9 0.3
C7 A:YWV203 2.9 10.8 0.3
C1 A:YWV203 2.9 11.5 0.3
CG A:ASP119 2.9 21.5 1.0
CZ A:ARG125 3.0 16.6 0.5
O2 A:YWV203 3.0 11.7 0.3
N2 A:YWV203 3.1 10.2 0.3
C8 A:YWV203 3.1 12.3 0.3
OD2 A:ASP119 3.2 23.0 1.0
NH1 A:ARG125 3.2 18.3 0.5
C9 A:YWV203 3.5 12.5 0.3
NE A:ARG125 4.1 16.8 0.5
C13 A:YWV203 4.3 11.9 0.3
CB A:ASP119 4.3 18.0 1.0
CB A:GLN121 4.3 22.6 1.0
C15 A:YWV203 4.5 11.5 0.3
N A:GLN121 4.6 16.0 1.0
O A:HOH429 4.6 15.9 0.3
CA A:ASP119 4.6 15.1 1.0
CA A:GLN121 4.8 18.6 1.0
C10 A:YWV203 4.8 13.8 0.3
C A:ASP119 4.8 15.0 1.0
N A:ALA122 4.9 14.6 1.0
C A:GLN121 5.0 15.3 1.0
O A:ASP119 5.0 15.3 1.0

Ruthenium binding site 6 out of 10 in 8ph6

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Ruthenium binding site 6 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru203

b:10.9
occ:0.30
 RU2 A:YWV203 0.0 10.9 0.3
N2 A:YWV203 2.0 10.2 0.3
O2 A:YWV203 2.0 11.7 0.3
OD2 A:ASP119 2.2 23.0 1.0
NH1 A:ARG125 2.2 18.3 0.5
RU1 A:YWV203 2.3 10.6 0.3
O A:HOH429 2.3 15.9 0.3
CG A:ASP119 2.9 21.5 1.0
C1 A:YWV203 2.9 11.5 0.3
NH2 A:ARG125 2.9 15.7 0.5
C7 A:YWV203 2.9 10.8 0.3
OD1 A:ASP119 2.9 22.7 1.0
CZ A:ARG125 3.0 16.6 0.5
N1 A:YWV203 3.1 10.5 0.3
O1 A:YWV203 3.1 11.6 0.3
C15 A:YWV203 3.1 11.5 0.3
C16 A:YWV203 3.6 7.6 0.3
NE A:ARG125 4.3 16.8 0.5
CB A:ASP119 4.3 18.0 1.0
C20 A:YWV203 4.3 13.0 0.3
C8 A:YWV203 4.5 12.3 0.3
C17 A:YWV203 4.9 14.8 0.3

Ruthenium binding site 7 out of 10 in 8ph6

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Ruthenium binding site 7 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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 7 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru204

b:11.5
occ:0.35
 RU1 A:ZWO204 0.0 11.5 0.3
O1 A:ZWO204 2.0 9.9 0.3
O5 A:ZWO204 2.0 12.8 0.3
N1 A:ZWO204 2.1 11.7 0.3
O3 A:ZWO204 2.1 12.8 0.3
RU2 A:ZWO204 2.3 10.4 0.3
C1 A:ZWO204 2.8 9.5 0.3
C7 A:ZWO204 2.9 11.5 0.3
C3 A:ZWO204 2.9 14.4 0.3
C5 A:ZWO204 3.0 13.2 0.3
O6 A:ZWO204 3.0 10.7 0.3
N2 A:ZWO204 3.0 10.2 0.3
O4 A:ZWO204 3.1 11.9 0.3
O2 A:ZWO204 3.1 9.4 0.3
C8 A:ZWO204 3.1 13.1 0.3
C9 A:ZWO204 3.6 13.0 0.3
O9 A:ZWO204 4.1 17.4 0.3
O7 A:ZWO204 4.2 13.6 0.3
C13 A:ZWO204 4.2 15.1 0.3
O8 A:ZWO204 4.2 8.4 0.3
O A:HOH348 4.4 11.0 0.3
C15 A:ZWO204 4.4 10.8 0.3
C10 A:ZWO204 4.9 14.6 0.3

Ruthenium binding site 8 out of 10 in 8ph6

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Ruthenium binding site 8 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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 8 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru204

b:10.4
occ:0.35
 RU2 A:ZWO204 0.0 10.4 0.3
O2 A:ZWO204 2.0 9.4 0.3
O6 A:ZWO204 2.0 10.7 0.3
N2 A:ZWO204 2.0 10.2 0.3
O4 A:ZWO204 2.1 11.9 0.3
O A:HOH348 2.2 11.0 0.3
RU1 A:ZWO204 2.3 11.5 0.3
C1 A:ZWO204 2.8 9.5 0.3
C3 A:ZWO204 2.9 14.4 0.3
C7 A:ZWO204 3.0 11.5 0.3
C5 A:ZWO204 3.0 13.2 0.3
O1 A:ZWO204 3.0 9.9 0.3
O5 A:ZWO204 3.0 12.8 0.3
O3 A:ZWO204 3.0 12.8 0.3
C15 A:ZWO204 3.1 10.8 0.3
N1 A:ZWO204 3.1 11.7 0.3
C16 A:ZWO204 3.6 11.3 0.3
O A:HOH375 4.0 30.2 1.0
O9 A:ZWO204 4.1 17.4 0.3
O7 A:ZWO204 4.1 13.6 0.3
C20 A:ZWO204 4.1 10.9 0.3
O8 A:ZWO204 4.1 8.4 0.3
C8 A:ZWO204 4.5 13.1 0.3
C17 A:ZWO204 4.9 11.8 0.3

Ruthenium binding site 9 out of 10 in 8ph6

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Ruthenium binding site 9 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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 9 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru205

b:11.0
occ:0.30
 RU1 A:ZXE205 0.0 11.0 0.3
O1 A:ZXE205 2.0 11.3 0.3
O5 A:ZXE205 2.0 11.5 0.3
N1 A:ZXE205 2.0 11.8 0.3
O3 A:ZXE205 2.0 12.7 0.3
RU2 A:ZXE205 2.3 11.1 0.3
C1 A:ZXE205 2.8 11.9 0.3
C3 A:ZXE205 2.9 13.5 0.3
C5 A:ZXE205 2.9 12.4 0.3
C7 A:ZXE205 2.9 11.4 0.3
O6 A:ZXE205 3.0 11.8 0.3
O2 A:ZXE205 3.0 11.5 0.3
O4 A:ZXE205 3.1 14.1 0.3
C8 A:ZXE205 3.1 11.7 0.3
N2 A:ZXE205 3.1 11.7 0.3
O A:HOH304 3.3 36.9 1.0
C13 A:ZXE205 3.7 12.5 0.3
C9 A:ZXE205 4.0 11.8 0.3
O9 A:ZXE205 4.0 14.6 0.3
O8 A:ZXE205 4.2 13.0 0.3
O A:HOH301 4.5 12.7 0.3
C15 A:ZXE205 4.5 10.8 0.3
CE1 A:PHE34 4.9 12.0 1.0
C12 A:ZXE205 4.9 13.1 0.3

Ruthenium binding site 10 out of 10 in 8ph6

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Ruthenium binding site 10 out of 10 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(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 10 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Dphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru205

b:11.1
occ:0.30
 RU2 A:ZXE205 0.0 11.1 0.3
O6 A:ZXE205 2.0 11.8 0.3
O2 A:ZXE205 2.0 11.5 0.3
N2 A:ZXE205 2.0 11.7 0.3
O4 A:ZXE205 2.1 14.1 0.3
O A:HOH301 2.2 12.7 0.3
RU1 A:ZXE205 2.3 11.0 0.3
C1 A:ZXE205 2.8 11.9 0.3
C5 A:ZXE205 2.9 12.4 0.3
C7 A:ZXE205 2.9 11.4 0.3
C3 A:ZXE205 2.9 13.5 0.3
N1 A:ZXE205 3.0 11.8 0.3
O5 A:ZXE205 3.1 11.5 0.3
C15 A:ZXE205 3.1 10.8 0.3
O3 A:ZXE205 3.1 12.7 0.3
O1 A:ZXE205 3.1 11.3 0.3
CE A:LYS33 3.5 22.4 1.0
NZ A:LYS33 3.5 26.7 1.0
C16 A:ZXE205 3.6 11.4 0.3
O9 A:ZXE205 4.1 14.6 0.3
C20 A:ZXE205 4.1 11.2 0.3
O8 A:ZXE205 4.2 13.0 0.3
O A:HOH367 4.3 38.6 1.0
C8 A:ZXE205 4.5 11.7 0.3
CD A:LYS33 4.8 19.0 1.0
C17 A:ZXE205 4.9 12.1 0.3

Reference:

A.Teran, G.Ferraro, P.Imbimbo, A.E.Sanchez-Pelaez, D.M.Monti, S.Herrero, A.Merlino. Steric Hindrance and Charge Influence on the Cytotoxic Activity and Protein Binding Properties of Diruthenium Complexes. Int.J.Biol.Macromol. 26666 2023.
ISSN: ISSN 0141-8130
PubMed: 37660867
DOI: 10.1016/J.IJBIOMAC.2023.126666
Page generated: Thu Oct 10 13:14:15 2024

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