Atomistry » Ruthenium » PDB 8p6b-8s90 » 8ph6
Atomistry »
  Ruthenium »
    PDB 8p6b-8s90 »
      8ph6 »

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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

Go back to Ruthenium Binding Sites List in 8ph6
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

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