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Ruthenium in PDB 8ph7: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)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 [RU2CL(Dphf)(O2CCH3)3] in Condition A, PDB code: 8ph7 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) 54.92 / 1.41
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.67, 77.67, 38.28, 90, 90, 90
R / Rfree (%) 22.6 / 26.6

Other elements in 8ph7:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A also contains other interesting chemical elements:

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 [RU2CL(Dphf)(O2CCH3)3] in Condition A (pdb code 8ph7). 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 [RU2CL(Dphf)(O2CCH3)3] in Condition A, PDB code: 8ph7:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in 8ph7

Go back to Ruthenium Binding Sites List in 8ph7
Ruthenium binding site 1 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)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 [RU2CL(Dphf)(O2CCH3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru201

b:37.5
occ:0.40
 RU1 A:ZQ2201 0.0 37.5 0.4
N1 A:ZQ2201 2.0 33.2 0.4
O5 A:ZQ2201 2.1 33.5 0.4
RU2 A:ZQ2201 2.3 32.8 0.4
OD1 A:ASP101 2.6 51.3 1.0
O2 A:SIN202 2.7 26.1 0.4
C1 A:ZQ2201 2.8 31.5 0.4
C3 A:SIN202 2.9 31.5 0.4
C18 A:ZQ2201 2.9 32.8 0.4
C2 A:ZQ2201 3.0 36.1 0.4
N2 A:ZQ2201 3.0 28.8 0.4
C7 A:ZQ2201 3.1 37.0 0.4
C2 A:SIN202 3.1 30.4 0.4
O6 A:ZQ2201 3.1 34.9 0.4
C1 A:SIN202 3.2 29.9 0.4
CG A:ASP101 3.8 53.2 1.0
C4 A:SIN202 4.3 32.2 0.4
C3 A:ZQ2201 4.3 36.6 0.4
C19 A:ZQ2201 4.3 32.4 0.4
O1 A:SIN202 4.3 28.0 0.4
C6 A:ZQ2201 4.4 37.0 0.4
C8 A:ZQ2201 4.4 25.7 0.4
OD2 A:ASP101 4.5 61.2 1.0
CB A:ASP101 4.8 49.4 1.0
O A:HOH305 4.9 15.4 0.4
O A:ASP101 4.9 59.9 1.0
O4 A:SIN202 4.9 32.0 0.4
CA A:ASP101 4.9 47.7 1.0

Ruthenium binding site 2 out of 4 in 8ph7

Go back to Ruthenium Binding Sites List in 8ph7
Ruthenium binding site 2 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)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 [RU2CL(Dphf)(O2CCH3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru201

b:32.8
occ:0.40
 RU2 A:ZQ2201 0.0 32.8 0.4
N2 A:ZQ2201 2.0 28.8 0.4
O6 A:ZQ2201 2.0 34.9 0.4
OD1 A:ASP101 2.1 51.3 1.0
RU1 A:ZQ2201 2.3 37.5 0.4
O A:HOH305 2.6 15.4 0.4
C18 A:ZQ2201 2.8 32.8 0.4
CG A:ASP101 2.9 53.2 1.0
C1 A:ZQ2201 2.9 31.5 0.4
O5 A:ZQ2201 3.0 33.5 0.4
OD2 A:ASP101 3.0 61.2 1.0
C8 A:ZQ2201 3.1 25.7 0.4
N1 A:ZQ2201 3.1 33.2 0.4
C9 A:ZQ2201 3.6 24.0 0.4
O2 A:SIN202 3.8 26.1 0.4
C1 A:SIN202 3.9 29.9 0.4
C2 A:SIN202 3.9 30.4 0.4
C19 A:ZQ2201 4.2 32.4 0.4
C13 A:ZQ2201 4.2 25.1 0.4
CB A:ASP101 4.3 49.4 1.0
C2 A:ZQ2201 4.4 36.1 0.4
C3 A:SIN202 4.5 31.5 0.4
O1 A:SIN202 4.5 28.0 0.4
O A:ASP101 4.8 59.9 1.0
C10 A:ZQ2201 4.9 26.9 0.4

Ruthenium binding site 3 out of 4 in 8ph7

Go back to Ruthenium Binding Sites List in 8ph7
Ruthenium binding site 3 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)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 [RU2CL(Dphf)(O2CCH3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru203

b:28.2
occ:0.45
 RU1 A:ZWH203 0.0 28.2 0.5
O4 A:ZWH203 1.6 35.1 0.5
N1 A:ZWH203 2.0 27.3 0.5
O1 A:ZWH203 2.0 30.6 0.5
O41 A:ZWH203 2.2 26.1 0.5
RU2 A:ZWH203 2.3 30.9 0.5
NZ A:LYS33 2.5 31.3 1.0
C41 A:ZWH203 2.6 39.1 0.5
C14 A:ZWH203 2.8 33.3 0.5
C1 A:ZWH203 2.8 28.5 0.5
C42 A:ZWH203 2.9 27.8 0.5
O31 A:ZWH203 3.0 29.2 0.5
N2 A:ZWH203 3.0 29.0 0.5
O2 A:ZWH203 3.0 31.8 0.5
C2 A:ZWH203 3.1 25.5 0.5
O3 A:ZWH203 3.1 37.4 0.5
CE A:LYS33 3.5 29.6 1.0
C3 A:ZWH203 3.7 24.2 0.5
C31 A:ZWH203 3.9 39.6 0.5
C7 A:ZWH203 4.0 26.2 0.5
C15 A:ZWH203 4.1 35.3 0.5
C21 A:ZWH203 4.2 41.2 0.5
O A:HOH303 4.3 19.1 0.5
C32 A:ZWH203 4.4 27.0 0.5
C8 A:ZWH203 4.4 30.5 0.5
CD A:LYS33 4.8 25.0 1.0
OD1 A:ASN37 4.9 30.8 1.0
C4 A:ZWH203 4.9 24.9 0.5
C22 A:ZWH203 4.9 25.6 0.5

Ruthenium binding site 4 out of 4 in 8ph7

Go back to Ruthenium Binding Sites List in 8ph7
Ruthenium binding site 4 out of 4 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)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 [RU2CL(Dphf)(O2CCH3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru203

b:30.9
occ:0.45
 RU2 A:ZWH203 0.0 30.9 0.5
O31 A:ZWH203 1.8 29.2 0.5
N2 A:ZWH203 2.0 29.0 0.5
O2 A:ZWH203 2.0 31.8 0.5
O A:HOH303 2.1 19.1 0.5
O3 A:ZWH203 2.1 37.4 0.5
RU1 A:ZWH203 2.3 28.2 0.5
O4 A:ZWH203 2.7 35.1 0.5
C41 A:ZWH203 2.7 39.1 0.5
C42 A:ZWH203 2.7 27.8 0.5
C14 A:ZWH203 2.9 33.3 0.5
C1 A:ZWH203 2.9 28.5 0.5
O41 A:ZWH203 3.0 26.1 0.5
C8 A:ZWH203 3.0 30.5 0.5
O1 A:ZWH203 3.1 30.6 0.5
N1 A:ZWH203 3.1 27.3 0.5
C13 A:ZWH203 3.6 31.5 0.5
C9 A:ZWH203 4.1 33.4 0.5
C32 A:ZWH203 4.1 27.0 0.5
C31 A:ZWH203 4.2 39.6 0.5
C15 A:ZWH203 4.2 35.3 0.5
C2 A:ZWH203 4.6 25.5 0.5
NZ A:LYS33 4.7 31.3 1.0
C12 A:ZWH203 4.8 31.1 0.5

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 Dec 28 12:00:00 2023

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