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Ruthenium in PDB 5ob6: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole, PDB code: 5ob6 was solved by N.Pontillo, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.41 / 1.88
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.776, 79.776, 36.637, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 24.2

Other elements in 5ob6:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole also contains other interesting chemical elements:

Chlorine (Cl) 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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole (pdb code 5ob6). 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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole, PDB code: 5ob6:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5; 6;

Ruthenium binding site 1 out of 6 in 5ob6

Go back to Ruthenium Binding Sites List in 5ob6
Ruthenium binding site 1 out of 6 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole


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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru205

b:38.6
occ:0.80
 RU A:9Q8205 0.0 38.6 0.8
C3 A:9Q8205 1.7 40.7 0.8
C2 A:9Q8205 1.7 35.9 0.8
C1 A:9Q8205 1.8 42.4 0.8
NE2 A:HIS15 2.1 42.3 1.0
O4 A:9Q8205 2.3 43.2 0.8
O5 A:9Q8205 2.3 40.4 0.8
O2 A:9Q8205 2.7 36.1 0.8
O3 A:9Q8205 2.8 44.2 0.8
O1 A:9Q8205 2.9 42.5 0.8
CD2 A:HIS15 3.1 39.4 1.0
CE1 A:HIS15 3.2 43.5 1.0
O A:HOH395 3.8 13.8 0.2
CG A:HIS15 4.3 36.5 1.0
ND1 A:HIS15 4.3 39.3 1.0
OD1 A:ASP87 4.7 41.9 1.0

Ruthenium binding site 2 out of 6 in 5ob6

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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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole


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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru206

b:54.8
occ:0.50
 RU A:RU2206 0.0 54.8 0.5
C2 A:RU2206 1.9 49.6 0.5
OD2 A:ASP18 2.3 46.3 1.0
O5 A:RU2206 2.3 48.0 0.5
O1 A:RU2206 2.4 46.9 0.5
O3 A:RU2206 2.4 44.3 0.5
O4 A:RU2206 2.5 49.2 0.5
O2 A:RU2206 3.0 50.2 0.5
CG A:ASP18 3.0 40.5 1.0
OD1 A:ASP18 3.1 41.2 1.0
NZ A:LYS13 3.8 58.0 1.0
CB A:ASP18 4.5 39.6 1.0
CE A:LYS13 4.6 54.9 1.0

Ruthenium binding site 3 out of 6 in 5ob6

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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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole


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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:52.1
occ:0.30
 RU A:RU2207 0.0 52.1 0.3
RU A:RU2207 2.0 52.5 0.3
O A:HOH349 2.1 9.7 0.3
OD2 A:ASP52 2.3 35.7 1.0
CG A:ASP52 3.3 30.0 1.0
O A:HOH378 3.4 34.5 1.0
OD1 A:ASP52 3.7 28.6 1.0
O A:HOH336 3.9 29.8 1.0
O A:HOH316 4.0 40.5 0.7
O A:HOH304 4.0 39.4 1.0
O A:HOH402 4.2 45.3 1.0
O A:HOH414 4.2 46.5 1.0
O A:GLN57 4.3 21.3 1.0
OD1 A:ASN46 4.4 34.8 1.0
CB A:ASP52 4.4 23.1 1.0
OE1 A:GLU35 4.6 24.8 1.0
CB A:GLN57 4.8 25.6 1.0

Ruthenium binding site 4 out of 6 in 5ob6

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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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole


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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru207

b:52.5
occ:0.30
 RU A:RU2207 0.0 52.5 0.3
RU A:RU2207 2.0 52.1 0.3
OD2 A:ASP52 2.0 35.7 1.0
OD1 A:ASN46 2.4 34.8 1.0
O A:HOH316 2.7 40.5 0.7
CG A:ASP52 2.9 30.0 1.0
CG A:ASN46 3.2 33.9 1.0
OD1 A:ASP52 3.3 28.6 1.0
O A:HOH349 3.5 9.7 0.3
ND2 A:ASN46 3.6 32.5 1.0
O A:HOH336 4.1 29.8 1.0
ND2 A:ASN44 4.2 26.6 0.3
CB A:ASP52 4.2 23.1 1.0
ND2 A:ASN59 4.5 44.2 1.0
CB A:ASN46 4.5 31.3 1.0
O A:HOH402 4.9 45.3 1.0

Ruthenium binding site 5 out of 6 in 5ob6

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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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole


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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru208

b:58.5
occ:0.50
 RU A:RU1208 0.0 58.5 0.5
C2 A:RU1208 2.0 55.7 0.5
C1 A:RU1208 2.0 57.9 0.5
OD2 A:ASP119 2.5 66.1 1.0
NH2 A:ARG125 2.7 71.8 1.0
NH1 A:ARG125 2.8 72.7 1.0
CZ A:ARG125 3.1 72.7 1.0
CG A:ASP119 3.1 52.9 1.0
OD1 A:ASP119 3.1 58.7 1.0
O2 A:RU1208 3.2 53.0 0.5
O1 A:RU1208 3.2 52.3 0.5
NE A:ARG125 4.3 70.2 1.0
CB A:ASP119 4.6 47.0 1.0
OE1 A:GLN121 4.7 46.2 0.5
CB A:GLN121 4.9 42.4 0.5
CB A:GLN121 4.9 43.0 0.5

Ruthenium binding site 6 out of 6 in 5ob6

Go back to Ruthenium Binding Sites List in 5ob6
Ruthenium binding site 6 out of 6 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole


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 the Compound Fac-[Ruii(Co)3CL2(N3-Im), Im=Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru209

b:50.0
occ:0.30
 RU A:RU2209 0.0 50.0 0.3
O4 A:RU2209 2.3 41.2 0.3
O3 A:RU2209 2.3 41.5 0.3
O5 A:RU2209 2.3 37.8 0.3
OXT A:LEU129 2.4 81.0 1.0
O A:LEU129 2.6 74.1 1.0
C A:LEU129 2.9 75.1 1.0
O2 A:GOL201 4.0 80.0 0.5
C2 A:GOL201 4.1 68.1 0.5
CA A:LEU129 4.4 65.0 1.0
C3 A:GOL201 4.6 75.2 0.5
O A:HOH310 4.7 57.9 1.0

Reference:

N.Pontillo, G.Ferraro, L.Messori, G.Tamasi, A.Merlino. Ru-Based Co Releasing Molecules with Azole Ligands: Interaction with Proteins and the Co Release Mechanism Disclosed By X-Ray Crystallography. Dalton Trans V. 46 9621 2017.
ISSN: ESSN 1477-9234
PubMed: 28702564
DOI: 10.1039/C7DT01991B
Page generated: Wed Dec 16 02:08:38 2020

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