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Ruthenium in PDB 4ooo: X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex

Enzymatic activity of X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex

All present enzymatic activity of X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex, PDB code: 4ooo was solved by A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.36 / 2.15
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.292, 78.292, 37.119, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 25.4

Other elements in 4ooo:

The structure of X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex 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 Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex (pdb code 4ooo). 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 Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex, PDB code: 4ooo:
Jump to Ruthenium binding site number: 1; 2; 3; 4;

Ruthenium binding site 1 out of 4 in 4ooo

Go back to Ruthenium Binding Sites List in 4ooo
Ruthenium binding site 1 out of 4 in the X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex


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 Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru204

b:51.6
occ:0.50
 RU1 A:RU0204 0.0 51.6 0.5
O A:HOH395 1.7 31.6 0.5
O22 A:RU0204 2.0 49.8 0.5
O1 A:RU0204 2.0 50.6 0.5
OD1 A:ASP101 2.0 47.1 1.0
RU2 A:RU0204 2.2 46.0 0.5
O A:HOH396 2.5 45.6 0.5
O A:HOH380 2.6 38.7 1.0
C2 A:RU0204 2.9 49.2 0.5
CG A:ASP101 2.9 41.2 1.0
O2 A:RU0204 3.0 49.0 0.5
C1 A:RU0204 3.0 50.5 0.5
OD2 A:ASP101 3.0 47.0 1.0
O11 A:RU0204 3.3 50.2 0.5
O A:ASP101 4.2 34.7 1.0
C20 A:RU0204 4.3 49.1 0.5
CB A:ASP101 4.3 36.5 1.0
C6 A:RU0204 4.4 50.7 0.5
CA A:ASP101 4.9 34.9 1.0

Ruthenium binding site 2 out of 4 in 4ooo

Go back to Ruthenium Binding Sites List in 4ooo
Ruthenium binding site 2 out of 4 in the X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex


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 Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru204

b:46.0
occ:0.50
 RU2 A:RU0204 0.0 46.0 0.5
O2 A:RU0204 2.0 49.0 0.5
O A:HOH396 2.0 45.6 0.5
O11 A:RU0204 2.0 50.2 0.5
OD2 A:ASP101 2.0 47.0 1.0
RU1 A:RU0204 2.2 51.6 0.5
O A:HOH395 2.6 31.6 0.5
O1 A:RU0204 2.6 50.6 0.5
C1 A:RU0204 2.7 50.5 0.5
CG A:ASP101 2.8 41.2 1.0
C2 A:RU0204 2.9 49.2 0.5
O22 A:RU0204 3.0 49.8 0.5
OD1 A:ASP101 3.0 47.1 1.0
O A:ASP101 4.0 34.7 1.0
C6 A:RU0204 4.2 50.7 0.5
C20 A:RU0204 4.2 49.1 0.5
CB A:ASP101 4.3 36.5 1.0
O A:HOH380 4.8 38.7 1.0
C A:ASP101 4.8 34.3 1.0

Ruthenium binding site 3 out of 4 in 4ooo

Go back to Ruthenium Binding Sites List in 4ooo
Ruthenium binding site 3 out of 4 in the X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex


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 Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru205

b:35.0
occ:0.50
 RU1 A:RU0205 0.0 35.0 0.5
O22 A:RU0205 2.0 32.6 0.5
O33 A:RU0205 2.0 36.4 0.5
OD1 A:ASP119 2.0 32.6 0.5
RU2 A:RU0205 2.3 36.4 0.5
O A:HOH394 2.6 31.8 0.5
O A:HOH392 2.7 10.1 0.5
O2 A:RU0205 2.8 33.5 0.5
C2 A:RU0205 2.8 32.4 0.5
CG A:ASP119 2.9 31.7 0.5
C3 A:RU0205 3.0 37.1 0.5
OD2 A:ASP119 3.1 34.2 0.5
O3 A:RU0205 3.4 37.1 0.5
O A:HOH393 3.4 27.9 0.5
CB A:ALA122 4.0 30.6 1.0
C20 A:RU0205 4.2 32.0 0.5
C30 A:RU0205 4.2 37.4 0.5
CB A:ASP119 4.4 31.4 0.5
OD2 A:ASP119 4.5 31.2 0.5
CB A:ASP119 4.6 30.8 0.5
O A:ASP119 4.9 31.4 1.0
CG A:ASP119 5.0 30.1 0.5

Ruthenium binding site 4 out of 4 in 4ooo

Go back to Ruthenium Binding Sites List in 4ooo
Ruthenium binding site 4 out of 4 in the X-Ray Structure of the Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex


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 Lysozyme Derivative of Tetrakis(Acetato) Chlorido Diruthenium(II,III) Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru205

b:36.4
occ:0.50
 RU2 A:RU0205 0.0 36.4 0.5
O2 A:RU0205 2.0 33.5 0.5
OD2 A:ASP119 2.0 34.2 0.5
O3 A:RU0205 2.0 37.1 0.5
RU1 A:RU0205 2.3 35.0 0.5
O33 A:RU0205 2.5 36.4 0.5
C3 A:RU0205 2.7 37.1 0.5
O A:HOH393 2.7 27.9 0.5
O A:HOH391 2.8 13.4 0.5
CG A:ASP119 2.8 31.7 0.5
OD1 A:ASP119 3.0 32.6 0.5
C2 A:RU0205 3.0 32.4 0.5
O22 A:RU0205 3.1 32.6 0.5
O A:HOH394 3.4 31.8 0.5
O A:HOH345 3.7 34.7 1.0
O A:HOH348 3.8 35.4 1.0
C30 A:RU0205 4.1 37.4 0.5
CB A:ASP119 4.3 31.4 0.5
C20 A:RU0205 4.3 32.0 0.5
CB A:ASP119 4.5 30.8 0.5
O A:ASP119 4.7 31.4 1.0
N A:ASP119 4.7 30.6 1.0
CA A:ASP119 4.9 31.2 0.5
CA A:ASP119 5.0 30.9 0.5

Reference:

L.Messori, T.Marzo, R.N.Sanches, Hanif-Ur-Rehman, D.De Oliveira Silva, A.Merlino. Unusual Structural Features in the Lysozyme Derivative of the Tetrakis(Acetato)Chloridodiruthenium(II,III) Complex. Angew.Chem.Int.Ed.Engl. V. 53 6172 2014.
ISSN: ISSN 1433-7851
PubMed: 24796316
DOI: 10.1002/ANIE.201403337
Page generated: Thu Oct 10 12:54:49 2024

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