Atomistry » Ruthenium » PDB 4l55-5ira » 4ooo
Atomistry »
  Ruthenium »
    PDB 4l55-5ira »
      4ooo »

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: Wed Dec 16 02:08:22 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy