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Ruthenium in PDB 5v4g: Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

Enzymatic activity of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites

All present enzymatic activity of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites:
3.2.1.17;

Protein crystallography data

The structure of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites, PDB code: 5v4g was solved by M.P.Sullivan, C.G.Hartinger, D.C.Goldstone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.77 / 1.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.282, 80.282, 36.928, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.6

Other elements in 5v4g:

The structure of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Sodium (Na) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites (pdb code 5v4g). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 3 binding sites of Ruthenium where determined in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites, PDB code: 5v4g:
Jump to Ruthenium binding site number: 1; 2; 3;

Ruthenium binding site 1 out of 3 in 5v4g

Go back to Ruthenium Binding Sites List in 5v4g
Ruthenium binding site 1 out of 3 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru202

b:23.7
occ:0.90
RU1 A:RU7202 0.0 23.7 0.9
C6 A:RU7202 2.2 26.2 0.9
NE2 A:HIS15 2.2 19.0 1.0
C5 A:RU7202 2.2 24.2 0.9
C3 A:RU7202 2.2 24.8 0.9
C2 A:RU7202 2.2 25.1 0.9
C1 A:RU7202 2.2 25.3 0.9
C4 A:RU7202 2.2 25.4 0.9
CL1 A:RU7202 2.4 27.1 0.9
CL2 A:RU7202 2.5 26.7 0.9
CE1 A:HIS15 3.1 20.6 1.0
CD2 A:HIS15 3.2 19.4 1.0
C7 A:RU7202 3.4 29.5 0.9
C8 A:RU7202 3.4 27.6 0.9
C10 A:RU7202 3.9 28.4 0.9
ND1 A:HIS15 4.2 19.9 1.0
CG A:HIS15 4.3 17.8 1.0
OD1 A:ASP87 4.6 22.6 1.0
C9 A:RU7202 4.7 30.4 0.9
OG1 A:THR89 4.9 19.0 1.0

Ruthenium binding site 2 out of 3 in 5v4g

Go back to Ruthenium Binding Sites List in 5v4g
Ruthenium binding site 2 out of 3 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru203

b:40.2
occ:0.50
RU1 A:RU7203 0.0 40.2 0.5
C6 A:RU7203 2.2 30.1 0.5
C3 A:RU7203 2.2 35.4 0.5
C2 A:RU7203 2.2 33.0 0.5
C5 A:RU7203 2.2 29.6 0.5
C1 A:RU7203 2.2 32.3 0.5
C4 A:RU7203 2.2 32.9 0.5
CL1 A:RU7203 2.4 41.0 0.5
CL1 A:RU7204 2.4 42.4 0.5
OD2 A:ASP101 2.6 33.3 1.0
RU1 A:RU7204 3.2 42.1 0.5
C7 A:RU7203 3.3 31.6 0.5
C8 A:RU7203 3.4 29.0 0.5
CG A:ASP101 3.5 34.5 1.0
OD1 A:ASP101 3.7 34.3 1.0
C10 A:RU7203 3.9 25.6 0.5
C9 A:RU7203 4.7 28.4 0.5
CB A:ASP101 4.9 30.0 1.0

Ruthenium binding site 3 out of 3 in 5v4g

Go back to Ruthenium Binding Sites List in 5v4g
Ruthenium binding site 3 out of 3 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru204

b:42.1
occ:0.50
RU1 A:RU7204 0.0 42.1 0.5
OD1 A:ASP101 2.2 34.3 1.0
CL1 A:RU7204 2.2 42.4 0.5
CL1 A:RU7203 2.6 41.0 0.5
CG A:ASP101 3.2 34.5 1.0
RU1 A:RU7203 3.2 40.2 0.5
OD2 A:ASP101 3.4 33.3 1.0
N A:GLY102 4.1 27.5 1.0
CB A:ASP101 4.5 30.0 1.0
C3 A:RU7203 4.5 35.4 0.5
C2 A:RU7203 4.6 33.0 0.5
CA A:GLY102 4.8 26.8 1.0
C4 A:RU7203 4.9 32.9 0.5
CA A:ASP101 5.0 27.8 1.0

Reference:

M.P.Sullivan, M.Groessl, S.M.Meier, R.L.Kingston, D.C.Goldstone, C.G.Hartinger. The Metalation of Hen Egg White Lysozyme Impacts Protein Stability As Shown By Ion Mobility Mass Spectrometry, Differential Scanning Calorimetry, and X-Ray Crystallography. Chem. Commun. (Camb.) V. 53 4246 2017.
ISSN: ESSN 1364-548X
PubMed: 28361137
DOI: 10.1039/C6CC10150J
Page generated: Wed Dec 16 02:08:41 2020

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