Chlorine 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:

Ruthenium (Ru) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites, PDB code: 5v4g:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5v4g

Go back to Chlorine Binding Sites List in 5v4g
Chlorine binding site 1 out of 4 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl202

b:27.1
occ:0.90
 CL1 A:RU7202 0.0 27.1 0.9
RU1 A:RU7202 2.4 23.7 0.9
NE2 A:HIS15 3.2 19.0 1.0
CL2 A:RU7202 3.2 26.7 0.9
CD2 A:HIS15 3.2 19.4 1.0
C6 A:RU7202 3.2 26.2 0.9
C5 A:RU7202 3.3 24.2 0.9
CB A:ALA11 3.6 16.8 1.0
CA A:ALA11 3.7 17.3 1.0
C1 A:RU7202 3.9 25.3 0.9
O A:ALA11 4.0 16.7 1.0
C4 A:RU7202 4.0 25.4 0.9
CB A:ARG14 4.3 24.0 1.0
C A:ALA11 4.3 15.8 1.0
CG A:ARG14 4.3 29.1 1.0
CE1 A:HIS15 4.5 20.6 1.0
C2 A:RU7202 4.5 25.1 0.9
C3 A:RU7202 4.5 24.8 0.9
CG A:HIS15 4.6 17.8 1.0
C7 A:RU7202 4.6 29.5 0.9
C10 A:RU7202 4.7 28.4 0.9
C8 A:RU7202 4.9 27.6 0.9
N A:ALA11 4.9 16.6 1.0

Chlorine binding site 2 out of 4 in 5v4g

Go back to Chlorine Binding Sites List in 5v4g
Chlorine binding site 2 out of 4 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl202

b:26.7
occ:0.90
 CL2 A:RU7202 0.0 26.7 0.9
RU1 A:RU7202 2.5 23.7 0.9
NE2 A:HIS15 3.1 19.0 1.0
CL1 A:RU7202 3.2 27.1 0.9
N A:ILE88 3.3 15.5 1.0
C1 A:RU7202 3.3 25.3 0.9
C2 A:RU7202 3.4 25.1 0.9
C7 A:RU7202 3.5 29.5 0.9
CG1 A:ILE88 3.7 15.5 1.0
CE1 A:HIS15 3.8 20.6 1.0
CA A:ASP87 3.8 17.2 1.0
O A:HOH335 3.9 24.8 1.0
C6 A:RU7202 3.9 26.2 0.9
OD1 A:ASP87 4.0 22.6 1.0
CD2 A:HIS15 4.0 19.4 1.0
C3 A:RU7202 4.0 24.8 0.9
C A:ASP87 4.0 16.3 1.0
CA A:ILE88 4.3 14.8 1.0
CB A:ILE88 4.3 15.1 1.0
O A:SER86 4.3 19.7 1.0
CG2 A:ILE88 4.4 16.6 1.0
CG A:ASP87 4.5 22.2 1.0
C5 A:RU7202 4.5 24.2 0.9
CD1 A:ILE88 4.6 16.2 1.0
C4 A:RU7202 4.6 25.4 0.9
CB A:ASP87 4.7 19.7 1.0
N A:THR89 4.8 15.3 1.0
CB A:ALA11 4.9 16.8 1.0
ND1 A:HIS15 4.9 19.9 1.0
N A:ASP87 4.9 15.8 1.0
C A:ILE88 5.0 13.7 1.0

Chlorine binding site 3 out of 4 in 5v4g

Go back to Chlorine Binding Sites List in 5v4g
Chlorine binding site 3 out of 4 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl203

b:41.0
occ:0.50
 CL1 A:RU7203 0.0 41.0 0.5
RU1 A:RU7203 2.4 40.2 0.5
RU1 A:RU7204 2.6 42.1 0.5
C1 A:RU7203 3.2 32.3 0.5
OD2 A:ASP101 3.2 33.3 1.0
C2 A:RU7203 3.3 33.0 0.5
OD1 A:ASP101 3.3 34.3 1.0
C7 A:RU7203 3.3 31.6 0.5
CG A:ASP101 3.5 34.5 1.0
CL1 A:RU7204 3.6 42.4 0.5
C6 A:RU7203 3.8 30.1 0.5
C3 A:RU7203 4.0 35.4 0.5
C5 A:RU7203 4.5 29.6 0.5
C4 A:RU7203 4.5 32.9 0.5
CB A:ASP101 4.7 30.0 1.0

Chlorine binding site 4 out of 4 in 5v4g

Go back to Chlorine Binding Sites List in 5v4g
Chlorine binding site 4 out of 4 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:42.4
occ:0.50
 CL1 A:RU7204 0.0 42.4 0.5
RU1 A:RU7204 2.2 42.1 0.5
RU1 A:RU7203 2.4 40.2 0.5
C10 A:RU7203 3.0 25.6 0.5
C4 A:RU7203 3.1 32.9 0.5
C8 A:RU7203 3.1 29.0 0.5
OD1 A:ASP101 3.2 34.3 1.0
C3 A:RU7203 3.2 35.4 0.5
OD2 A:ASP101 3.3 33.3 1.0
CL1 A:RU7203 3.6 41.0 0.5
CG A:ASP101 3.6 34.5 1.0
C5 A:RU7203 3.8 29.6 0.5
C2 A:RU7203 3.9 33.0 0.5
C6 A:RU7203 4.4 30.1 0.5
C1 A:RU7203 4.5 32.3 0.5
C9 A:RU7203 4.7 28.4 0.5

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: Fri Jul 26 18:37:19 2024

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