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Chlorine in PDB 5v4h: Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site

Enzymatic activity of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site

All present enzymatic activity of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site:
3.2.1.17;

Protein crystallography data

The structure of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site, PDB code: 5v4h 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) 56.79 / 1.22
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 80.320, 80.320, 36.590, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19

Other elements in 5v4h:

The structure of Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site (pdb code 5v4h). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site, PDB code: 5v4h:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 5v4h

Go back to Chlorine Binding Sites List in 5v4h
Chlorine binding site 1 out of 2 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site


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 Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:24.6
occ:0.80
 CL1 A:RU7202 0.0 24.6 0.8
RU1 A:RU7202 2.4 21.9 0.8
NE2 A:HIS15 3.2 19.8 1.0
CD2 A:HIS15 3.2 19.1 1.0
CL2 A:RU7202 3.3 23.1 0.8
C5 A:RU7202 3.3 24.8 0.8
C6 A:RU7202 3.3 25.1 0.8
CB A:ALA11 3.6 16.6 1.0
CA A:ALA11 3.7 16.3 1.0
C4 A:RU7202 4.0 25.6 0.8
C1 A:RU7202 4.0 23.4 0.8
O A:ALA11 4.0 16.7 1.0
CG A:ARG14 4.1 29.0 0.5
CB A:ARG14 4.1 23.5 0.5
CB A:ARG14 4.2 24.6 0.5
CG A:ARG14 4.3 27.6 0.5
C A:ALA11 4.3 15.9 1.0
C3 A:RU7202 4.5 24.4 0.8
CE1 A:HIS15 4.5 20.2 1.0
C2 A:RU7202 4.5 22.5 0.8
CG A:HIS15 4.6 18.2 1.0
CD A:ARG14 4.6 30.9 0.5
NE A:ARG14 4.7 31.3 0.5
C7 A:RU7202 4.7 26.2 0.8
C10 A:RU7202 4.8 30.4 0.8
C8 A:RU7202 4.8 29.7 0.8
N A:ALA11 4.9 17.2 1.0

Chlorine binding site 2 out of 2 in 5v4h

Go back to Chlorine Binding Sites List in 5v4h
Chlorine binding site 2 out of 2 in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site


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 Formed When Ruthenium(II)(Cymene)(Bromido)2 Underwent Ligand Exchange, Resulting in One Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:23.1
occ:0.80
 CL2 A:RU7202 0.0 23.1 0.8
RU1 A:RU7202 2.4 21.9 0.8
NE2 A:HIS15 3.1 19.8 1.0
CL1 A:RU7202 3.3 24.6 0.8
C1 A:RU7202 3.3 23.4 0.8
N A:ILE88 3.3 14.7 1.0
C7 A:RU7202 3.3 26.2 0.8
C2 A:RU7202 3.4 22.5 0.8
CE1 A:HIS15 3.7 20.2 1.0
CG1 A:ILE88 3.8 15.2 1.0
O A:HOH317 3.8 24.6 1.0
CA A:ASP87 3.8 17.3 1.0
C6 A:RU7202 3.9 25.1 0.8
CD2 A:HIS15 4.0 19.1 1.0
C3 A:RU7202 4.0 24.4 0.8
OD1 A:ASP87 4.0 21.0 1.0
C A:ASP87 4.0 15.6 1.0
O A:SER86 4.2 19.0 1.0
CA A:ILE88 4.3 14.2 1.0
CB A:ILE88 4.3 15.2 1.0
CG2 A:ILE88 4.4 16.4 1.0
CG A:ASP87 4.4 21.3 1.0
C5 A:RU7202 4.5 24.8 0.8
C4 A:RU7202 4.6 25.6 0.8
CB A:ASP87 4.6 19.2 1.0
CD1 A:ILE88 4.6 16.4 1.0
ND1 A:HIS15 4.8 18.8 1.0
N A:ASP87 4.8 15.7 1.0
CB A:ALA11 4.8 16.6 1.0
N A:THR89 4.8 16.1 1.0
C A:SER86 5.0 16.4 1.0
CG A:HIS15 5.0 18.2 1.0
C A:ILE88 5.0 15.0 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: Fri Jul 26 18:37:19 2024

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