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: Sat Dec 12 12:33:14 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