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Sodium 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
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was 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:

Sodium binding site 1 out of 1 in 5v4h

Go back to Sodium Binding Sites List in 5v4h
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na201

b:15.3
occ:1.00
 O A:SER60 2.3 15.4 1.0
O A:HOH371 2.4 17.7 1.0
O A:ARG73 2.4 17.4 1.0
O A:CYS64 2.4 12.4 1.0
O A:HOH352 2.4 12.6 1.0
OG A:SER72 2.5 17.5 1.0
CB A:SER72 3.3 17.6 1.0
C A:ARG73 3.5 16.1 1.0
C A:SER60 3.5 12.8 1.0
C A:CYS64 3.5 12.0 1.0
CA A:ASN65 3.9 12.2 1.0
N A:ARG73 3.9 18.5 1.0
CA A:SER60 4.1 12.3 1.0
N A:ASN65 4.1 12.6 1.0
C A:SER72 4.2 19.2 1.0
CB A:SER60 4.2 11.9 1.0
CA A:ARG73 4.3 19.1 1.0
CA A:SER72 4.3 17.3 1.0
N A:ASN74 4.4 15.5 1.0
N A:CYS64 4.5 12.8 1.0
O A:ARG61 4.5 19.5 1.0
N A:ARG61 4.6 14.2 1.0
C A:ARG61 4.6 17.0 1.0
CA A:ASN74 4.6 15.3 1.0
N A:ASP66 4.6 11.6 1.0
CA A:CYS64 4.6 12.5 1.0
OD1 A:ASN65 4.7 15.3 1.0
CB A:THR69 4.7 13.1 1.0
O A:HOH382 4.7 7.6 1.0
CB A:ASN74 4.8 15.8 1.0
CB A:ASN65 4.8 13.6 1.0
O A:SER72 4.8 20.8 1.0
CA A:ARG61 4.8 17.4 0.5
CA A:ARG61 4.8 17.3 0.5
C A:ASN65 4.8 11.7 1.0
N A:TRP62 4.9 15.5 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: Tue Oct 8 00:43:13 2024

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