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Sodium 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
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Ruthenium(II)(Cymene)(Chlorido)2-Lysozyme Adduct with Two Binding Sites, PDB code: 5v4g:

Sodium binding site 1 out of 1 in 5v4g

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


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 with Two Binding Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:12.9
occ:1.00
 O A:SER60 2.3 13.5 1.0
O A:CYS64 2.4 12.0 1.0
O A:ARG73 2.4 14.9 1.0
O A:HOH355 2.4 15.4 1.0
O A:HOH338 2.5 11.9 1.0
OG A:SER72 2.5 14.6 1.0
CB A:SER72 3.3 13.8 1.0
C A:ARG73 3.5 15.3 1.0
C A:CYS64 3.5 11.5 1.0
C A:SER60 3.5 12.1 1.0
N A:ARG73 3.9 16.3 1.0
CA A:ASN65 3.9 11.7 1.0
CA A:SER60 4.1 11.5 1.0
C A:SER72 4.1 16.1 1.0
N A:ASN65 4.1 11.6 1.0
CB A:SER60 4.2 11.8 1.0
CA A:ARG73 4.3 17.3 1.0
CA A:SER72 4.3 15.1 1.0
N A:ASN74 4.4 15.6 1.0
N A:CYS64 4.5 12.3 1.0
O A:ARG61 4.5 16.8 1.0
C A:ARG61 4.6 15.0 1.0
N A:ARG61 4.6 13.0 1.0
CA A:ASN74 4.6 14.2 1.0
N A:ASP66 4.6 11.4 1.0
CA A:CYS64 4.6 11.9 1.0
OD1 A:ASN65 4.7 14.2 1.0
O A:SER72 4.7 18.5 1.0
CB A:THR69 4.7 11.6 1.0
CB A:ASN74 4.8 15.4 1.0
CB A:ASN65 4.8 12.2 1.0
CA A:ARG61 4.8 15.9 1.0
C A:ASN65 4.8 10.8 1.0
N A:TRP62 4.9 14.8 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: Tue Oct 8 00:43:11 2024

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