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Sodium in PDB 5lvj: Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]

Enzymatic activity of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]

All present enzymatic activity of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)], PDB code: 5lvj was solved by K.Kurpiewska, P.Halajko, K.Lewinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.83 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.609, 77.609, 37.205, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 21.4

Other elements in 5lvj:

The structure of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] also contains other interesting chemical elements:

Ruthenium (Ru) 1 atom
Chlorine (Cl) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] (pdb code 5lvj). 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 Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)], PDB code: 5lvj:

Sodium binding site 1 out of 1 in 5lvj

Go back to Sodium Binding Sites List in 5lvj
Sodium binding site 1 out of 1 in the Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)]


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg White Lysozyme Soaked with [H2IND][Trans-RUCL4(Dmso)(Hind)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:24.2
occ:1.00
O A:SER60 2.1 17.6 1.0
O A:HOH313 2.3 17.7 1.0
O A:HOH390 2.3 12.1 1.0
OG A:SER72 2.5 28.1 1.0
O A:ARG73 2.6 24.5 0.5
O A:ARG73 2.6 24.4 0.5
O A:CYS64 2.6 11.3 1.0
C A:SER60 3.3 15.6 1.0
CB A:SER72 3.4 31.9 1.0
C A:ARG73 3.6 22.8 0.5
C A:ARG73 3.6 22.3 0.5
C A:CYS64 3.7 10.7 1.0
CA A:ASN65 4.0 10.9 1.0
N A:ARG73 4.0 26.0 0.5
N A:ARG73 4.0 25.3 0.5
CA A:SER60 4.0 13.2 1.0
C A:SER72 4.1 31.0 1.0
CB A:SER60 4.2 12.4 1.0
N A:ASN65 4.3 10.4 1.0
N A:ARG61 4.3 16.2 1.0
CA A:ARG73 4.4 23.2 0.5
CA A:SER72 4.4 33.6 1.0
CA A:ARG73 4.4 22.2 0.5
C A:ARG61 4.4 21.3 1.0
N A:ASN74 4.5 18.7 1.0
CA A:ARG61 4.5 20.6 1.0
O A:ARG61 4.5 24.3 1.0
CL A:CL206 4.5 23.6 1.0
O A:SER72 4.5 35.1 1.0
CB A:THR69 4.5 15.3 1.0
ND2 A:ASN65 4.6 12.6 1.0
N A:ASP66 4.7 10.5 1.0
OXT A:ACT210 4.7 40.6 1.0
N A:CYS64 4.7 11.8 1.0
CA A:ASN74 4.7 16.8 1.0
CB A:ASN65 4.8 12.3 1.0
O A:THR69 4.8 16.0 1.0
CA A:CYS64 4.8 11.9 1.0
N A:TRP62 4.8 17.9 1.0
O A:ACT210 4.9 39.9 1.0
C A:ASN65 4.9 11.0 1.0
CG2 A:THR69 4.9 15.4 1.0
CB A:ASN74 5.0 15.7 1.0
OG A:SER60 5.0 12.3 1.0

Reference:

M.Oszajca, K.Kurpiewska, P.Halajko, A.Szura, K.Lewinski, M.Brindell. Ligand-Dependent Interaction of Anticancer Ruthenium Complexes with Hen Egg White Lysozyme and Human Lysozyme To Be Published.
Page generated: Tue Dec 15 11:14:23 2020

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