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Sodium in PDB 6tvl: Hen Egg White Lysozyme in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound

Enzymatic activity of Hen Egg White Lysozyme in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound

All present enzymatic activity of Hen Egg White Lysozyme in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg White Lysozyme in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound, PDB code: 6tvl was solved by L.Chiniadis, P.Giastas, I.Bratsos, A.Papakyriakou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.45 / 1.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.270, 79.270, 35.910, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 24.3

Other elements in 6tvl:

The structure of Hen Egg White Lysozyme in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Ruthenium (Ru) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Egg White Lysozyme in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound (pdb code 6tvl). 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 in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound, PDB code: 6tvl:

Sodium binding site 1 out of 1 in 6tvl

Go back to Sodium Binding Sites List in 6tvl
Sodium binding site 1 out of 1 in the Hen Egg White Lysozyme in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound


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 in Complex with A "Half Sandwich"-Type Ru(II) Coordination Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:21.9
occ:1.00
 O A:SER60 2.3 22.4 1.0
O A:HOH378 2.3 24.3 1.0
OG A:SER72 2.4 25.4 1.0
O A:ARG73 2.4 28.7 1.0
O A:HOH366 2.4 23.3 1.0
O A:CYS64 2.4 25.4 1.0
CB A:SER72 3.2 30.5 1.0
C A:SER60 3.5 22.9 1.0
C A:ARG73 3.5 26.7 1.0
C A:CYS64 3.6 22.7 1.0
CA A:ASN65 4.0 22.7 1.0
N A:ARG73 4.0 26.8 1.0
C A:SER72 4.1 33.5 1.0
CA A:SER60 4.1 19.5 1.0
N A:ASN65 4.2 22.0 1.0
CA A:SER72 4.2 27.9 1.0
CB A:SER60 4.3 17.9 1.0
N A:ASN74 4.4 28.7 1.0
CA A:ARG73 4.4 29.1 1.0
O A:ARG61 4.5 24.4 1.0
N A:CYS64 4.5 21.4 1.0
N A:ARG61 4.5 24.2 1.0
CA A:ASN74 4.5 27.1 1.0
C A:ARG61 4.6 26.5 1.0
O A:HOH404 4.6 45.4 1.0
CB A:ASN74 4.7 27.6 1.0
O A:SER72 4.7 31.5 1.0
CB A:THR69 4.7 24.9 1.0
O A:HOH387 4.7 18.9 1.0
CA A:CYS64 4.7 21.1 1.0
OD1 A:ASN65 4.7 31.2 1.0
CB A:ASN65 4.8 25.4 1.0
N A:ASP66 4.8 24.9 1.0
N A:TRP62 4.8 22.2 1.0
CA A:ARG61 4.9 22.3 1.0
C A:ASN65 4.9 27.3 1.0
O A:THR69 5.0 28.1 1.0

Reference:

L.Chiniadis, I.Bratsos, K.Bethanis, M.Karpusas, P.Giastas, A.Papakyriakou. High-Resolution Crystal Structures of A "Half Sandwich"-Type Ru(II) Coordination Compound Bound to Hen Egg-White Lysozyme and Proteinase K. J.Biol.Inorg.Chem. 2020.
ISSN: ESSN 1432-1327
PubMed: 32266561
DOI: 10.1007/S00775-020-01786-Z
Page generated: Tue Oct 8 14:04:58 2024

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