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Sodium in PDB 8ph7: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A, PDB code: 8ph7 was solved by A.Teran, G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.92 / 1.41
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.67, 77.67, 38.28, 90, 90, 90
R / Rfree (%) 22.6 / 26.6

Other elements in 8ph7:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A also contains other interesting chemical elements:

Ruthenium (Ru) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A (pdb code 8ph7). 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 X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A, PDB code: 8ph7:

Sodium binding site 1 out of 1 in 8ph7

Go back to Sodium Binding Sites List in 8ph7
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with [RU2CL(Dphf)(O2CCH3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:44.1
occ:1.00
 O A:SER60 2.2 27.0 1.0
O A:HOH368 2.3 26.4 1.0
O A:HOH326 2.4 37.9 1.0
OG A:SER72 2.5 46.5 1.0
O A:ARG73 2.6 42.7 1.0
O A:CYS64 2.7 23.3 1.0
CB A:SER72 3.1 51.2 1.0
C A:SER60 3.4 26.1 1.0
C A:ARG73 3.6 40.4 1.0
C A:CYS64 3.7 22.1 1.0
CA A:ASN65 3.9 23.4 0.6
CA A:ASN65 4.0 21.4 0.4
N A:ARG73 4.0 42.7 1.0
C A:SER72 4.0 46.9 1.0
CA A:SER72 4.2 50.5 1.0
CA A:SER60 4.2 21.4 1.0
N A:ASN65 4.2 22.5 0.6
N A:ASN65 4.2 21.5 0.4
O A:ARG61 4.3 31.6 1.0
C A:ARG61 4.4 31.1 1.0
N A:ARG61 4.4 28.6 1.0
CA A:ARG73 4.4 44.7 1.0
O A:SER72 4.5 47.9 1.0
CB A:SER60 4.5 19.3 1.0
CA A:ARG61 4.5 34.0 1.0
N A:ASN74 4.5 34.5 1.0
O A:HOH362 4.5 29.2 1.0
OD1 A:ASN65 4.6 22.7 0.4
O A:HOH306 4.6 39.8 1.0
CB A:ASN65 4.7 25.7 0.6
CB A:THR69 4.7 26.9 1.0
ND2 A:ASN65 4.7 32.0 0.6
CB A:ASN65 4.7 21.8 0.4
N A:ASP66 4.7 20.4 1.0
CB A:ASN74 4.8 27.3 1.0
CA A:ASN74 4.8 30.1 1.0
N A:CYS64 4.8 23.8 1.0
CG A:ASN65 4.8 30.1 0.6
N A:TRP62 4.9 28.5 0.5
CA A:CYS64 4.9 22.5 1.0
N A:TRP62 4.9 29.4 0.5
C A:ASN65 4.9 20.6 0.6
C A:ASN65 4.9 20.2 0.4
O A:THR69 4.9 31.8 1.0

Reference:

A.Teran, G.Ferraro, P.Imbimbo, A.E.Sanchez-Pelaez, D.M.Monti, S.Herrero, A.Merlino. Steric Hindrance and Charge Influence on the Cytotoxic Activity and Protein Binding Properties of Diruthenium Complexes. Int.J.Biol.Macromol. 26666 2023.
ISSN: ISSN 0141-8130
PubMed: 37660867
DOI: 10.1016/J.IJBIOMAC.2023.126666
Page generated: Thu Dec 28 11:44:37 2023

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