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Sodium in PDB 8pfw: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A

Enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)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 K2[RU2(Danif)(CO3)3] in Condition A, PDB code: 8pfw 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) 55.02 / 1.12
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.81, 77.81, 37.39, 90, 90, 90
R / Rfree (%) 20.1 / 23.9

Other elements in 8pfw:

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A also contains other interesting chemical elements:

Ruthenium (Ru) 6 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)3] in Condition A (pdb code 8pfw). 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 K2[RU2(Danif)(CO3)3] in Condition A, PDB code: 8pfw:

Sodium binding site 1 out of 1 in 8pfw

Go back to Sodium Binding Sites List in 8pfw
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(Danif)(CO3)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 K2[RU2(Danif)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:19.9
occ:1.00
 O A:HOH375 2.3 23.1 1.0
O A:SER60 2.3 18.9 1.0
O A:ARG73 2.4 25.3 1.0
O A:CYS64 2.5 15.8 1.0
OG A:SER72 2.6 23.6 1.0
O A:HOH374 2.7 23.9 1.0
C A:ARG73 3.4 22.6 1.0
C A:CYS64 3.5 14.5 1.0
C A:SER60 3.5 16.7 1.0
CB A:SER72 3.5 24.8 1.0
N A:ARG73 3.8 25.5 1.0
CA A:ASN65 4.1 16.2 1.0
CA A:SER60 4.1 16.0 1.0
C A:SER72 4.1 28.6 1.0
N A:ASN65 4.2 16.5 1.0
CA A:ARG73 4.2 25.7 1.0
N A:ASN74 4.2 22.1 1.0
N A:CYS64 4.3 16.1 1.0
CB A:SER60 4.3 15.4 1.0
CA A:SER72 4.4 28.0 1.0
CA A:ASN74 4.4 21.3 1.0
C A:ARG61 4.5 20.3 1.0
O A:ARG61 4.5 22.2 1.0
CA A:CYS64 4.5 15.8 1.0
N A:ARG61 4.6 16.8 1.0
CB A:ASN74 4.6 19.2 1.0
O A:SER72 4.7 30.0 1.0
CB A:THR69 4.7 16.6 1.0
N A:TRP62 4.7 18.7 1.0
O A:HOH335 4.8 26.2 1.0
CA A:ARG61 4.8 20.1 1.0
CB A:ASN65 4.9 19.8 1.0
N A:TRP63 4.9 16.6 1.0
C A:TRP62 4.9 18.4 1.0
O A:THR69 4.9 21.5 1.0
N A:ASP66 4.9 14.7 1.0

Reference:

S.Herrero Dominguez, A.Teran, G.Ferraro, A.E.Sanchez-Pelaez, A.Merlino. Charge Effect in Protein Metalation Reactions By Diruthenium Complexes Inorg Chem Front 2023.
DOI: 10.1039/D3QI01192E
Page generated: Wed Oct 9 12:55:54 2024

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