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Sodium in PDB 8pfx: X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition B

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

All present enzymatic activity of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition B:
3.2.1.17;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition B, PDB code: 8pfx 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) 38.36 / 1.03
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.72, 76.72, 38.39, 90, 90, 90
R / Rfree (%) 19.2 / 21.4

Other elements in 8pfx:

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

Ruthenium (Ru) 6 atoms
Fluorine (F) 2 atoms

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(D-P-Fphf)(CO3)3] in Condition B (pdb code 8pfx). 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(D-P-Fphf)(CO3)3] in Condition B, PDB code: 8pfx:

Sodium binding site 1 out of 1 in 8pfx

Go back to Sodium Binding Sites List in 8pfx
Sodium binding site 1 out of 1 in the X-Ray Structure of the Adduct Formed Upon Reaction of Lysozyme with K2[RU2(D-P-Fphf)(CO3)3] in Condition B


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(D-P-Fphf)(CO3)3] in Condition B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:12.7
occ:1.00
 O A:SER60 2.3 11.5 1.0
O A:ARG73 2.4 15.5 1.0
O A:CYS64 2.4 10.9 1.0
O A:HOH406 2.4 16.6 1.0
O A:HOH389 2.5 14.0 1.0
OG A:SER72 2.5 17.0 1.0
CB A:SER72 3.3 17.1 1.0
C A:CYS64 3.4 10.3 1.0
C A:ARG73 3.4 15.2 1.0
C A:SER60 3.5 10.2 1.0
CA A:ASN65 3.9 10.3 1.0
N A:ARG73 4.0 17.1 1.0
N A:ASN65 4.1 10.3 1.0
CA A:SER60 4.1 9.2 1.0
C A:SER72 4.2 18.2 1.0
N A:ASN74 4.3 15.4 1.0
CB A:SER60 4.3 9.1 1.0
CA A:ARG73 4.3 17.7 1.0
CA A:SER72 4.4 17.9 1.0
N A:CYS64 4.4 10.7 1.0
C A:ARG61 4.5 12.3 1.0
CA A:ASN74 4.5 14.4 1.0
O A:HOH371 4.5 17.6 1.0
N A:ARG61 4.5 10.7 1.0
CA A:CYS64 4.6 10.5 1.0
O A:HOH422 4.6 31.8 1.0
O A:ARG61 4.6 14.8 1.0
CB A:ASN74 4.6 14.9 1.0
O A:SER72 4.7 21.8 1.0
N A:ASP66 4.7 9.8 1.0
OD1 A:ASN65 4.7 17.6 1.0
CA A:ARG61 4.7 13.5 1.0
CB A:THR69 4.8 12.7 1.0
N A:TRP62 4.8 11.8 1.0
CB A:ASN65 4.8 11.7 1.0
C A:ASN65 4.9 9.5 1.0
O A:THR69 5.0 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: Mon Aug 18 15:01:07 2025

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