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

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

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 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(D-P-Fphf)(CO3)3] in Condition A, PDB code: 8pft 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) 54.98 / 1.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.75, 77.75, 37.34, 90, 90, 90
R / Rfree (%) 20.3 / 24.6

Other elements in 8pft:

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

Fluorine (F) 4 atoms
Chlorine (Cl) 1 atom
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 K2[RU2(D-P-Fphf)(CO3)3] in Condition A (pdb code 8pft). 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 A, PDB code: 8pft:

Sodium binding site 1 out of 1 in 8pft

Go back to Sodium Binding Sites List in 8pft
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 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(D-P-Fphf)(CO3)3] in Condition A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:27.2
occ:1.00
 O A:SER60 2.2 25.2 1.0
O A:ARG73 2.4 32.6 1.0
O A:HOH384 2.4 30.8 1.0
OG A:SER72 2.5 33.5 1.0
O A:CYS64 2.5 21.0 1.0
O A:HOH369 2.7 30.1 1.0
CB A:SER72 3.3 36.0 1.0
C A:SER60 3.4 21.6 1.0
C A:ARG73 3.4 31.4 1.0
C A:CYS64 3.5 19.8 1.0
O A:HOH367 3.7 26.1 0.5
N A:ARG73 3.9 32.0 1.0
CA A:SER60 4.0 20.4 1.0
C A:SER72 4.1 37.6 1.0
CA A:ASN65 4.1 21.6 1.0
N A:ASN65 4.2 21.7 1.0
CA A:ARG73 4.3 33.9 1.0
CB A:SER60 4.3 22.1 1.0
CA A:SER72 4.3 42.6 1.0
N A:ASN74 4.3 28.3 1.0
N A:CYS64 4.4 23.1 1.0
O A:ARG61 4.4 31.1 1.0
C A:ARG61 4.4 27.4 1.0
N A:ARG61 4.5 23.9 1.0
CA A:CYS64 4.5 23.5 1.0
O A:SER72 4.6 40.1 1.0
CA A:ASN74 4.6 27.0 1.0
O A:HOH367 4.6 25.9 0.5
N A:TRP62 4.7 25.1 1.0
O A:HOH304 4.7 45.3 1.0
CB A:THR69 4.7 27.4 1.0
CB A:ASN74 4.7 27.0 1.0
CA A:ARG61 4.8 27.7 1.0
O A:THR69 4.9 27.7 1.0
N A:TRP63 4.9 20.1 1.0
CB A:ASN65 4.9 25.6 1.0
C A:TRP62 4.9 24.4 1.0
N A:ASP66 5.0 18.7 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 15:00:47 2025

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