Fluorine 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:

Sodium (Na) 1 atom
Chlorine (Cl) 1 atom
Ruthenium (Ru) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where 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:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8pft

Go back to Fluorine Binding Sites List in 8pft
Fluorine binding site 1 out of 4 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 Fluorine with other atoms in the F 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:F203

b:55.7
occ:0.35
 F1 A:YJT203 0.0 55.7 0.3
C5 A:YJT203 1.4 51.8 0.3
C6 A:YJT203 2.3 52.0 0.3
C4 A:YJT203 2.4 51.9 0.3
C7 A:YJT203 3.6 50.7 0.3
C3 A:YJT203 3.6 49.4 0.3
C2 A:YJT203 4.1 46.8 0.3

Fluorine binding site 2 out of 4 in 8pft

Go back to Fluorine Binding Sites List in 8pft
Fluorine binding site 2 out of 4 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 Fluorine with other atoms in the F binding site number 2 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:F203

b:39.0
occ:0.35
 F2 A:YJT203 0.0 39.0 0.3
C11 A:YJT203 1.3 43.7 0.3
C12 A:YJT203 2.3 45.2 0.3
C10 A:YJT203 2.3 44.0 0.3
C13 A:YJT203 3.6 42.3 0.3
C9 A:YJT203 3.6 45.5 0.3
C8 A:YJT203 4.1 42.0 0.3

Fluorine binding site 3 out of 4 in 8pft

Go back to Fluorine Binding Sites List in 8pft
Fluorine binding site 3 out of 4 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 Fluorine with other atoms in the F binding site number 3 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:F204

b:32.1
occ:0.35
 F1 A:YJT204 0.0 32.1 0.3
C5 A:YJT204 1.3 29.9 0.3
C6 A:YJT204 2.3 28.8 0.3
C4 A:YJT204 2.3 31.2 0.3
C7 A:YJT204 3.6 24.3 0.3
C3 A:YJT204 3.6 29.4 0.3
CA A:GLY117 3.8 24.4 1.0
O A:HOH350 4.0 31.7 1.0
C2 A:YJT204 4.1 30.1 0.3
O A:GLY117 4.1 34.3 1.0
C A:GLY117 4.2 27.5 1.0
O A:HOH345 4.5 29.8 1.0
N A:GLY117 4.7 21.9 1.0
O A:HOH390 4.9 32.7 1.0

Fluorine binding site 4 out of 4 in 8pft

Go back to Fluorine Binding Sites List in 8pft
Fluorine binding site 4 out of 4 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 Fluorine with other atoms in the F binding site number 4 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:F204

b:38.1
occ:0.35
 F2 A:YJT204 0.0 38.1 0.3
C11 A:YJT204 1.4 36.2 0.3
C12 A:YJT204 2.3 38.2 0.3
C10 A:YJT204 2.3 37.1 0.3
C9 A:YJT204 3.6 37.2 0.3
C13 A:YJT204 3.6 37.8 0.3
C8 A:YJT204 4.1 35.8 0.3
O A:HOH392 4.9 42.9 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: Fri Aug 2 22:00:52 2024

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