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Fluorine in PDB 7qpy: X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3)

Enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3)

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3):
4.6.1.18;

Protein crystallography data

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3), PDB code: 7qpy was solved by D.Loreto, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.12 / 1.42
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.22, 32.5, 72.38, 90, 90.41, 90
R / Rfree (%) 17.7 / 21.2

Other elements in 7qpy:

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3) also contains other interesting chemical elements:

Rhodium (Rh) 10 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3) (pdb code 7qpy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3), PDB code: 7qpy:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7qpy

Go back to Fluorine Binding Sites List in 7qpy
Fluorine binding site 1 out of 3 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3)


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 Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:44.9
occ:0.80
 F1 A:F5T201 0.0 44.9 0.8
C6 A:F5T201 1.4 39.0 0.8
F2 A:F5T201 2.2 45.1 0.8
F3 A:F5T201 2.2 37.5 0.8
C5 A:F5T201 2.3 30.3 0.8
O0 A:F5T201 2.6 22.2 0.8
O A:HOH305 2.9 39.0 1.0
O A:HOH369 3.1 34.6 1.0
HZ2 A:LYS41 3.2 36.4 1.0
O A:HOH420 3.2 34.0 1.0
O9 A:F5T201 3.3 24.5 0.8
O A:HOH425 3.5 46.7 1.0
HE3 A:LYS41 3.6 33.4 1.0
HZ1 A:LYS41 3.7 36.3 1.0
NZ A:LYS41 3.8 37.5 1.0
O A:HOH349 4.1 35.0 1.0
CE A:LYS41 4.2 33.9 1.0
HE21 A:GLN11 4.2 23.6 1.0
O A:HOH324 4.3 15.9 1.0
O A:HOH404 4.5 33.9 1.0
HZ3 A:LYS41 4.6 36.3 1.0
HE2 A:LYS41 4.6 33.4 1.0
HE1 A:HIS119 4.6 16.4 1.0
RH1 A:F5T201 4.7 17.7 0.8
O A:HOH407 4.9 29.7 1.0
O1 A:F5T201 4.9 19.1 0.8
HD1 A:HIS119 5.0 15.4 0.0

Fluorine binding site 2 out of 3 in 7qpy

Go back to Fluorine Binding Sites List in 7qpy
Fluorine binding site 2 out of 3 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3)


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 Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:45.1
occ:0.80
 F2 A:F5T201 0.0 45.1 0.8
C6 A:F5T201 1.3 39.0 0.8
F3 A:F5T201 2.2 37.5 0.8
F1 A:F5T201 2.2 44.9 0.8
C5 A:F5T201 2.4 30.3 0.8
O0 A:F5T201 3.0 22.2 0.8
O9 A:F5T201 3.1 24.5 0.8
O A:HOH425 3.5 46.7 1.0
O A:HOH420 4.5 34.0 1.0
O A:HOH369 4.5 34.6 1.0
O A:HOH349 4.6 35.0 1.0
O A:HOH404 4.6 33.9 1.0
HE1 A:HIS119 4.7 16.4 1.0
O3 A:F5T201 4.8 22.9 0.8
O A:HOH305 4.8 39.0 1.0
RH1 A:F5T201 4.9 17.7 0.8
O4 A:F5T201 4.9 25.5 0.8
RH2 A:F5T201 4.9 22.5 0.8

Fluorine binding site 3 out of 3 in 7qpy

Go back to Fluorine Binding Sites List in 7qpy
Fluorine binding site 3 out of 3 in the X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3)


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 Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:37.5
occ:0.80
 F3 A:F5T201 0.0 37.5 0.8
C6 A:F5T201 1.4 39.0 0.8
F2 A:F5T201 2.2 45.1 0.8
F1 A:F5T201 2.2 44.9 0.8
C5 A:F5T201 2.4 30.3 0.8
O9 A:F5T201 2.6 24.5 0.8
O A:HOH349 2.6 35.0 1.0
O0 A:F5T201 3.5 22.2 0.8
HZ1 A:LYS41 3.6 36.3 1.0
O A:HOH404 3.7 33.9 1.0
O A:HOH305 3.8 39.0 1.0
HE3 A:LYS41 4.0 33.4 1.0
HZ2 A:LYS41 4.0 36.4 1.0
NZ A:LYS41 4.2 37.5 1.0
HE21 A:GLN11 4.4 23.6 1.0
CE A:LYS41 4.6 33.9 1.0
RH2 A:F5T201 4.7 22.5 0.8
O A:HOH420 4.8 34.0 1.0
HD2 A:LYS41 4.9 30.1 1.0

Reference:

D.Loreto, A.Esposito, N.Demitri, A.Guaragna, A.Merlino. Reactivity of A Fluorine-Containing Dirhodium Tetracarboxylate Compound with Proteins. Dalton Trans V. 51 3695 2022.
ISSN: ESSN 1477-9234
PubMed: 35166290
DOI: 10.1039/D2DT00082B
Page generated: Fri Aug 2 11:46:42 2024

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