Fluorine in PDB 7qpz: X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)

Enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4)

All present enzymatic activity of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4):
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 (4), PDB code: 7qpz 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) 50.86 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.73, 32.87, 72.89, 90, 90.15, 90
R / Rfree (%) 16.2 / 20.2

Other elements in 7qpz:

The structure of X-Ray Structure of the Adduct Obtained Upon Reaction of [Cis- RH2(OCOCH3)2(OCOCF3)2] with Rnase A (4) also contains other interesting chemical elements:

Rhodium (Rh) 8 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 (4) (pdb code 7qpz). 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 (4), PDB code: 7qpz:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7qpz

Go back to Fluorine Binding Sites List in 7qpz
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 (4)


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 (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:33.5
occ:0.75
 F1 A:F5T201 0.0 33.5 0.8
C6 A:F5T201 1.4 33.2 0.8
O A:HOH367 2.0 13.8 0.3
F3 A:F5T201 2.2 41.5 0.8
F2 A:F5T201 2.2 43.6 0.8
C5 A:F5T201 2.5 24.6 0.8
O0 A:F5T201 2.7 18.9 0.8
O A:HOH418 3.1 24.9 1.0
O A:HOH303 3.3 38.7 1.0
O A:HOH441 3.4 27.3 1.0
HE2 A:LYS41 3.5 25.2 1.0
O9 A:F5T201 3.5 15.6 0.8
HE3 A:LYS41 4.0 25.3 1.0
CE A:LYS41 4.2 25.2 1.0
HZ2 A:LYS41 4.3 27.9 1.0
HE21 A:GLN11 4.4 18.2 1.0
O A:HOH460 4.4 34.4 1.0
NZ A:LYS41 4.8 29.2 1.0
RH1 A:F5T201 4.8 16.8 0.8
O A:HOH520 4.8 38.1 1.0
O A:HOH320 4.9 26.7 1.0

Fluorine binding site 2 out of 3 in 7qpz

Go back to Fluorine Binding Sites List in 7qpz
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 (4)


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 (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:43.6
occ:0.75
 F2 A:F5T201 0.0 43.6 0.8
C6 A:F5T201 1.3 33.2 0.8
F3 A:F5T201 2.2 41.5 0.8
F1 A:F5T201 2.2 33.5 0.8
C5 A:F5T201 2.3 24.6 0.8
O9 A:F5T201 2.6 15.6 0.8
O A:HOH389 3.1 23.0 1.0
O A:HOH520 3.2 38.1 1.0
O A:HOH460 3.2 34.4 1.0
O A:HOH303 3.3 38.7 1.0
O A:HOH484 3.3 30.6 1.0
O0 A:F5T201 3.4 18.9 0.8
O A:HOH320 3.5 26.7 1.0
HZ2 A:LYS41 3.8 27.9 1.0
HE2 A:LYS41 4.0 25.2 1.0
O A:HOH367 4.1 13.8 0.3
HE1 A:HIS119 4.3 11.9 1.0
O A:HOH441 4.5 27.3 1.0
NZ A:LYS41 4.5 29.2 1.0
O A:HOH329 4.6 12.2 1.0
CE A:LYS41 4.6 25.2 1.0
HE3 A:LYS41 4.6 25.3 1.0
RH2 A:F5T201 4.7 11.8 0.8
O A:HOH418 4.8 24.9 1.0
HE21 A:GLN11 4.8 18.2 1.0
HD1 A:HIS119 4.9 10.5 0.0
CE1 A:HIS119 5.0 12.9 1.0

Fluorine binding site 3 out of 3 in 7qpz

Go back to Fluorine Binding Sites List in 7qpz
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 (4)


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 (4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:41.5
occ:0.75
 F3 A:F5T201 0.0 41.5 0.8
C6 A:F5T201 1.3 33.2 0.8
F2 A:F5T201 2.2 43.6 0.8
F1 A:F5T201 2.2 33.5 0.8
C5 A:F5T201 2.4 24.6 0.8
O0 A:F5T201 3.0 18.9 0.8
O9 A:F5T201 3.1 15.6 0.8
O A:HOH367 3.2 13.8 0.3
O A:HOH520 3.8 38.1 1.0
O A:HOH484 4.1 30.6 1.0
O A:HOH441 4.5 27.3 1.0
O3 A:F5T201 4.6 19.6 0.8
O4 A:F5T201 4.7 16.2 0.8
O A:HOH303 4.8 38.7 1.0
O A:HOH418 4.8 24.9 1.0
O A:HOH460 4.8 34.4 1.0
RH1 A:F5T201 4.8 16.8 0.8
HE1 A:HIS119 4.9 11.9 1.0
RH2 A:F5T201 4.9 11.8 0.8
O A:HOH389 5.0 23.0 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: Wed Apr 5 00:50:06 2023

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