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 / R_free (%)*	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

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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

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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

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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: Tue Jul 15 23:17:34 2025

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