Fluorine in PDB 5qj8: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

All present enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829, PDB code: 5qj8 was solved by Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	77.81 / 1.76
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	49.530, 59.990, 79.650, 79.56, 81.09, 75.49
*R / R_free (%)*	23.5 / 27.8

Other elements in 5qj8:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829 also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Chlorine	(Cl)	1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829 (pdb code 5qj8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829, PDB code: 5qj8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5qj8

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Fluorine Binding Sites List in 5qj8

Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F305 b:59.3 occ:0.70	F16	B:ELQ305	0.0	59.3	0.7
	C14	B:ELQ305	1.3	59.7	0.7
	C13	B:ELQ305	2.3	61.0	0.7
	C15	B:ELQ305	2.4	60.2	0.7
	O	B:GLU47	2.5	34.5	1.0
	F17	B:ELQ305	2.6	56.2	0.7
	O	B:GLY135	3.1	29.4	1.0
	NE1	B:TRP46	3.3	30.4	1.0
	C12	B:ELQ305	3.6	62.5	0.7
	C10	B:ELQ305	3.6	61.9	0.7
	C	B:GLU47	3.7	33.6	1.0
	CG2	A:VAL29	3.8	35.7	1.0
	CD1	B:TRP46	3.8	31.9	1.0
	CE2	B:TRP46	4.1	34.0	1.0
	CA	B:LEU136	4.1	29.2	1.0
	C11	B:ELQ305	4.1	62.4	0.7
	CD1	B:LEU136	4.2	36.5	1.0
	C	B:GLY135	4.2	30.4	1.0
	N	B:GLU47	4.5	30.2	1.0
	CA	B:GLU47	4.5	35.0	1.0
	CB	B:GLU47	4.5	34.5	1.0
	N	B:LEU136	4.6	27.2	1.0
	CZ2	B:TRP46	4.7	36.0	1.0
	O	B:LEU136	4.7	35.5	1.0
	CG	B:TRP46	4.7	34.8	1.0
	CB	B:LEU136	4.8	33.1	1.0
	N	B:SER48	4.8	28.8	1.0
	C08	B:ELQ305	4.8	61.9	0.7
	CD2	B:TRP46	4.9	30.9	1.0
	C	B:LEU136	4.9	31.8	1.0
	O09	B:ELQ305	5.0	64.1	0.7
	NH1	A:ARG51	5.0	30.1	1.0

Fluorine binding site 2 out of 2 in 5qj8

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Fluorine Binding Sites List in 5qj8

Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z2856434829 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F305 b:56.2 occ:0.70	F17	B:ELQ305	0.0	56.2	0.7
	C13	B:ELQ305	1.3	61.0	0.7
	C14	B:ELQ305	2.3	59.7	0.7
	C12	B:ELQ305	2.4	62.5	0.7
	NH1	A:ARG51	2.6	30.1	1.0
	F16	B:ELQ305	2.6	59.3	0.7
	O	A:HOH425	3.1	45.0	1.0
	CZ	A:ARG51	3.3	32.1	1.0
	C15	B:ELQ305	3.6	60.2	0.7
	C11	B:ELQ305	3.7	62.4	0.7
	NH2	A:ARG51	3.7	33.4	1.0
	CG2	A:VAL29	3.8	35.7	1.0
	CD1	B:LEU136	3.9	36.5	1.0
	C10	B:ELQ305	4.1	61.9	0.7
	O	A:TRP28	4.2	34.1	0.7
	NE	A:ARG51	4.2	31.7	1.0
	CG	A:ARG51	4.3	27.3	1.0
	CB	A:TRP28	4.4	46.1	0.7
	O	B:GLY135	4.5	29.4	1.0
	CD	A:ARG51	4.6	30.3	1.0
	C	A:TRP28	4.7	38.1	0.7
	CB	B:LEU136	5.0	33.1	1.0

Reference:

Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft. Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) To Be Published.

Page generated: Tue Jul 15 06:26:53 2025

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