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

Go back to

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

Go back to

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

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy