Fluorine in PDB 5qtn: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432, PDB code: 5qtn was solved by Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.91 / 1.83
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	49.083, 59.814, 79.586, 79.55, 81.29, 75.78
*R / R_free (%)*	23.8 / 27.5

Other elements in 5qtn:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432 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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 (pdb code 5qtn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432, PDB code: 5qtn:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5qtn

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Fluorine Binding Sites List in 5qtn

Fluorine binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432

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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F304 b:37.1 occ:0.74	F	A:PWD304	0.0	37.1	0.7
	C	A:PWD304	1.3	36.5	0.7
	C1	A:PWD304	2.4	36.9	0.7
	C6	A:PWD304	2.4	34.7	0.7
	NE1	B:TRP28	3.5	47.8	0.7
	N	A:PWD304	3.6	34.1	0.7
	C5	A:PWD304	3.6	35.3	0.7
	CZ3	A:TRP46	3.7	34.6	1.0
	CE2	B:TRP28	3.7	48.2	0.7
	CE3	A:TRP46	3.8	34.7	1.0
	CZ2	B:TRP28	3.9	47.6	0.7
	C2	A:PWD304	4.0	34.8	0.7
	CD1	B:TRP28	4.1	47.7	0.7
	CH2	A:TRP46	4.2	35.1	1.0
	CD2	B:TRP28	4.3	47.1	0.7
	CD2	A:TRP46	4.5	35.5	1.0
	O	A:THR45	4.5	34.8	1.0
	CG	B:TRP28	4.6	47.7	0.7
	CH2	B:TRP28	4.7	47.6	0.7
	CZ2	A:TRP46	4.8	35.9	1.0
	CE2	A:TRP46	4.9	35.9	1.0
	C4	A:PWD304	5.0	35.3	0.7

Fluorine binding site 2 out of 3 in 5qtn

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Fluorine Binding Sites List in 5qtn

Fluorine binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432

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 -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:F304 b:35.3 occ:0.74	F	B:PWD304	0.0	35.3	0.7
	C	B:PWD304	1.3	31.8	0.7
	C1	B:PWD304	2.4	31.4	0.7
	C6	B:PWD304	2.4	31.7	0.7
	CZ3	B:TRP46	3.5	32.9	0.7
	CE2	A:TRP28	3.6	41.8	0.7
	N	B:PWD304	3.6	30.1	0.7
	C5	B:PWD304	3.6	30.1	0.7
	CZ2	A:TRP28	3.6	42.8	0.7
	NE1	A:TRP28	3.8	41.9	0.7
	CE3	B:TRP46	3.9	32.4	0.7
	CH2	B:TRP46	4.0	32.6	0.7
	C2	B:PWD304	4.0	29.7	0.7
	CD2	A:TRP28	4.2	40.3	0.7
	CH2	A:TRP28	4.2	42.6	0.7
	O	B:HOH459	4.3	43.4	1.0
	CD1	A:TRP28	4.4	40.6	0.7
	CD2	B:TRP46	4.6	31.2	0.7
	CZ2	B:TRP46	4.6	32.5	0.7
	O	B:THR45	4.7	36.5	1.0
	CG	A:TRP28	4.7	40.3	0.7
	CE3	A:TRP28	4.8	41.8	0.7
	CZ3	A:TRP28	4.8	42.0	0.7
	CE2	B:TRP46	4.9	32.3	0.7
	C4	B:PWD304	4.9	29.9	0.7

Fluorine binding site 3 out of 3 in 5qtn

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Fluorine Binding Sites List in 5qtn

Fluorine binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ss-4432 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:F304 b:46.6 occ:0.90	F	C:PWD304	0.0	46.6	0.9
	C	C:PWD304	1.3	44.2	0.9
	C6	C:PWD304	2.3	45.6	0.9
	C1	C:PWD304	2.4	43.8	0.9
	CE2	C:TRP28	3.2	57.6	0.9
	NE1	C:TRP28	3.2	59.3	0.9
	CZ2	C:TRP28	3.5	58.0	0.9
	C5	C:PWD304	3.6	43.9	0.9
	N	C:PWD304	3.6	42.7	0.9
	CD2	C:TRP28	3.8	58.7	0.9
	CD1	C:TRP28	3.8	57.9	0.9
	CZ3	D:TRP46	3.9	43.3	1.0
	CE3	D:TRP46	4.0	44.3	1.0
	C2	C:PWD304	4.0	43.4	0.9
	CG	C:TRP28	4.1	58.9	0.9
	CH2	C:TRP28	4.2	57.5	0.9
	CH2	D:TRP46	4.3	41.8	1.0
	CD2	D:TRP46	4.4	42.4	1.0
	CE3	C:TRP28	4.5	58.5	0.9
	CZ3	C:TRP28	4.7	58.0	0.9
	CZ2	D:TRP46	4.7	43.9	1.0
	CE2	D:TRP46	4.8	41.5	1.0
	C4	C:PWD304	4.9	45.8	0.9
	O	D:THR45	4.9	50.2	1.0

Reference:

Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft. Pandda Analysis Group Deposition To Be Published.

Page generated: Thu Aug 1 13:24:36 2024

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