Fluorine in PDB 7n70: Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State

Other elements in 7n70:

The structure of Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State (pdb code 7n70). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State, PDB code: 7n70:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7n70

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Fluorine Binding Sites List in 7n70

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F1201 b:32.4 occ:1.00	F1	A:BEF1201	0.0	32.4	1.0
	BE	A:BEF1201	1.5	32.4	1.0
	OD2	A:ASP508	2.1	31.7	1.0
	MG	A:MG1202	2.2	30.8	1.0
	OD1	A:ASP508	2.4	31.7	1.0
	F3	A:BEF1201	2.5	32.4	1.0
	F2	A:BEF1201	2.6	32.4	1.0
	CG	A:ASP508	2.6	31.7	1.0
	O	A:THR510	3.0	30.4	1.0
	CA	A:GLY342	3.7	31.8	1.0
	N	A:THR510	3.8	30.4	1.0
	ND2	A:ASN876	3.8	34.4	1.0
	CB	A:THR510	3.9	30.4	1.0
	C	A:THR510	3.9	30.4	1.0
	O	A:SER338	4.0	32.3	1.0
	CA	A:THR510	4.0	30.4	1.0
	CB	A:ASP508	4.1	31.7	1.0
	OD1	A:ASP873	4.2	36.1	1.0
	OD2	A:ASP877	4.2	36.6	1.0
	OD1	A:ASN876	4.4	34.4	1.0
	OG1	A:THR510	4.4	30.4	1.0
	NZ	A:LYS854	4.5	30.2	1.0
	N	A:LYS509	4.5	28.6	1.0
	O	A:GLY342	4.5	31.8	1.0
	CG	A:ASN876	4.5	34.4	1.0
	N	A:GLY342	4.6	31.8	1.0
	C	A:GLY342	4.6	31.8	1.0
	C	A:LYS509	4.8	28.6	1.0
	CA	A:ASP508	5.0	31.7	1.0
	OG1	A:THR745	5.0	28.8	1.0

Fluorine binding site 2 out of 3 in 7n70

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Fluorine Binding Sites List in 7n70

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F1201 b:32.4 occ:1.00	F2	A:BEF1201	0.0	32.4	1.0
	BE	A:BEF1201	1.6	32.4	1.0
	OG1	A:THR745	2.4	28.8	1.0
	OD1	A:ASP508	2.4	31.7	1.0
	F3	A:BEF1201	2.5	32.4	1.0
	F1	A:BEF1201	2.6	32.4	1.0
	N	A:THR510	3.2	30.4	1.0
	CB	A:THR745	3.3	28.8	1.0
	OG1	A:THR510	3.4	30.4	1.0
	N	A:GLY746	3.4	28.4	1.0
	CG	A:ASP508	3.5	31.7	1.0
	CA	A:THR745	3.5	28.8	1.0
	O	A:GLY342	3.6	31.8	1.0
	N	A:LYS509	3.6	28.6	1.0
	CB	A:THR510	3.7	30.4	1.0
	CA	A:GLY342	3.7	31.8	1.0
	OD2	A:ASP508	3.9	31.7	1.0
	C	A:THR745	4.0	28.8	1.0
	CA	A:THR510	4.0	30.4	1.0
	CB	A:LYS509	4.0	28.6	1.0
	CA	A:LYS509	4.1	28.6	1.0
	C	A:LYS509	4.1	28.6	1.0
	C	A:GLY342	4.1	31.8	1.0
	N	A:ASP747	4.4	30.7	1.0
	O	A:THR510	4.4	30.4	1.0
	CA	A:GLY746	4.5	28.4	1.0
	NZ	A:LYS854	4.5	30.2	1.0
	MG	A:MG1202	4.6	30.8	1.0
	C	A:ASP508	4.6	31.7	1.0
	CG2	A:THR745	4.7	28.8	1.0
	CB	A:ASP508	4.7	31.7	1.0
	C	A:THR510	4.7	30.4	1.0
	O	A:VAL744	4.8	28.6	1.0
	ND2	A:ASN876	4.8	34.4	1.0
	CA	A:ASP508	4.8	31.7	1.0
	N	A:THR745	4.8	28.8	1.0
	C	A:GLY746	4.9	28.4	1.0
	CE	A:LYS509	4.9	28.6	1.0
	CB	A:ASP747	5.0	30.7	1.0

Fluorine binding site 3 out of 3 in 7n70

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Fluorine Binding Sites List in 7n70

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State

Mono view

Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of ATP13A2 in the Bef-Bound E2P-Like State within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F1201 b:32.4 occ:1.00	F3	A:BEF1201	0.0	32.4	1.0
	BE	A:BEF1201	1.5	32.4	1.0
	OD1	A:ASP508	2.3	31.7	1.0
	NZ	A:LYS854	2.4	30.2	1.0
	F2	A:BEF1201	2.5	32.4	1.0
	ND2	A:ASN876	2.5	34.4	1.0
	F1	A:BEF1201	2.5	32.4	1.0
	CG	A:ASP508	3.2	31.7	1.0
	N	A:GLY746	3.3	28.4	1.0
	CE	A:LYS854	3.4	30.2	1.0
	OD2	A:ASP508	3.6	31.7	1.0
	CG	A:ASN876	3.7	34.4	1.0
	CA	A:THR745	3.8	28.8	1.0
	CA	A:GLY342	3.8	31.8	1.0
	C	A:THR745	3.9	28.8	1.0
	OD1	A:ASP877	4.0	36.6	1.0
	CA	A:GLY746	4.1	28.4	1.0
	OG1	A:THR745	4.1	28.8	1.0
	OD1	A:ASN876	4.3	34.4	1.0
	O	A:VAL744	4.3	28.6	1.0
	CB	A:ASP508	4.4	31.7	1.0
	OD2	A:ASP877	4.5	36.6	1.0
	MG	A:MG1202	4.5	30.8	1.0
	N	A:GLY342	4.5	31.8	1.0
	CB	A:THR745	4.6	28.8	1.0
	CG	A:ASP877	4.7	36.6	1.0
	O	A:THR341	4.7	32.6	1.0
	CD	A:LYS854	4.7	30.2	1.0
	N	A:THR745	4.9	28.8	1.0
	CB	A:ASN876	4.9	34.4	1.0
	C	A:GLY342	4.9	31.8	1.0
	C	A:THR341	4.9	32.6	1.0
	N	A:LYS509	4.9	28.6	1.0
	CA	A:ASP508	5.0	31.7	1.0
	O	A:GLY342	5.0	31.8	1.0
	O	A:THR745	5.0	28.8	1.0

Reference:

S.I.Sim, S.Von Bulow, G.Hummer, E.Park. Structural Basis of Polyamine Transport By Human ATP13A2 (PARK9). Mol.Cell 2021.
ISSN: ISSN 1097-2765
PubMed: 34715013
DOI: 10.1016/J.MOLCEL.2021.08.017

Page generated: Tue Jul 15 22:01:07 2025

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