Fluorine in PDB 7whv: Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State)

Enzymatic activity of Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State)

All present enzymatic activity of Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State):
7.6.2.1;

Other elements in 7whv:

The structure of Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P 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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) (pdb code 7whv). 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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State), PDB code: 7whv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7whv

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Fluorine Binding Sites List in 7whv

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P 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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F1602 b:26.5 occ:1.00	F1	A:BEF1602	0.0	26.5	1.0
	BE	A:BEF1602	1.7	26.5	1.0
	OD2	A:ASP667	2.1	23.9	1.0
	OD1	A:ASP1130	2.1	25.2	1.0
	O	A:THR669	2.2	26.0	1.0
	OG1	A:THR671	2.8	23.7	1.0
	O	A:ASP1130	2.8	25.2	1.0
	F2	A:BEF1602	3.0	26.5	1.0
	F3	A:BEF1602	3.0	26.5	1.0
	CG	A:ASP667	3.1	23.9	1.0
	C	A:THR669	3.2	26.0	1.0
	CG	A:ASP1130	3.2	25.2	1.0
	N	A:THR671	3.3	23.7	1.0
	CB	A:THR671	3.6	23.7	1.0
	OD2	A:ASP1134	3.6	25.2	1.0
	CB	A:ASP667	3.7	23.9	1.0
	N	A:ASP1130	3.7	25.2	1.0
	C	A:ASP1130	3.8	25.2	1.0
	OD2	A:ASP1130	3.8	25.2	1.0
	C	A:GLY670	3.9	25.6	1.0
	N	A:GLY670	4.0	25.6	1.0
	CA	A:GLY670	4.0	25.6	1.0
	N	A:THR669	4.0	26.0	1.0
	CA	A:THR671	4.0	23.7	1.0
	OD1	A:ASP667	4.1	23.9	1.0
	CA	A:THR669	4.1	26.0	1.0
	MG	A:MG1601	4.1	24.9	1.0
	CA	A:ASP1130	4.2	25.2	1.0
	CB	A:ASP1130	4.3	25.2	1.0
	C	A:LYS668	4.4	26.5	1.0
	O	A:LYS668	4.7	26.5	1.0
	CB	A:THR669	4.7	26.0	1.0
	CG	A:ASP1134	4.8	25.2	1.0
	O	A:GLY670	4.8	25.6	1.0
	N	A:LYS668	4.8	26.5	1.0
	C	A:GLY1129	4.8	21.3	1.0
	C	A:ASP667	4.8	23.9	1.0
	CA	A:ASP667	4.9	23.9	1.0
	CG2	A:THR671	4.9	23.7	1.0
	CA	A:GLY1129	5.0	21.3	1.0
	N	A:GLY1131	5.0	25.8	1.0

Fluorine binding site 2 out of 3 in 7whv

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Fluorine Binding Sites List in 7whv

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P 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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F1602 b:26.5 occ:1.00	F2	A:BEF1602	0.0	26.5	1.0
	BE	A:BEF1602	1.8	26.5	1.0
	OD1	A:ASN1133	2.3	25.8	1.0
	O	A:ASP1130	2.5	25.2	1.0
	OD2	A:ASP1134	2.8	25.2	1.0
	F1	A:BEF1602	3.0	26.5	1.0
	F3	A:BEF1602	3.1	26.5	1.0
	CG	A:ASN1133	3.1	25.8	1.0
	OD2	A:ASP667	3.1	23.9	1.0
	ND2	A:ASN1133	3.2	25.8	1.0
	CG	A:ASP667	3.5	23.9	1.0
	CG	A:ASP1134	3.6	25.2	1.0
	OD1	A:ASP667	3.6	23.9	1.0
	MG	A:MG1601	3.6	24.9	1.0
	C	A:ASP1130	3.7	25.2	1.0
	O	A:LYS436	3.8	30.9	1.0
	CA	A:GLY1131	3.9	25.8	1.0
	O	A:ASP439	4.0	32.7	1.0
	OD1	A:ASP1134	4.0	25.2	1.0
	O	A:THR669	4.2	26.0	1.0
	N	A:GLY1131	4.3	25.8	1.0
	C	A:GLY1131	4.3	25.8	1.0
	NZ	A:LYS1110	4.4	25.9	1.0
	OD1	A:ASP1130	4.4	25.2	1.0
	CB	A:ASP667	4.4	23.9	1.0
	CB	A:ASN1133	4.5	25.8	1.0
	N	A:ASP1134	4.5	25.2	1.0
	CB	A:ASP1134	4.6	25.2	1.0
	O	A:ASN437	4.6	31.4	1.0
	O	A:GLY1131	4.7	25.8	1.0
	N	A:ASP1130	4.7	25.2	1.0
	N	A:ASN1133	4.8	25.8	1.0
	C	A:ASP439	4.8	32.7	1.0
	CA	A:ASP1130	4.8	25.2	1.0
	N	A:SER1132	4.8	27.4	1.0

Fluorine binding site 3 out of 3 in 7whv

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Fluorine Binding Sites List in 7whv

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P 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 DNF1 From Saccharomyces Cerevisiae in Detergent with Beryllium Fluoride (E2P State) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:F1602 b:26.5 occ:1.00	F3	A:BEF1602	0.0	26.5	1.0
	BE	A:BEF1602	1.8	26.5	1.0
	O	A:THR669	2.4	26.0	1.0
	O	A:LYS436	2.4	30.9	1.0
	F1	A:BEF1602	3.0	26.5	1.0
	F2	A:BEF1602	3.1	26.5	1.0
	C	A:THR669	3.5	26.0	1.0
	C	A:LYS436	3.5	30.9	1.0
	O	A:ASP439	3.5	32.7	1.0
	CB	A:LYS436	3.7	30.9	1.0
	CB	A:THR669	3.8	26.0	1.0
	CG2	A:THR669	3.8	26.0	1.0
	O	A:ASP1130	3.9	25.2	1.0
	CA	A:LYS436	3.9	30.9	1.0
	OD2	A:ASP667	3.9	23.9	1.0
	CE	A:LYS436	4.0	30.9	1.0
	OD1	A:ASP1130	4.2	25.2	1.0
	CA	A:THR669	4.2	26.0	1.0
	CA	A:GLY440	4.2	31.6	1.0
	MG	A:MG1601	4.2	24.9	1.0
	N	A:GLY670	4.4	25.6	1.0
	NZ	A:LYS436	4.5	30.9	1.0
	CA	A:GLY670	4.5	25.6	1.0
	OD2	A:ASP1130	4.6	25.2	1.0
	CG	A:LYS436	4.6	30.9	1.0
	C	A:ASP439	4.6	32.7	1.0
	N	A:ASN437	4.6	31.4	1.0
	CG	A:ASP1130	4.6	25.2	1.0
	N	A:THR669	4.8	26.0	1.0
	C	A:ASP1130	4.8	25.2	1.0
	CD	A:LYS436	4.9	30.9	1.0
	OD1	A:ASN1133	4.9	25.8	1.0
	N	A:GLY440	4.9	31.6	1.0
	CG	A:ASP667	5.0	23.9	1.0

Reference:

J.Xu, Y.He, X.Wu, L.Li. Conformational Changes of A Phosphatidylcholine Flippase in Lipid Membranes. Cell Rep V. 38 10518 2022.
ISSN: ESSN 2211-1247
PubMed: 35294892
DOI: 10.1016/J.CELREP.2022.110518

Page generated: Fri Aug 2 14:49:22 2024

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