Magnesium in PDB 7jga: Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3

Enzymatic activity of Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3

All present enzymatic activity of Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3:
7.1.2.2;

Other elements in 7jga:

The structure of Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3 also contains other interesting chemical elements:

Bromine

(Br)

7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3 (pdb code 7jga). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3, PDB code: 7jga:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7jga

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Magnesium Binding Sites List in 7jga

Magnesium binding site 1 out of 4 in the Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg601 b:75.4 occ:1.00	O1B	A:ATP600	1.8	78.3	1.0
	O1G	A:ATP600	2.0	78.3	1.0
	OG1	A:THR179	2.0	75.9	1.0
	PG	A:ATP600	2.9	78.3	1.0
	PB	A:ATP600	2.9	78.3	1.0
	O3G	A:ATP600	3.0	78.3	1.0
	CB	A:THR179	3.2	75.9	1.0
	O3B	A:ATP600	3.4	78.3	1.0
	O2B	A:ATP600	3.7	78.3	1.0
	NE2	A:GLN211	3.8	74.4	1.0
	CG2	A:THR179	3.9	75.9	1.0
	O1A	A:ATP600	4.0	78.3	1.0
	OD2	A:ASP272	4.0	74.1	1.0
	OD1	A:ASP272	4.2	74.1	1.0
	O3A	A:ATP600	4.2	78.3	1.0
	O2G	A:ATP600	4.3	78.3	1.0
	CA	A:THR179	4.3	75.9	1.0
	N	A:THR179	4.4	75.9	1.0
	CG	A:ASP272	4.5	74.1	1.0
	PA	A:ATP600	4.6	78.3	1.0
	CD	A:GLN211	4.8	74.4	1.0
	OE1	A:GLN211	4.8	74.4	1.0

Magnesium binding site 2 out of 4 in 7jga

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Magnesium Binding Sites List in 7jga

Magnesium binding site 2 out of 4 in the Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg601 b:75.1 occ:1.00	O2B	B:ATP600	2.0	82.2	1.0
	O3G	B:ATP600	2.0	82.2	1.0
	OG1	B:THR179	2.1	75.3	1.0
	OD2	B:ASP272	3.1	71.7	1.0
	CB	B:THR179	3.2	75.3	1.0
	PB	B:ATP600	3.2	82.2	1.0
	PG	B:ATP600	3.3	82.2	1.0
	NE2	B:GLN211	3.4	73.7	1.0
	O1B	B:ATP600	3.7	82.2	1.0
	O3B	B:ATP600	3.8	82.2	1.0
	OD1	B:ASP272	3.8	71.7	1.0
	CG	B:ASP272	3.9	71.7	1.0
	O2G	B:ATP600	3.9	82.2	1.0
	CG2	B:THR179	4.0	75.3	1.0
	CD	B:GLN211	4.1	73.7	1.0
	O1A	B:ATP600	4.1	82.2	1.0
	N	B:THR179	4.3	75.3	1.0
	CA	B:THR179	4.3	75.3	1.0
	O3A	B:ATP600	4.5	82.2	1.0
	O1G	B:ATP600	4.5	82.2	1.0
	OE1	B:GLN211	4.6	73.7	1.0
	PA	B:ATP600	4.8	82.2	1.0
	CG2	B:THR215	4.8	74.1	1.0
	CG	B:GLN211	4.9	73.7	1.0

Magnesium binding site 3 out of 4 in 7jga

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Magnesium Binding Sites List in 7jga

Magnesium binding site 3 out of 4 in the Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg601 b:79.5 occ:1.00	O2B	C:ATP600	1.8	76.4	1.0
	O1B	C:ATP600	2.1	76.4	1.0
	OG1	C:THR179	2.1	73.3	1.0
	O1G	C:ATP600	2.1	76.4	1.0
	PB	C:ATP600	2.1	76.4	1.0
	O3B	C:ATP600	3.0	76.4	1.0
	PG	C:ATP600	3.1	76.4	1.0
	CB	C:THR179	3.4	73.3	1.0
	O3A	C:ATP600	3.6	76.4	1.0
	O2G	C:ATP600	3.8	76.4	1.0
	O1A	C:ATP600	3.9	76.4	1.0
	OD2	C:ASP272	4.0	72.1	1.0
	OD1	C:ASP272	4.1	72.1	1.0
	N	C:THR179	4.2	73.3	1.0
	CG2	C:THR179	4.2	73.3	1.0
	PA	C:ATP600	4.3	76.4	1.0
	NE2	C:GLN211	4.3	72.4	1.0
	O3G	C:ATP600	4.3	76.4	1.0
	CA	C:THR179	4.4	73.3	1.0
	CG	C:ASP272	4.5	72.1	1.0
	NZ	C:LYS178	4.6	73.9	1.0
	O2A	C:ATP600	4.6	76.4	1.0
	CE	C:LYS178	4.8	73.9	1.0
	OD1	C:ASP273	4.9	73.5	1.0
	OD2	C:ASP273	4.9	73.5	1.0

Magnesium binding site 4 out of 4 in 7jga

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Magnesium Binding Sites List in 7jga

Magnesium binding site 4 out of 4 in the Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Bedaquiline-Saturated Mycobacterium Smegmatis Atp Synthase Rotational State 3 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
E:Mg601 b:75.4 occ:1.00	OG1	E:THR167	2.1	76.8	1.0
	OE2	E:GLU192	2.1	76.0	1.0
	O2B	E:ADP600	2.2	77.4	1.0
	O3B	E:ADP600	2.5	77.4	1.0
	PB	E:ADP600	2.8	77.4	1.0
	CD	E:GLU192	3.2	76.0	1.0
	CB	E:THR167	3.4	76.8	1.0
	O3A	E:ADP600	3.9	77.4	1.0
	NH1	E:ARG193	3.9	74.5	1.0
	N	E:THR167	4.0	76.8	1.0
	OE1	E:GLU192	4.0	76.0	1.0
	CG	E:GLU192	4.1	76.0	1.0
	O1B	E:ADP600	4.1	77.4	1.0
	CA	E:THR167	4.3	76.8	1.0
	O2A	E:ADP600	4.3	77.4	1.0
	NZ	E:LYS166	4.3	75.2	1.0
	CE	E:LYS166	4.3	75.2	1.0
	CG2	E:THR167	4.4	76.8	1.0
	PA	E:ADP600	4.5	77.4	1.0
	CB	E:LYS166	4.7	75.2	1.0
	O1A	E:ADP600	4.8	77.4	1.0
	CZ	E:ARG193	4.8	74.5	1.0
	C	E:LYS166	5.0	75.2	1.0

Reference:

H.Guo, G.M.Courbon, S.A.Bueler, J.Mai, J.Liu, J.L.Rubinstein. Structure of Mycobacterial Atp Synthase with the Tb Drug Bedaquiline Biorxiv 2020.
DOI: 10.1101/2020.08.06.225375

Page generated: Wed Oct 2 21:51:21 2024

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