Magnesium in PDB 9ggq: E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin

Enzymatic activity of E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin

All present enzymatic activity of E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin:
5.6.2.2;

Other elements in 9ggq:

The structure of E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin (pdb code 9ggq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin, PDB code: 9ggq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 9ggq

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Magnesium Binding Sites List in 9ggq

Magnesium binding site 1 out of 4 in the E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg901 b:43.0 occ:1.00	O03	F:MFX201	1.9	38.1	1.0
	O	F:HOH304	1.9	39.2	1.0
	O	F:HOH303	1.9	43.8	1.0
	O	F:HOH301	1.9	72.0	1.0
	O	F:HOH302	1.9	42.5	1.0
	O02	F:MFX201	1.9	39.9	1.0
	C19	F:MFX201	2.9	38.9	1.0
	C20	F:MFX201	3.0	38.2	1.0
	C18	F:MFX201	3.3	38.0	1.0
	O	F:MFX201	4.0	37.8	1.0
	O4	G:DT20	4.1	38.4	1.0
	C14	F:MFX201	4.2	38.8	1.0
	O6	H:DG1	4.3	38.3	1.0
	OG	A:SER83	4.6	76.2	1.0
	C17	F:MFX201	4.6	39.5	1.0
	C16	F:MFX201	4.7	37.6	1.0
	N6	F:DA5	4.8	40.7	1.0
	N4	F:DC4	5.0	41.9	1.0
	CB	A:SER83	5.0	74.7	1.0
	C6	H:DG1	5.0	37.3	1.0

Magnesium binding site 2 out of 4 in 9ggq

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Magnesium Binding Sites List in 9ggq

Magnesium binding site 2 out of 4 in the E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg901 b:75.7 occ:1.00	OD2	B:ASP500	2.8	76.5	1.0
	OD2	B:ASP498	3.3	77.8	1.0
	CG	B:ASP500	3.9	75.8	1.0
	OP1	G:DT20	4.2	36.5	1.0
	CG	B:ASP498	4.4	77.2	1.0
	OD1	B:ASP500	4.4	76.8	1.0
	OE2	B:GLU424	4.6	74.1	1.0
	CB	B:ASP498	4.6	75.3	1.0
	O3'	G:DT20	4.8	37.3	1.0
	C5'	G:DT20	5.0	36.2	1.0

Magnesium binding site 3 out of 4 in 9ggq

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Magnesium Binding Sites List in 9ggq

Magnesium binding site 3 out of 4 in the E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg901 b:74.0 occ:1.00	O03	H:MFX201	1.8	102.4	1.0
	O02	H:MFX201	1.9	103.7	1.0
	O	H:HOH301	1.9	56.2	1.0
	O	H:HOH303	1.9	30.8	1.0
	O	H:HOH302	1.9	75.3	1.0
	O	H:HOH304	1.9	55.4	1.0
	C19	H:MFX201	2.9	103.2	1.0
	C20	H:MFX201	3.0	101.7	1.0
	C18	H:MFX201	3.3	102.6	1.0
	N6	F:DA1	4.0	39.5	1.0
	O	H:MFX201	4.0	100.5	1.0
	C14	H:MFX201	4.2	103.0	1.0
	N6	E:DA18	4.2	37.4	1.0
	OG	C:SER83	4.5	76.5	1.0
	C17	H:MFX201	4.6	103.2	1.0
	C16	H:MFX201	4.7	102.4	1.0
	CB	C:SER83	4.9	75.3	1.0
	C6	F:DA1	4.9	39.2	1.0

Magnesium binding site 4 out of 4 in 9ggq

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Magnesium Binding Sites List in 9ggq

Magnesium binding site 4 out of 4 in the E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E.Coli Gyrase Holocomplex with Cleaved Chirally Wrapped 217 Bp Dna Fragment and Moxifloxacin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg901 b:77.3 occ:1.00	OD2	D:ASP500	3.0	79.0	1.0
	OD2	D:ASP498	3.3	79.3	1.0
	CG	D:ASP500	4.2	78.6	1.0
	OP1	E:DA18	4.3	35.8	1.0
	CG	D:ASP498	4.4	78.3	1.0
	OD1	D:ASP500	4.6	80.0	1.0
	CB	D:ASP498	4.7	77.1	1.0
	OE2	D:GLU424	4.8	74.9	1.0
	O3'	E:DA18	4.8	36.3	1.0
	O	D:LYS740	4.9	85.9	1.0
	C5'	E:DA18	5.0	35.5	1.0
	OD2	D:ASP502	5.0	78.5	1.0

Reference:

E.Michalczyk, Z.Pakosz-Stepien, J.D.Liston, O.Gittins, M.Pabis, J.G.Heddle, D.Ghilarov. Structural Basis of Chiral Wrap and T-Segment Capture By Escherichia Coli Dna Gyrase Proceedings of the National 2024ACADEMY of Sciences Usa.

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