Sodium in PDB 6qtk: 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna

Enzymatic activity of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna

All present enzymatic activity of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna:
5.99.1.3;

Protein crystallography data

The structure of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna, PDB code: 6qtk was solved by B.D.Bax, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	39.99 / 2.31
*Space group*	P 6₁
*Cell size a, b, c (Å), α, β, γ (°)*	92.730, 92.730, 408.775, 90.00, 90.00, 120.00
*R / R_free (%)*	16.3 / 20.3

Other elements in 6qtk:

The structure of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna (pdb code 6qtk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna, PDB code: 6qtk:

Sodium binding site 1 out of 1 in 6qtk

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Sodium Binding Sites List in 6qtk

Sodium binding site 1 out of 1 in the 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.31A Structure of Gepotidacin with S.Aureus Dna Gyrase and Doubly Nicked Dna within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na502 b:33.1 occ:1.00	O	A:HOH795	2.2	35.9	1.0
	O	A:TYR322	2.3	28.4	1.0
	O	A:THR325	2.4	27.6	1.0
	O	A:GLN328	2.4	28.6	1.0
	O	A:HOH833	2.5	45.3	1.0
	C	A:GLN328	3.4	33.0	1.0
	C	A:TYR322	3.5	29.3	1.0
	C	A:THR325	3.5	29.2	1.0
	O	A:LYS323	3.7	34.7	1.0
	N	A:GLN328	3.9	29.6	1.0
	CB	A:GLN328	3.9	28.5	1.0
	C	A:LYS323	3.9	31.4	1.0
	CA	A:GLN328	4.0	31.7	1.0
	N	A:THR325	4.0	28.9	1.0
	N	A:LYS323	4.3	32.9	1.0
	CA	A:LYS323	4.3	30.0	1.0
	N	A:PRO326	4.4	29.5	1.0
	CA	A:THR325	4.4	28.6	1.0
	O	A:HOH645	4.4	40.7	1.0
	N	A:GLN324	4.4	28.3	1.0
	CA	A:PRO326	4.4	30.6	1.0
	CG	A:GLN328	4.5	30.1	1.0
	O	A:HOH863	4.5	44.1	1.0
	CA	A:TYR322	4.5	30.6	1.0
	N	A:THR329	4.5	30.2	1.0
	C	A:PRO326	4.7	32.0	1.0
	O	A:LEU321	4.7	30.4	1.0
	C	A:GLN324	4.8	31.9	1.0
	N	A:LEU327	4.9	29.2	1.0
	CA	A:THR329	5.0	33.4	1.0

Reference:

E.G.Gibson, B.Bax, P.F.Chan, N.Osheroff. Mechanistic and Structural Basis For the Actions of the Antibacterial Gepotidacin Against Staphylococcus Aureus Gyrase. Acs Infect Dis. V. 5 570 2019.
ISSN: ESSN 2373-8227
PubMed: 30757898
DOI: 10.1021/ACSINFECDIS.8B00315

Page generated: Mon Aug 18 06:48:05 2025

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