Sodium in PDB 6m1j: The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X

Enzymatic activity of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X

All present enzymatic activity of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X:
5.6.2.2;

Protein crystallography data

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X, PDB code: 6m1j was solved by Z.H.Xu, Z.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.92 / 1.70
*Space group*	C 2 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	145.216, 160.743, 41.421, 90.00, 90.00, 90.00
*R / R_free (%)*	19.2 / 23.1

Other elements in 6m1j:

The structure of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X also contains other interesting chemical elements:

Fluorine

(F)

8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X (pdb code 6m1j). 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 The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X, PDB code: 6m1j:

Sodium binding site 1 out of 1 in 6m1j

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Sodium Binding Sites List in 6m1j

Sodium binding site 1 out of 1 in the The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Dna Gyrase B Atp Binding Domain of Pseudomonas Aeruginosa in Complex with Compound 12X within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na304 b:25.0 occ:1.00	OG	A:SER165	2.2	18.8	1.0
	O	A:ASN76	2.3	12.6	1.0
	O	A:HOH548	2.3	35.3	1.0
	O	A:HOH552	2.3	37.3	1.0
	O	A:GLY77	2.6	12.8	1.0
	O	A:SER165	2.6	14.6	1.0
	C	A:ASN76	3.0	10.5	1.0
	C	A:SER165	3.2	14.6	1.0
	CB	A:SER165	3.3	18.4	1.0
	C	A:GLY77	3.4	14.1	1.0
	CA	A:SER165	3.6	12.5	1.0
	N	A:GLY77	3.7	13.8	1.0
	N	A:SER165	3.7	18.3	1.0
	O	A:HOH469	3.8	21.1	1.0
	O	A:HOH554	3.8	32.7	1.0
	CA	A:GLY77	3.8	12.4	1.0
	CA	A:ASN76	3.9	10.3	1.0
	O	A:HOH592	4.0	45.9	1.0
	O	A:HOH492	4.1	29.8	1.0
	N	A:GLY166	4.1	12.3	1.0
	CB	A:ASN76	4.2	13.6	1.0
	N	A:ARG78	4.4	11.1	1.0
	O	A:HOH579	4.6	42.3	1.0
	CA	A:GLY166	4.6	12.0	1.0
	O	A:TYR57	4.7	18.5	1.0
	CA	A:ARG78	4.8	12.5	1.0
	CG	A:ASN76	4.8	16.1	1.0
	C	A:GLY164	5.0	32.0	1.0

Reference:

Y.Hu, H.Shi, M.Zhou, Q.Ren, W.Zhu, W.Zhang, Z.Zhang, C.Zhou, Y.Liu, X.Ding, H.C.Shen, S.F.Yan, F.Dey, W.Wu, G.Zhai, Z.Zhou, Z.Xu, Y.Ji, H.Lv, T.Jiang, W.Wang, Y.Xu, M.Vercruysse, X.Yao, Y.Mao, X.Yu, K.Bradley, X.Tan. Discovery of Pyrido[2,3-B]Indole Derivatives with Gram-Negative Activity Targeting Both Dna Gyrase and Topoisomerase IV. J.Med.Chem. V. 63 9623 2020.
ISSN: ISSN 0022-2623
PubMed: 32787097
DOI: 10.1021/ACS.JMEDCHEM.0C00768

Page generated: Tue Oct 8 11:48:29 2024

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