Sodium in PDB 6yen: Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133)

Enzymatic activity of Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133)

All present enzymatic activity of Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133):
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133), PDB code: 6yen was solved by P.A.Lang, J.Brem, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	97.04 / 1.42
*Space group*	P 4₃ 3 2
*Cell size a, b, c (Å), α, β, γ (°)*	137.229, 137.229, 137.229, 90.00, 90.00, 90.00
*R / R_free (%)*	14.4 / 16.9

Other elements in 6yen:

The structure of Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133) also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Chlorine	(Cl)	3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133) (pdb code 6yen). 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 Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133), PDB code: 6yen:

Sodium binding site 1 out of 1 in 6yen

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Sodium Binding Sites List in 6yen

Sodium binding site 1 out of 1 in the Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Ampc From E. Coli with Taniborbactam (Vnrx-5133) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na413 b:40.2 occ:1.00	OD1	A:ASP217	2.2	27.3	1.0
	O	A:HOH742	2.2	37.7	1.0
	O	A:HOH646	2.2	52.5	1.0
	O	A:HOH521	2.5	47.0	1.0
	CG	A:ASP217	3.1	27.4	1.0
	OD2	A:ASP217	3.3	29.1	1.0
	O	A:HOH620	3.3	47.5	1.0
	N	A:ALA218	4.2	22.9	1.0
	O	A:GLY214	4.3	30.3	1.0
	O	A:HOH762	4.4	32.6	1.0
	CB	A:ASP217	4.5	25.5	1.0
	CB	A:ALA218	4.5	24.9	1.0
	O	A:HOH697	4.7	42.4	1.0
	OE1	A:GLU171	4.7	38.7	0.5
	N	A:ASP217	4.7	22.4	1.0
	CA	A:ALA218	4.9	22.3	1.0
	CA	A:ASP217	5.0	22.7	1.0

Reference:

P.A.Lang, A.Parkova, T.M.Leissing, K.Calvopina, R.Cain, A.Krajnc, T.D.Panduwawala, J.Philippe, C.W.G.Fishwick, P.Trapencieris, M.G.P.Page, C.J.Schofield, J.Brem. Bicyclic Boronates As Potent Inhibitors of Ampc, the Class C Beta-Lactamase From Escherichia Coli Biomolecules 2020.
ISSN: ESSN 2218-273X
DOI: 10.3390/BIOM10060899

Page generated: Tue Oct 8 15:07:13 2024

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