Sodium in PDB 6d4o: Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate

Enzymatic activity of Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate

All present enzymatic activity of Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate:
3.2.1.31;

Protein crystallography data

The structure of Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate, PDB code: 6d4o was solved by S.J.Pellock, W.G.Walton, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	29.45 / 2.90
*Space group*	P 6₄ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	179.954, 179.954, 134.941, 90.00, 90.00, 120.00
*R / R_free (%)*	19.9 / 24.4

Other elements in 6d4o:

The structure of Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate (pdb code 6d4o). 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 Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate, PDB code: 6d4o:

Sodium binding site 1 out of 1 in 6d4o

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Sodium Binding Sites List in 6d4o

Sodium binding site 1 out of 1 in the Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Eubacterium Eligens Beta-Glucuronidase Bound to An Amoxapine- Glucuronide Conjugate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na703 b:34.9 occ:1.00	OH	A:TYR542	2.6	29.8	1.0
	O	A:LYS580	2.6	35.7	1.0
	NE2	A:GLN538	2.9	25.2	1.0
	O	A:TRP561	3.1	34.1	1.0
	N	A:ALA519	3.1	31.4	1.0
	CA	A:GLY518	3.2	32.6	1.0
	CE2	A:TYR542	3.3	29.9	1.0
	CZ	A:TYR542	3.3	28.3	1.0
	O	A:ALA519	3.5	27.7	1.0
	C	A:LYS580	3.6	31.3	1.0
	C	A:GLY518	3.7	33.7	1.0
	CA	A:LYS580	3.9	28.6	1.0
	CD	A:GLN538	3.9	24.8	1.0
	CB	A:LYS580	3.9	27.1	1.0
	CG	A:GLN538	4.1	27.5	1.0
	C	A:TRP561	4.1	33.6	1.0
	C	A:ALA519	4.1	30.0	1.0
	CA	A:ALA519	4.2	33.6	1.0
	CD2	A:LEU582	4.4	26.3	1.0
	O	A:TYR517	4.5	38.0	1.0
	N	A:ASN562	4.6	35.0	1.0
	N	A:GLY518	4.6	36.2	1.0
	CD2	A:TYR542	4.6	31.1	1.0
	CG	A:LYS580	4.6	34.6	1.0
	CE1	A:TYR542	4.7	27.9	1.0
	N	A:GLY581	4.7	26.0	1.0
	O	A:GLY581	4.8	28.5	1.0
	C	A:GLY581	4.9	30.7	1.0
	O	A:GLY518	4.9	37.5	1.0
	C	A:TYR517	5.0	33.6	1.0
	CB	A:ALA519	5.0	29.2	1.0

Reference:

S.J.Pellock, B.C.Creekmore, W.G.Walton, N.Mehta, K.A.Biernat, A.P.Cesmat, Y.Ariyarathna, Z.D.Dunn, B.Li, J.Jin, L.I.James, M.R.Redinbo. Gut Microbial Beta-Glucuronidase Inhibition Via Catalytic Cycle Interception. Acs Cent Sci V. 4 868 2018.
ISSN: ESSN 2374-7943
PubMed: 30062115
DOI: 10.1021/ACSCENTSCI.8B00239

Page generated: Tue Dec 15 12:07:21 2020

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