Sodium in PDB 8djz: Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product

Enzymatic activity of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product

All present enzymatic activity of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product:
3.1.1.17;

Protein crystallography data

The structure of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product, PDB code: 8djz was solved by C.A.Bingman, B.W.Hall, R.W.Smith, B.G.Fox, T.J.Donohue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	38.03 / 1.55
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	47.51, 47.51, 199.02, 90, 90, 120
*R / R_free (%)*	18 / 21.1

Other elements in 8djz:

The structure of Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product (pdb code 8djz). 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 RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product, PDB code: 8djz:

Sodium binding site 1 out of 1 in 8djz

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Sodium Binding Sites List in 8djz

Sodium binding site 1 out of 1 in the Crystal Structure of RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product

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 RPA3624, A Beta-Propeller Lactonase From Rhodopseudomonas Palustris, with Active-Site Bound Product within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na402 b:25.0 occ:1.00	O	A:HOH599	2.3	28.2	1.0
	O	A:ILE272	2.4	25.1	1.0
	OD1	A:ASN271	2.5	23.5	1.0
	O	A:HOH551	2.6	27.8	1.0
	O	A:HOH608	2.6	24.8	1.0
	O	A:LEU231	2.7	24.6	1.0
	HB2	A:ALA232	3.2	29.8	1.0
	H	A:ILE272	3.3	30.2	1.0
	C	A:ILE272	3.5	23.0	1.0
	CG	A:ASN271	3.5	23.2	1.0
	HB2	A:ALA273	3.6	32.3	1.0
	HD21	A:ASN271	3.6	25.8	1.0
	C	A:LEU231	3.7	22.9	1.0
	HA	A:ALA273	3.9	32.7	1.0
	ND2	A:ASN271	4.0	21.5	1.0
	H	A:LEU231	4.0	28.2	1.0
	O	A:HOH613	4.1	28.1	1.0
	N	A:ILE272	4.1	25.2	1.0
	CB	A:ALA232	4.1	24.8	1.0
	HB3	A:SER230	4.1	31.4	1.0
	HA	A:ALA232	4.2	28.6	1.0
	HG23	A:ILE272	4.2	32.7	1.0
	HG2	A:PRO17	4.3	29.9	1.0
	O	A:HOH552	4.3	23.1	1.0
	N	A:ALA273	4.3	25.9	1.0
	CB	A:ALA273	4.4	26.9	1.0
	O	A:HOH568	4.4	22.7	1.0
	CA	A:ALA273	4.4	27.3	1.0
	N	A:ALA232	4.4	23.7	1.0
	CA	A:ILE272	4.5	27.2	1.0
	CA	A:ALA232	4.5	23.9	1.0
	N	A:LEU231	4.5	23.5	1.0
	HD2	A:PRO17	4.5	29.4	1.0
	HB1	A:ALA232	4.6	29.8	1.0
	O	A:HOH517	4.6	29.2	1.0
	OD2	A:ASP124	4.6	24.0	1.0
	O	A:HOH536	4.6	26.0	1.0
	HB3	A:ALA232	4.6	29.8	1.0
	CA	A:LEU231	4.7	21.9	1.0
	CB	A:ASN271	4.8	26.1	1.0
	HB1	A:ALA273	4.8	32.3	1.0
	HD22	A:ASN271	4.8	25.8	1.0
	HG22	A:ILE272	4.8	32.7	1.0
	O	A:PRO17	4.9	25.3	1.0
	HB3	A:ASN271	4.9	31.3	1.0
	CG2	A:ILE272	4.9	27.2	1.0
	HA	A:ASN271	4.9	29.9	1.0
	HA	A:LEU231	5.0	26.3	1.0

Reference:

B.W.Hall, C.A.Bingman, B.G.Fox, D.R.Noguera, T.J.Donohue. A Broad Specificity Beta-Propeller Enzyme From Rhodopseudomonas Palustris That Hydrolyzes Many Lactones Including Gamma-Valerolactone. J.Biol.Chem. 02782 2022.
ISSN: ESSN 1083-351X
PubMed: 36502920
DOI: 10.1016/J.JBC.2022.102782

Page generated: Wed Oct 9 11:31:44 2024

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