Sodium in PDB 4k8e: OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation

Enzymatic activity of OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation

All present enzymatic activity of OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation:
1.6.99.1;

Protein crystallography data

The structure of OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation, PDB code: 4k8e was solved by B.Sullivan, Y.A.Pompeu, J.D.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	24.20 / 1.27
*Space group*	P 4₃ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	141.135, 141.135, 42.850, 90.00, 90.00, 90.00
*R / R_free (%)*	10.7 / 12.7

Other elements in 4k8e:

The structure of OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation (pdb code 4k8e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation, PDB code: 4k8e:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4k8e

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Sodium Binding Sites List in 4k8e

Sodium binding site 1 out of 4 in the OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na408 b:30.0 occ:0.82	HE1	A:TRP52	2.1	14.4	1.0
	O2	A:PGE415	2.8	21.9	0.6
	O4	A:PGE415	2.8	21.9	0.6
	NE1	A:TRP52	2.9	12.0	1.0
	O1	A:PGE415	3.0	21.9	0.6
	O3	A:PGE415	3.0	21.9	0.6
	C1	A:PGE415	3.3	21.9	0.6
	O	A:HOH961	3.4	40.1	1.0
	C2	A:PGE415	3.6	21.9	0.6
	C4	A:PGE415	3.7	21.9	0.6
	C5	A:PGE415	3.7	21.9	0.6
	HD1	A:TRP52	3.7	13.3	1.0
	HB3	A:ASP51	3.8	13.8	1.0
	CD1	A:TRP52	3.8	11.1	1.0
	C3	A:PGE415	3.8	21.9	0.6
	C6	A:PGE415	3.8	21.9	0.6
	CE2	A:TRP52	4.0	11.9	1.0
	HZ2	A:TRP52	4.1	15.0	1.0
	O	A:HOH945	4.4	38.3	1.0
	CZ2	A:TRP52	4.5	12.5	1.0
	HB2	A:ALA379	4.5	13.3	1.0
	CB	A:ASP51	4.7	11.5	1.0
	HB2	A:ASP51	4.9	13.8	1.0

Sodium binding site 2 out of 4 in 4k8e

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Sodium Binding Sites List in 4k8e

Sodium binding site 2 out of 4 in the OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na410 b:30.0 occ:0.90	H	A:ALA10	2.0	15.5	1.0
	O2	A:PGE409	2.6	21.9	0.5
	HA	A:GLN9	2.8	18.3	0.4
	HA	A:GLN9	2.9	19.2	0.6
	N	A:ALA10	2.9	12.9	1.0
	O3	A:PGE409	3.0	21.9	0.5
	O4	A:PGE409	3.1	21.9	0.5
	HB3	A:ALA10	3.1	15.9	1.0
	HB2	A:ALA10	3.4	15.9	1.0
	O1	A:PGE409	3.4	21.9	0.5
	C4	A:PGE409	3.5	21.9	0.5
	C3	A:PGE409	3.5	21.9	0.5
	CB	A:ALA10	3.6	13.2	1.0
	C1	A:PGE409	3.6	21.9	0.5
	CA	A:GLN9	3.6	15.3	0.4
	C6	A:PGE409	3.6	21.9	0.5
	CA	A:GLN9	3.7	16.0	0.6
	C2	A:PGE409	3.7	21.9	0.5
	C	A:GLN9	3.7	14.2	1.0
	HG2	A:GLN9	3.7	27.7	0.6
	C5	A:PGE409	3.8	21.9	0.5
	CA	A:ALA10	3.8	12.7	1.0
	HB3	A:GLN9	4.1	21.3	0.4
	HG3	A:GLN9	4.1	27.7	0.6
	HA3	A:GLY363	4.2	13.5	1.0
	CG	A:GLN9	4.3	23.1	0.6
	CB	A:GLN9	4.4	17.7	0.4
	O	A:PRO8	4.4	17.1	1.0
	HA	A:ALA10	4.5	15.2	1.0
	HB1	A:ALA10	4.5	15.9	1.0
	O	A:ALA10	4.5	15.6	1.0
	CB	A:GLN9	4.5	20.4	0.6
	HG2	A:GLN9	4.6	23.1	0.4
	C	A:ALA10	4.7	12.8	1.0
	N	A:GLN9	4.7	15.1	1.0
	O	A:GLN9	4.9	15.1	1.0
	C	A:PRO8	4.9	15.9	1.0

Sodium binding site 3 out of 4 in 4k8e

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Sodium Binding Sites List in 4k8e

Sodium binding site 3 out of 4 in the OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na411 b:30.0 occ:0.79	O1	A:PGE412	2.7	21.9	0.4
	O3	A:PGE412	3.0	21.9	0.4
	HD2	A:TYR375	3.0	13.0	0.8
	O	A:HOH939	3.0	40.3	1.0
	O2	A:PGE412	3.1	21.9	0.4
	O4	A:PGE412	3.2	21.9	0.4
	HE2	A:TYR375	3.3	12.7	0.8
	C2	A:PGE412	3.5	21.9	0.4
	C1	A:PGE412	3.7	21.9	0.4
	C3	A:PGE412	3.7	21.9	0.4
	CD2	A:TYR375	3.7	10.9	0.8
	C6	A:PGE412	3.8	21.9	0.4
	CE2	A:TYR375	3.8	10.6	0.8
	C5	A:PGE412	3.9	21.9	0.4
	C4	A:PGE412	3.9	21.9	0.4
	HZ	A:PHE123	4.7	24.6	1.0
	CG	A:TYR375	4.9	10.2	0.9

Sodium binding site 4 out of 4 in 4k8e

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Sodium Binding Sites List in 4k8e

Sodium binding site 4 out of 4 in the OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of OYE1-W116V Complexed with the Aromatic Product of (R)-Carvone Dismutation within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na413 b:30.0 occ:0.59	O2	A:PGE414	2.4	21.9	0.5
	O4	A:PGE414	2.9	21.9	0.5
	O1	A:PGE414	2.9	21.9	0.5
	C4	A:PGE414	2.9	21.9	0.5
	O3	A:PGE414	3.0	21.9	0.5
	C3	A:PGE414	3.1	21.9	0.5
	C5	A:PGE414	3.4	21.9	0.5
	C2	A:PGE414	3.5	21.9	0.5
	C1	A:PGE414	3.6	21.9	0.5
	C6	A:PGE414	3.7	21.9	0.5
	HB2	A:SER308	4.1	11.7	1.0
	HB3	A:SER308	4.3	11.7	1.0
	CB	A:SER308	4.7	9.7	1.0

Reference:

Y.A.Pompeu, B.Sullivan, J.D.Stewart. X‑Ray Crystallography Reveals How Subtle Changes Control the Orientation of Substrate Binding in An Alkene Reductase Acs Catalysis V. 3 2376 2013.
ISSN: ESSN 2155-5435
DOI: 10.1021/CS400622E

Page generated: Mon Oct 7 16:26:51 2024

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