Sodium in PDB 1l8s: Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions)

Enzymatic activity of Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions)

All present enzymatic activity of Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions):
3.1.1.4;

Protein crystallography data

The structure of Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions), PDB code: 1l8s was solved by Y.H.Pan, B.J.Bahnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	8.00 / 1.55
*Space group*	P 3₁
*Cell size a, b, c (Å), α, β, γ (°)*	65.166, 65.166, 62.963, 90.00, 90.00, 120.00
*R / R_free (%)*	18.3 / 24.6

Other elements in 1l8s:

The structure of Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions) (pdb code 1l8s). 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 Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions), PDB code: 1l8s:

Sodium binding site 1 out of 1 in 1l8s

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Sodium Binding Sites List in 1l8s

Sodium binding site 1 out of 1 in the Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Carboxylic Ester Hydrolase Complex (Dimeric PLA2 + Lpc-Ether + Acetate + Phosphate Ions) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na315 b:27.2 occ:1.00	OD1	A:ASN23	3.0	39.8	1.0
	O	A:HOH408	3.1	25.8	1.0
	O	A:LEU19	3.2	28.5	1.0
	N	B:TRP3	3.3	20.7	1.0
	N	B:LEU2	3.5	19.3	1.0
	CB	B:LEU2	3.5	23.2	1.0
	CD1	B:TRP3	3.5	23.5	1.0
	O	A:HOH435	3.5	29.7	1.0
	CG	A:ASN23	3.8	33.7	1.0
	CA	B:LEU2	3.9	20.8	1.0
	CB	A:ASN23	4.0	34.5	1.0
	C	B:LEU2	4.0	21.9	1.0
	C	A:LEU19	4.1	25.3	1.0
	CG	B:TRP3	4.2	20.8	1.0
	CB	B:TRP3	4.2	25.1	1.0
	CA	B:TRP3	4.3	21.2	1.0
	O	B:TYR69	4.3	28.2	1.0
	C	B:ALA1	4.4	27.8	1.0
	CB	B:ALA1	4.4	19.9	1.0
	CG	B:LEU2	4.5	17.0	1.0
	CB	A:LEU19	4.6	24.2	1.0
	NE1	B:TRP3	4.6	28.1	1.0
	O	A:ASN23	4.7	29.8	1.0
	CA	A:MET20	4.7	24.4	1.0
	N	A:MET20	4.8	21.7	1.0
	CD2	B:LEU2	4.9	19.7	1.0
	CA	B:ALA1	4.9	20.4	1.0
	CA	A:LEU19	4.9	25.1	1.0

Reference:

Y.H.Pan, B.-Z.Yu, O.G.Berg, M.K.Jain, B.J.Bahnson. Crystal Structure of Phospholipase A2 Complex with the Hydrolysis Products of Platelet Activating Factor: Equilibrium Binding of Fatty Acid and Lysophospholipid-Ether at the Active Site May Be Mutually Exclusive Biochemistry V. 41 14790 2002.
ISSN: ISSN 0006-2960
PubMed: 12475227
DOI: 10.1021/BI026922R

Page generated: Sun Oct 6 20:16:25 2024

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