Sodium in PDB 2wg9: Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid

Enzymatic activity of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid

All present enzymatic activity of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid:
3.1.1.4;

Protein crystallography data

The structure of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid, PDB code: 2wg9 was solved by J.E.Guy, U.Stahl, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	27.05 / 2.00
*Space group*	P 6₂
*Cell size a, b, c (Å), α, β, γ (°)*	109.159, 109.159, 41.394, 90.00, 90.00, 120.00
*R / R_free (%)*	18.7 / 22

Other elements in 2wg9:

The structure of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid (pdb code 2wg9). 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 Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid, PDB code: 2wg9:

Sodium binding site 1 out of 1 in 2wg9

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Sodium Binding Sites List in 2wg9

Sodium binding site 1 out of 1 in the Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Oryza Sativa (Rice) PLA2, Complex with Octanoic Acid within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Na1126 b:27.9 occ:1.00	O	B:HOH2067	2.3	37.9	1.0
	O	B:ARG87	2.4	19.3	1.0
	O	A:HOH2033	2.4	28.0	1.0
	O	A:HOH2030	2.4	22.9	1.0
	O	A:HOH2032	2.6	17.5	1.0
	OG	B:SER89	2.6	23.0	1.0
	C	B:ARG87	3.6	19.5	1.0
	N	B:SER89	3.7	20.8	1.0
	CB	B:SER89	3.8	22.1	1.0
	OE2	A:GLU48	4.2	15.6	1.0
	C	B:VAL88	4.2	20.5	1.0
	O	A:GLY47	4.2	12.2	1.0
	CA	B:SER89	4.3	21.8	1.0
	O	A:HOH2036	4.3	9.8	1.0
	CA	B:VAL88	4.4	20.1	1.0
	N	B:VAL88	4.4	19.7	1.0
	C	A:GLY47	4.5	12.4	1.0
	CA	B:ARG87	4.6	19.4	1.0
	CB	B:ARG87	4.6	19.6	1.0
	CD	A:GLU48	4.8	13.9	1.0
	O	B:SER89	4.8	22.4	1.0
	C	B:SER89	4.9	21.9	1.0
	O	B:VAL88	4.9	20.3	1.0
	N	A:GLU48	4.9	12.0	1.0

Reference:

J.E.Guy, U.Stahl, Y.Lindqvist. Crystal Structure of A Class Xib Phospholipase A2 (PLA2): Rice (Oryza Sativa) Isoform-2 PLA2 and An Octanoate Complex. J.Biol.Chem. V. 284 19371 2009.
ISSN: ISSN 0021-9258
PubMed: 19457861
DOI: 10.1074/JBC.M109.008466

Page generated: Mon Oct 7 04:39:20 2024

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