Sodium in PDB 3akg: Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose

Enzymatic activity of Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose

All present enzymatic activity of Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose:
3.2.1.55;

Protein crystallography data

The structure of Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose, PDB code: 3akg was solved by Z.Fujimoto, H.Ichinose, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	40.42 / 1.80
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	41.052, 91.765, 135.053, 90.00, 90.00, 90.00
*R / R_free (%)*	18.7 / 22.1

Other elements in 3akg:

The structure of Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose (pdb code 3akg). 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 Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose, PDB code: 3akg:

Sodium binding site 1 out of 1 in 3akg

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Sodium Binding Sites List in 3akg

Sodium binding site 1 out of 1 in the Crystal Structure of Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose

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 Exo-1,5-Alpha-L-Arabinofuranosidase Complexed with Alpha-1,5-L-Arabinofuranobiose within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na502 b:25.1 occ:1.00	OE2	A:GLU79	2.2	20.6	1.0
	O	A:HOH718	2.3	24.5	1.0
	O	A:HOH706	2.3	18.5	1.0
	O	A:HOH686	2.3	17.4	1.0
	O	A:HOH693	2.4	25.5	1.0
	CE1	A:HIS260	3.2	22.6	1.0
	CD	A:GLU79	3.4	19.8	1.0
	O	A:HOH785	3.5	31.6	1.0
	CG	A:GLU79	3.8	19.4	1.0
	O	A:PRO198	3.9	16.3	1.0
	ND1	A:HIS260	4.0	21.1	1.0
	O	A:HOH620	4.0	19.1	1.0
	NE2	A:HIS260	4.0	20.9	1.0
	O	A:ASN261	4.4	17.9	1.0
	OE1	A:GLU79	4.4	18.3	1.0
	O	A:HOH638	4.7	22.3	1.0
	CA	A:GLY197	4.7	17.1	1.0
	O	A:ASP135	4.7	17.7	1.0
	C	A:GLY197	4.7	16.7	1.0
	CB	A:THR137	4.8	15.5	1.0
	O	A:ALA136	4.9	15.9	1.0
	O	A:GLY197	4.9	17.5	1.0

Reference:

Z.Fujimoto, H.Ichinose, T.Maehara, M.Honda, M.Kitaoka, S.Kaneko. Crystal Structure of An Exo-1,5-{Alpha}-L-Arabinofuranosidase From Streptomyces Avermitilis Provides Insights Into the Mechanism of Substrate Discrimination Between Exo- and Endo-Type Enzymes in Glycoside Hydrolase Family 43. J.Biol.Chem. V. 285 34134 2010.
ISSN: ISSN 0021-9258
PubMed: 20739278
DOI: 10.1074/JBC.M110.164251

Page generated: Mon Oct 7 05:50:28 2024

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