Sodium in PDB 3vij: Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose

Enzymatic activity of Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose

All present enzymatic activity of Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose:
3.2.1.21;

Protein crystallography data

The structure of Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose, PDB code: 3vij was solved by W.Y.Jeng, C.I.Liu, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	26.40 / 1.03
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	92.948, 68.403, 75.052, 90.00, 95.48, 90.00
*R / R_free (%)*	12 / 13.5

Other elements in 3vij:

The structure of Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose (pdb code 3vij). 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 Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose, PDB code: 3vij:

Sodium binding site 1 out of 1 in 3vij

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Sodium Binding Sites List in 3vij

Sodium binding site 1 out of 1 in the Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose

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 Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glucose within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na509 b:14.9 occ:1.00	O	A:HOH856	3.0	19.8	1.0
	NZ	A:LYS179	3.2	24.9	1.0
	ND2	A:ASN180	3.2	9.5	1.0
	O	A:HOH779	3.3	27.5	1.0
	CE	A:LYS179	3.8	22.6	1.0
	CD	A:LYS179	3.9	19.9	1.0
	CG2	A:VAL120	4.0	11.5	1.0
	CG1	A:VAL176	4.2	8.5	1.0
	CG	A:ASN180	4.2	10.2	1.0
	CG1	A:VAL120	4.2	12.0	1.0
	OD1	A:ASN180	4.3	12.1	1.0
	O	A:HOH1018	4.4	41.8	1.0
	CB	A:VAL120	4.5	10.3	1.0
	CG2	A:VAL176	4.6	8.2	1.0
	CB	A:VAL176	4.8	7.3	1.0
	O	A:HOH864	4.9	24.3	1.0
	CA	A:VAL176	5.0	7.2	1.0
	CG	A:LYS179	5.0	14.7	1.0

Reference:

W.Y.Jeng, N.C.Wang, C.T.Lin, W.J.Chang, C.I.Liu, A.H.J.Wang. High-Resolution Structures of Neotermes Koshunensis Beta-Glucosidase Mutants Provide Insights Into the Catalytic Mechanism and the Synthesis of Glucoconjugates Acta Crystallogr.,Sect.D V. 68 829 2012.
ISSN: ISSN 0907-4449
PubMed: 22751668
DOI: 10.1107/S0907444912013224

Page generated: Mon Oct 7 13:51:31 2024

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