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

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

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

Protein crystallography data

The structure of Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glycerol, PDB code: 3vih 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) 28.00 / 1.03
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 93.155, 68.526, 75.469, 90.00, 95.58, 90.00
R / Rfree (%) 14.8 / 16.8

Other elements in 3vih:

The structure of Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glycerol 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 Glycerol (pdb code 3vih). 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 Glycerol, PDB code: 3vih:

Sodium binding site 1 out of 1 in 3vih

Go back to Sodium Binding Sites List in 3vih
Sodium binding site 1 out of 1 in the Crystal Structure of Beta-Glucosidase From Termite Neotermes Koshunensis in Complex with Glycerol


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 Glycerol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na509

b:15.2
occ:1.00
O A:HOH830 3.1 20.2 1.0
O A:HOH914 3.2 26.4 1.0
ND2 A:ASN180 3.3 11.1 1.0
NZ A:LYS179 3.3 25.1 1.0
CD A:LYS179 3.8 20.4 1.0
CE A:LYS179 3.8 23.1 1.0
CG2 A:VAL120 4.0 13.1 1.0
CG1 A:VAL176 4.2 10.2 1.0
CG A:ASN180 4.2 10.8 1.0
CG1 A:VAL120 4.3 13.7 1.0
OD1 A:ASN180 4.3 13.1 1.0
CB A:VAL120 4.6 12.1 1.0
O A:HOH1045 4.6 40.0 1.0
CG2 A:VAL176 4.6 10.1 1.0
CB A:VAL176 4.8 9.2 1.0
CG A:LYS179 4.9 15.6 1.0
O A:HOH701 5.0 24.4 1.0
CA A:VAL176 5.0 9.2 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: Tue Dec 15 06:29:01 2020

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