Calcium in PDB 5yj7: Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis

All present enzymatic activity of Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis:
3.2.1.21;

The structure of Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis, PDB code: 5yj7 was solved by S.Dong, Y.J.Liu, H.X.Zhou, Y.Xiao, J.Xu, Q.Cui, X.Q.Wang, Y.G.Feng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.31 / 1.61
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.720, 74.750, 102.940, 105.29, 96.10, 90.32
R / Rfree (%)	13.4 / 15.2

The binding sites of Calcium atom in the Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis (pdb code 5yj7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis, PDB code: 5yj7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:16.9 occ:1.00 OD1 A:ASN147 2.3 19.8 1.0 O A:HOH877 2.4 24.5 1.0 O A:HOH773 2.5 21.8 1.0 CG A:ASN147 3.5 19.3 1.0 HD22 A:ASN150 3.7 27.4 1.0 HA A:ASN147 3.9 16.9 1.0 HD21 A:ASN147 4.0 21.4 1.0 O A:HOH1196 4.1 31.8 1.0 HG3 A:GLU143 4.1 38.2 1.0 ND2 A:ASN147 4.2 17.8 1.0 ND2 A:ASN150 4.4 22.9 1.0 HD21 A:ASN150 4.4 27.4 1.0 CA A:ASN147 4.5 14.1 1.0 HB3 A:GLN146 4.6 22.6 1.0 CB A:ASN147 4.6 15.4 1.0 N A:ASN147 4.6 13.9 1.0 H A:ASN147 4.7 16.6 1.0 HB2 A:GLN146 4.8 22.6 1.0 O A:HOH726 4.8 22.4 1.0 HG2 A:GLU143 4.8 38.2 1.0 CG A:GLU143 4.9 31.9 1.0

Calcium binding site 2 out of 2 in the Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca601 b:26.1 occ:1.00 O C:THR506 2.3 30.8 1.0 O C:PRO508 2.3 31.5 1.0 OD2 C:ASP505 2.4 26.1 1.0 OD2 C:ASP510 2.5 29.8 1.0 O C:HOH803 2.5 26.7 1.0 OD1 C:ASP510 2.6 35.6 1.0 CG C:ASP510 2.9 34.3 1.0 CG C:ASP505 3.4 34.8 1.0 C C:THR506 3.5 39.0 1.0 C C:PRO508 3.6 41.1 1.0 HG1 C:THR506 3.7 53.1 1.0 OD1 C:ASP505 3.8 35.4 1.0 N C:PRO508 3.9 45.4 1.0 C C:ALA507 3.9 40.9 1.0 HD2 C:PRO508 4.0 55.4 1.0 HA C:ALA507 4.1 52.6 1.0 O C:HOH749 4.2 35.4 1.0 O C:ALA507 4.3 33.1 1.0 CA C:PRO508 4.3 44.0 1.0 O C:HOH729 4.3 44.0 1.0 N C:ALA507 4.3 37.6 1.0 CA C:ALA507 4.3 43.9 1.0 CB C:ASP510 4.3 30.5 1.0 O C:PRO509 4.4 48.4 1.0 H C:THR506 4.4 49.0 1.0 C C:PRO509 4.4 45.9 1.0 N C:THR506 4.4 40.9 1.0 OG1 C:THR506 4.4 44.2 1.0 HB2 C:PRO508 4.5 55.2 1.0 CA C:THR506 4.5 39.2 1.0 CD C:PRO508 4.5 46.2 1.0 HB3 C:ASP505 4.6 51.0 1.0 N C:PRO509 4.6 46.2 1.0 HA C:PRO509 4.6 55.9 1.0 CB C:ASP505 4.6 42.5 1.0 N C:ASP510 4.7 35.8 1.0 HB2 C:ASP510 4.7 36.6 1.0 CA C:PRO509 4.8 46.6 1.0 HB3 C:ASP510 4.8 36.6 1.0 HA C:ASP510 4.9 43.1 1.0 CB C:PRO508 4.9 46.0 1.0 C C:ASP505 4.9 46.6 1.0 CA C:ASP510 5.0 35.9 1.0

S.Dong, Y.J.Liu, H.X.Zhou, Y.Xiao, J.Xu, Q.Cui, X.Q.Wang, Y.G.Feng. Structural Insight Into the Beta-GH1 Glucosidase BGLN1 From Oleaginous Microalgae Nannochloropsis To Be Published.