Calcium in PDB 5avn: The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel

All present enzymatic activity of The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel:
5.3.1.5;

The structure of The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel, PDB code: 5avn was solved by S.Sugiyama, N.Shimizu, N.Maruyama, G.Sazaki, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, H.Matsumura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.03
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.082, 98.285, 85.777, 90.00, 90.00, 90.00
R / Rfree (%)	12.7 / 15

The structure of The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel (pdb code 5avn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel, PDB code: 5avn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:10.3 occ:0.20 OE1 A:GLU217 1.9 7.3 1.0 OE2 A:GLU181 1.9 8.6 1.0 OD2 A:ASP245 2.0 8.1 1.0 OD2 A:ASP287 2.0 7.8 1.0 CD A:GLU181 2.8 8.6 1.0 CG A:ASP287 3.0 6.4 1.0 CG A:ASP245 3.1 6.7 1.0 CD A:GLU217 3.1 6.7 1.0 CB A:ASP287 3.3 6.8 1.0 O A:HOH708 3.4 21.2 1.0 OE1 A:GLU181 3.4 11.3 1.0 O A:HOH711 3.5 8.8 0.5 O A:HOH675 3.6 9.9 1.0 CB A:ASP245 3.6 6.9 1.0 O A:HOH711 3.7 12.1 0.5 CG A:GLU217 3.8 6.1 1.0 CG A:GLU181 3.8 7.5 1.0 CB A:GLU217 3.8 6.0 1.0 OD1 A:ASP287 4.1 7.3 1.0 OD1 A:ASP245 4.1 7.5 1.0 OE2 A:GLU217 4.1 7.0 1.0 CE1 A:HIS220 4.2 7.0 1.0 O A:HOH569 4.7 16.9 1.0 ND1 A:HIS220 4.8 6.3 1.0 ND2 A:ASN215 4.8 7.3 1.0 NE2 A:HIS220 4.8 7.4 1.0 CA A:ASP287 4.8 6.4 1.0 O A:HOH610 4.8 17.9 1.0 MN A:MN401 4.9 7.6 1.0

Calcium binding site 2 out of 2 in the The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:17.0 occ:0.30 OE2 B:GLU181 1.9 9.2 1.0 OE1 B:GLU217 1.9 7.9 1.0 OD2 B:ASP287 1.9 8.4 1.0 OD2 B:ASP245 2.0 8.4 1.0 CD B:GLU181 2.8 8.8 1.0 CG B:ASP287 2.9 6.5 1.0 CD B:GLU217 3.1 7.1 1.0 CG B:ASP245 3.1 7.1 1.0 CB B:ASP287 3.4 7.0 1.0 O B:HOH769 3.4 16.8 0.5 OE1 B:GLU181 3.5 12.1 1.0 O B:HOH730 3.5 12.5 1.0 O B:HOH687 3.5 10.2 1.0 CB B:ASP245 3.7 7.0 1.0 O B:HOH769 3.8 15.8 0.5 CG B:GLU181 3.8 7.5 1.0 CG B:GLU217 3.9 6.7 1.0 CB B:GLU217 3.9 6.5 1.0 OD1 B:ASP287 4.1 7.5 1.0 OE2 B:GLU217 4.1 6.8 1.0 OD1 B:ASP245 4.2 7.8 1.0 CE1 B:HIS220 4.2 7.3 1.0 O B:HOH556 4.4 16.9 0.5 O B:HOH545 4.8 17.4 1.0 ND1 B:HIS220 4.8 7.0 1.0 NE2 B:HIS220 4.8 7.3 1.0 ND2 B:ASN215 4.9 7.6 1.0 CA B:ASP287 4.9 6.8 1.0 O B:HOH556 4.9 10.7 0.5 MN B:MN401 4.9 7.7 1.0

S.Sugiyama, M.Maruyama, G.Sazaki, M.Hirose, H.Adachi, K.Takano, S.Murakami, T.Inoue, Y.Mori, H.Matsumura. Growth of Protein Crystals in Hydrogels Prevents Osmotic Shock J.Am.Chem.Soc. V. 134 5786 2012.
ISSN: ESSN 1520-5126
PubMed: 22435400
DOI: 10.1021/JA301584Y