Manganese 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:

Calcium

(Ca)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the The 1.03 Angstrom Structure (P212121) of Glucose Isomerase Crystallized in High-Strength Agarose Hydrogel, PDB code: 5avn:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn401 b:7.6 occ:1.00 OE2 A:GLU217 2.1 7.0 1.0 O A:HOH675 2.1 9.9 1.0 OD1 A:ASP257 2.2 7.9 1.0 OD2 A:ASP255 2.2 8.5 1.0 OD1 A:ASP255 2.3 7.3 1.0 NE2 A:HIS220 2.4 7.4 1.0 CG A:ASP255 2.6 7.1 1.0 CD A:GLU217 3.0 6.7 1.0 CD2 A:HIS220 3.1 6.9 1.0 CG A:ASP257 3.2 8.0 1.0 OE1 A:GLU217 3.3 7.3 1.0 CE1 A:HIS220 3.4 7.0 1.0 OD2 A:ASP257 3.5 12.5 1.0 O A:HOH761 3.7 13.5 1.0 O A:HOH520 3.9 22.5 1.0 O A:HOH621 4.0 7.5 1.0 ND2 A:ASN247 4.0 6.6 1.0 CB A:ASP255 4.1 7.0 1.0 O A:HOH610 4.2 17.9 1.0 CG A:HIS220 4.3 5.8 1.0 ND1 A:HIS220 4.4 6.3 1.0 CG A:GLU217 4.4 6.1 1.0 CB A:ASP257 4.5 7.8 1.0 CE A:LYS183 4.8 7.2 1.0 NZ A:LYS183 4.8 9.0 1.0 CA A:CA402 4.9 10.3 0.2 N A:ASP257 4.9 6.4 1.0 CA A:ASP257 4.9 7.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn401 b:7.7 occ:1.00 OE2 B:GLU217 2.1 6.8 1.0 O B:HOH687 2.1 10.2 1.0 OD1 B:ASP257 2.2 7.6 1.0 OD2 B:ASP255 2.2 8.0 1.0 OD1 B:ASP255 2.3 7.5 1.0 NE2 B:HIS220 2.4 7.3 1.0 CG B:ASP255 2.6 7.1 1.0 CD B:GLU217 3.1 7.1 1.0 CD2 B:HIS220 3.1 6.4 1.0 CG B:ASP257 3.2 7.5 1.0 CE1 B:HIS220 3.4 7.3 1.0 OE1 B:GLU217 3.4 7.9 1.0 OD2 B:ASP257 3.5 11.4 1.0 O B:HOH764 3.7 12.3 1.0 O B:HOH521 4.0 18.1 1.0 ND2 B:ASN247 4.0 7.0 1.0 O B:HOH642 4.0 7.8 1.0 CB B:ASP255 4.1 6.9 1.0 O B:HOH556 4.1 10.7 0.5 CG B:HIS220 4.3 6.2 1.0 ND1 B:HIS220 4.4 7.0 1.0 CG B:GLU217 4.4 6.7 1.0 CB B:ASP257 4.5 7.5 1.0 O B:HOH556 4.6 16.9 0.5 CE B:LYS183 4.8 7.5 1.0 NZ B:LYS183 4.9 8.7 1.0 O B:HOH769 4.9 15.8 0.5 CA B:ASP257 4.9 6.9 1.0 CA B:CA402 4.9 17.0 0.3 N B:ASP257 4.9 6.7 1.0 OD2 B:ASP287 5.0 8.4 1.0 CA B:ASP255 5.0 6.2 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