Manganese in PDB 7dmm: Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants

All present enzymatic activity of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants:
5.3.1.5;

The structure of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants, PDB code: 7dmm was solved by Y.Suzuki, N.Maita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.16 / 0.99
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.61, 98.46, 102.3, 90, 90, 90
R / Rfree (%)	15.7 / 16.6

The structure of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Manganese atom in the Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants (pdb code 7dmm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants, PDB code: 7dmm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:7.4 occ:1.00 OE2 A:GLU217 2.1 6.2 1.0 O A:HOH521 2.2 9.0 1.0 OD1 A:ASP257 2.2 7.3 1.0 OD2 A:ASP255 2.2 8.4 1.0 OD1 A:ASP255 2.3 6.7 1.0 NE2 A:HIS220 2.3 6.6 1.0 CG A:ASP255 2.6 6.7 1.0 CD A:GLU217 3.0 5.1 1.0 CD2 A:HIS220 3.1 6.3 1.0 CG A:ASP257 3.1 6.6 1.0 OE1 A:GLU217 3.2 7.1 1.0 CE1 A:HIS220 3.3 6.3 1.0 OD2 A:ASP257 3.4 10.1 1.0 O A:HOH648 3.7 13.6 1.0 ND2 A:ASN247 4.0 5.7 1.0 O A:HOH587 4.1 6.5 1.0 CB A:ASP255 4.1 7.1 1.0 O1 A:GOL401 4.3 7.8 1.0 CG A:HIS220 4.3 5.4 1.0 CG A:GLU217 4.3 5.2 1.0 ND1 A:HIS220 4.4 6.1 1.0 OD2 A:ASP287 4.5 7.3 1.0 CB A:ASP257 4.5 6.3 1.0 MN A:MN405 4.7 9.2 1.0 CE A:LYS183 4.9 6.9 1.0 CA A:ASP257 5.0 5.4 1.0 NZ A:LYS183 5.0 9.5 1.0

Manganese binding site 2 out of 2 in the Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of A Glucose Isomerase Crystal Grown in An Aqueous Glycerol Solution Without Any Precipitants within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn405 b:9.2 occ:1.00 OD2 A:ASP245 2.0 7.1 1.0 OE1 A:GLU217 2.1 7.1 1.0 OE2 A:GLU181 2.1 6.2 1.0 OD2 A:ASP287 2.1 7.3 1.0 O2 A:GOL401 2.2 6.8 1.0 O1 A:GOL401 2.3 7.8 1.0 CD A:GLU181 3.0 6.0 1.0 C1 A:GOL401 3.1 7.8 1.0 C2 A:GOL401 3.1 7.4 1.0 CG A:ASP287 3.2 6.1 1.0 CG A:ASP245 3.3 5.4 1.0 CD A:GLU217 3.3 5.1 1.0 OE1 A:GLU181 3.3 7.1 1.0 CB A:ASP287 3.6 6.0 1.0 O A:HOH521 3.8 9.0 1.0 CB A:ASP245 3.9 5.7 1.0 CE1 A:HIS220 4.0 6.3 1.0 CG A:GLU217 4.1 5.2 1.0 O A:HOH663 4.1 8.3 1.0 CB A:GLU217 4.1 5.1 1.0 OD1 A:ASP245 4.2 6.2 1.0 OE2 A:GLU217 4.2 6.2 1.0 OD1 A:ASP287 4.3 6.9 1.0 CG A:GLU181 4.3 6.1 1.0 C3 A:GOL401 4.4 7.1 1.0 NE2 A:HIS220 4.6 6.6 1.0 MN A:MN404 4.7 7.4 1.0 ND1 A:HIS220 4.7 6.1 1.0 ND2 A:ASN215 4.9 7.3 1.0

Y.Suzuki, N.Ikemitsu, N.Maita. Extraordinarily Fast Growth of High-Quality Glucose Isomerase Crystals Simply By Concentration in A Precipitant-Free Solution with A Cryoprotectant To Be Published.