Magnesium in PDB 8wdg: Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus

The structure of Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus, PDB code: 8wdg was solved by K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.77 / 0.99
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.675, 98.626, 102.137, 90, 90, 90
R / Rfree (%)	15.8 / 17.1

The binding sites of Magnesium atom in the Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus (pdb code 8wdg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus, PDB code: 8wdg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:9.1 occ:1.00 HE2 A:HIS220 1.9 12.5 0.0 OE2 A:GLU217 2.1 14.1 1.0 O A:HOH552 2.2 18.7 1.0 OD1 A:ASP257 2.3 12.3 1.0 OD2 A:ASP255 2.3 9.5 0.8 OD1 A:ASP255 2.3 9.1 0.8 NE2 A:HIS220 2.6 12.4 1.0 OD2 A:ASP255 2.6 9.5 0.2 CG A:ASP255 2.7 8.0 0.8 HO2 A:XYL403 3.1 18.0 0.0 HD2 A:HIS220 3.1 9.5 1.0 CD A:GLU217 3.1 10.9 1.0 CD2 A:HIS220 3.2 9.5 1.0 CG A:ASP257 3.2 11.0 1.0 HB2 A:ASP255 3.3 8.1 0.2 HD21 A:ASN247 3.3 7.3 1.0 OD2 A:ASP257 3.5 15.9 1.0 O1 A:XYL403 3.5 17.2 1.0 CE1 A:HIS220 3.6 10.9 1.0 CG A:ASP255 3.7 8.0 0.2 OE1 A:GLU217 3.7 16.3 1.0 HO1 A:XYL403 3.8 17.9 1.0 HZ1 A:LYS183 3.8 10.1 1.0 O2 A:XYL403 3.9 17.9 1.0 HE1 A:HIS220 3.9 10.7 1.0 HE3 A:LYS183 3.9 9.0 1.0 HD22 A:ASN247 3.9 7.3 1.0 ND2 A:ASN247 4.0 7.8 1.0 CB A:ASP255 4.0 8.4 0.2 H12 A:XYL403 4.1 19.2 1.0 CB A:ASP255 4.2 8.4 0.8 O A:HOH592 4.2 11.2 1.0 C1 A:XYL403 4.3 20.2 1.0 HG2 A:GLU217 4.3 7.6 1.0 CG A:GLU217 4.4 6.9 1.0 CG A:HIS220 4.4 7.5 1.0 HB2 A:ASP255 4.5 8.1 0.8 NZ A:LYS183 4.6 10.6 1.0 HB3 A:ASP255 4.6 8.1 0.8 HA A:ASP257 4.6 7.7 1.0 ND1 A:HIS220 4.6 9.3 1.0 O A:HOH767 4.6 32.3 1.0 CB A:ASP257 4.6 9.4 1.0 CE A:LYS183 4.7 8.9 1.0 C2 A:XYL403 4.7 19.0 1.0 HB3 A:ASP255 4.7 8.1 0.2 OD2 A:ASP287 4.7 14.6 1.0 H A:ASP257 4.7 7.4 1.0 OD1 A:ASP255 4.7 9.1 0.2 HZ2 A:LYS183 4.8 10.1 1.0 MG A:MG402 4.9 5.9 1.0 HA3 A:GLY219 5.0 5.6 1.0 HG3 A:GLU217 5.0 7.6 1.0 HA A:ASP255 5.0 7.8 0.8 HD2 A:LYS183 5.0 7.8 1.0 HO3 A:XYL403 5.0 18.1 0.0

Magnesium binding site 2 out of 3 in the Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:5.9 occ:1.00 HO4 A:XYL403 1.7 11.8 0.0 OE1 A:GLU217 2.0 16.3 1.0 OD2 A:ASP287 2.1 14.6 1.0 O2 A:XYL403 2.1 17.9 1.0 OE2 A:GLU181 2.1 11.4 1.0 OD2 A:ASP245 2.2 11.6 1.0 O4 A:XYL403 2.3 11.8 1.0 HO2 A:XYL403 2.6 18.0 0.0 CD A:GLU181 3.1 11.3 1.0 CG A:ASP287 3.2 9.4 1.0 CD A:GLU217 3.2 10.9 1.0 C2 A:XYL403 3.3 19.0 1.0 C4 A:XYL403 3.3 14.1 1.0 OE1 A:GLU181 3.3 11.6 1.0 CG A:ASP245 3.3 8.9 1.0 HB3 A:ASP287 3.4 8.2 1.0 HO3 A:XYL403 3.5 18.1 0.0 HB2 A:GLU217 3.5 6.4 1.0 H4 A:XYL403 3.5 13.8 1.0 H2 A:XYL403 3.5 18.7 1.0 C3 A:XYL403 3.5 17.4 1.0 HB2 A:ASP287 3.6 8.2 1.0 CB A:ASP287 3.6 8.3 1.0 O3 A:XYL403 3.7 17.9 1.0 HE1 A:HIS220 3.7 10.7 1.0 HB3 A:ASP245 3.7 7.9 1.0 HB2 A:ASP245 3.9 7.9 1.0 CB A:ASP245 3.9 8.1 1.0 O A:HOH783 3.9 13.5 1.0 O A:HOH552 3.9 18.7 1.0 OE2 A:GLU217 4.0 14.1 1.0 CE1 A:HIS220 4.1 10.9 1.0 CG A:GLU217 4.2 6.9 1.0 CB A:GLU217 4.2 6.5 1.0 OD1 A:ASP287 4.2 9.5 1.0 OD1 A:ASP245 4.3 10.2 1.0 HG3 A:GLU217 4.3 7.6 1.0 CG A:GLU181 4.4 9.1 1.0 C1 A:XYL403 4.5 20.2 1.0 HD22 A:ASN215 4.5 10.0 1.0 H3 A:XYL403 4.5 17.1 1.0 HB3 A:GLU217 4.5 6.4 1.0 HE2 A:HIS220 4.6 12.5 0.0 HD21 A:ASN215 4.6 10.0 1.0 C5 A:XYL403 4.6 12.0 1.0 H12 A:XYL403 4.6 19.2 1.0 HG3 A:GLU181 4.6 9.5 1.0 NE2 A:HIS220 4.6 12.4 1.0 HZ2 A:TRP16 4.6 8.5 1.0 HG2 A:GLU181 4.7 9.5 1.0 H52 A:XYL403 4.7 12.3 1.0 ND2 A:ASN215 4.8 10.4 1.0 H51 A:XYL403 4.8 12.3 1.0 HO1 A:XYL403 4.9 17.9 1.0 ND1 A:HIS220 4.9 9.3 1.0 MG A:MG401 4.9 9.1 1.0 O1 A:XYL403 4.9 17.2 1.0

Magnesium binding site 3 out of 3 in the Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Subatomic Crystal Structure of Glucose Isomerase From Streptomyces Rubiginosus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:11.9 occ:1.00 H A:ASP264 2.0 6.8 1.0 H A:GLN249 2.1 5.8 1.0 OE1 A:GLN222 2.7 8.9 1.0 HA2 A:GLY248 2.7 6.2 1.0 O A:HOH742 2.9 8.8 1.0 N A:ASP264 2.9 6.7 1.0 HA3 A:GLY263 2.9 8.2 1.0 N A:GLN249 3.0 5.8 1.0 HB3 A:ASP264 3.0 7.2 1.0 O A:GLN249 3.1 7.6 1.0 HE21 A:GLN222 3.1 8.2 1.0 HG11 A:VAL218 3.4 6.3 1.0 CA A:GLY248 3.5 6.4 1.0 HB3 A:GLN249 3.5 6.2 1.0 HG12 A:VAL218 3.5 6.3 1.0 O A:ALA262 3.5 8.9 1.0 CD A:GLN222 3.6 8.0 1.0 CB A:ASP264 3.6 7.2 1.0 HB2 A:ASP264 3.6 7.2 1.0 O A:HOH695 3.7 8.3 1.0 NE2 A:GLN222 3.7 8.4 1.0 CA A:GLY263 3.7 8.6 1.0 C A:GLY248 3.7 5.8 1.0 C A:GLY263 3.7 7.3 1.0 CA A:ASP264 3.7 6.5 1.0 HA3 A:GLY248 3.8 6.2 1.0 C A:GLN249 3.8 6.4 1.0 CA A:GLN249 3.8 5.5 1.0 CG1 A:VAL218 3.9 6.6 1.0 O A:ASP264 4.1 6.7 1.0 CB A:GLN249 4.2 6.3 1.0 HG13 A:VAL218 4.2 6.3 1.0 C A:ASP264 4.3 6.2 1.0 HA2 A:GLY263 4.3 8.2 1.0 O A:ASN247 4.4 6.5 1.0 O A:HOH639 4.4 15.9 1.0 C A:ALA262 4.5 7.5 1.0 HB2 A:GLN249 4.5 6.2 1.0 HE22 A:GLN222 4.5 8.2 1.0 HA A:ASP264 4.6 6.6 1.0 N A:GLY263 4.6 8.3 1.0 N A:GLY248 4.7 6.1 1.0 HA A:GLN249 4.7 5.9 1.0 HB3 A:ALA267 4.7 6.4 1.0 O A:GLY248 4.9 7.1 1.0 O A:GLY263 5.0 9.6 1.0 C A:ASN247 5.0 5.5 1.0

K.H.Nam, K.H.Nam. N/A N/A.