Magnesium in PDB 7cjo: Crystal Structure of Metal-Bound State of Glucose Isomerase

All present enzymatic activity of Crystal Structure of Metal-Bound State of Glucose Isomerase:
5.3.1.5;

The structure of Crystal Structure of Metal-Bound State of Glucose Isomerase, PDB code: 7cjo 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)	31.46 / 1.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.718, 92.765, 98.822, 90, 90, 90
R / Rfree (%)	13.5 / 14.7

The binding sites of Magnesium atom in the Crystal Structure of Metal-Bound State of Glucose Isomerase (pdb code 7cjo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Metal-Bound State of Glucose Isomerase, PDB code: 7cjo:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Metal-Bound State of Glucose Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Metal-Bound State of Glucose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg412 b:6.3 occ:1.00 OE2 A:GLU217 2.0 17.0 1.0 OD2 A:ASP287 2.0 13.0 1.0 OE2 A:GLU181 2.1 15.8 1.0 OD2 A:ASP245 2.3 13.2 1.0 O1 A:EDO401 2.3 21.0 1.0 HO1 A:EDO401 2.5 25.2 1.0 O A:HOH664 2.6 32.9 1.0 CD A:GLU181 3.0 13.8 1.0 CG A:ASP287 3.1 10.0 1.0 CD A:GLU217 3.2 8.4 1.0 OE1 A:GLU181 3.3 12.5 1.0 C1 A:EDO401 3.3 18.9 1.0 H11 A:EDO401 3.4 22.8 1.0 HB3 A:ASP287 3.4 8.2 1.0 HB2 A:ASP287 3.4 8.2 1.0 CG A:ASP245 3.5 8.4 1.0 HB2 A:GLU217 3.5 7.7 1.0 CB A:ASP287 3.5 6.8 1.0 H12 A:EDO401 3.6 22.8 1.0 HE1 A:HIS220 3.7 10.0 1.0 HB3 A:ASP245 3.7 6.7 1.0 O A:HOH520 3.8 17.1 1.0 O A:HOH719 3.9 17.7 1.0 CB A:ASP245 4.0 5.6 1.0 OE1 A:GLU217 4.0 10.1 1.0 HB2 A:ASP245 4.1 6.7 1.0 CE1 A:HIS220 4.1 8.3 1.0 CG A:GLU217 4.2 5.0 1.0 OD1 A:ASP287 4.2 9.1 1.0 CB A:GLU217 4.2 6.4 1.0 CG A:GLU181 4.3 7.5 1.0 HG3 A:GLU217 4.3 6.0 1.0 HG3 A:GLU181 4.4 9.0 1.0 OD1 A:ASP245 4.5 10.3 1.0 HG2 A:GLU181 4.5 9.0 1.0 HB3 A:GLU217 4.6 7.7 1.0 HD21 A:ASN215 4.6 9.2 1.0 NE2 A:HIS220 4.6 10.9 1.0 C2 A:EDO401 4.6 19.9 1.0 HZ2 A:TRP16 4.6 9.4 1.0 HD22 A:ASN215 4.8 9.2 1.0 H22 A:EDO401 4.8 23.8 1.0 MG A:MG413 4.9 6.6 1.0 ND1 A:HIS220 4.9 9.5 1.0 O A:HOH770 4.9 21.3 1.0 ND2 A:ASN215 5.0 7.7 1.0 H21 A:EDO401 5.0 23.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Metal-Bound State of Glucose Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Metal-Bound State of Glucose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:6.6 occ:1.00 OE1 A:GLU217 2.1 10.1 1.0 O A:HOH719 2.2 17.7 1.0 OD1 A:ASP257 2.3 11.6 1.0 OD2 A:ASP255 2.4 15.0 1.0 OD1 A:ASP255 2.4 13.6 1.0 NE2 A:HIS220 2.6 10.9 1.0 CG A:ASP255 2.7 14.5 1.0 CD A:GLU217 3.1 8.4 1.0 HD2 A:HIS220 3.2 11.2 1.0 CD2 A:HIS220 3.2 9.3 1.0 CG A:ASP257 3.3 15.3 1.0 HD21 A:ASN247 3.3 8.6 1.0 O A:HOH770 3.4 21.3 1.0 OD2 A:ASP257 3.5 19.5 1.0 OE2 A:GLU217 3.6 17.0 1.0 CE1 A:HIS220 3.7 8.3 1.0 HD22 A:ASN247 3.9 8.6 1.0 ND2 A:ASN247 3.9 7.1 1.0 O A:HOH664 4.0 32.9 1.0 HZ2 A:LYS183 4.0 14.6 1.0 HE3 A:LYS183 4.0 9.7 1.0 HE1 A:HIS220 4.0 10.0 1.0 O A:HOH647 4.1 10.2 1.0 CB A:ASP255 4.2 10.2 1.0 HG2 A:GLU217 4.3 6.0 1.0 CG A:GLU217 4.4 5.0 1.0 CG A:HIS220 4.4 6.4 1.0 HZ1 A:LYS183 4.5 14.6 1.0 OD2 A:ASP287 4.5 13.0 1.0 NZ A:LYS183 4.5 12.1 1.0 HB2 A:ASP255 4.5 12.3 1.0 HB3 A:ASP255 4.6 12.3 1.0 H A:ASP257 4.6 7.2 1.0 HA A:ASP257 4.6 6.3 1.0 ND1 A:HIS220 4.7 9.5 1.0 CB A:ASP257 4.7 7.3 1.0 O A:HOH678 4.7 36.5 1.0 CE A:LYS183 4.7 8.1 1.0 MG A:MG412 4.9 6.3 1.0 HD2 A:LYS183 4.9 6.2 1.0 HG3 A:GLU217 5.0 6.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Metal-Bound State of Glucose Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Metal-Bound State of Glucose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1211 b:6.3 occ:1.00 OE2 B:GLU217 2.0 13.7 1.0 OD2 B:ASP287 2.1 12.4 1.0 OE2 B:GLU181 2.1 15.9 1.0 OD2 B:ASP245 2.3 12.7 1.0 O1 B:EDO1203 2.3 24.0 1.0 HO1 B:EDO1203 2.4 28.8 1.0 CD B:GLU181 3.0 13.9 1.0 CG B:ASP287 3.1 9.2 1.0 CD B:GLU217 3.2 10.2 1.0 H11 B:EDO1203 3.2 32.4 1.0 OE1 B:GLU181 3.2 12.7 1.0 C1 B:EDO1203 3.2 27.0 1.0 HB3 B:ASP287 3.4 8.6 1.0 HB2 B:ASP287 3.4 8.6 1.0 CG B:ASP245 3.5 8.6 1.0 HB2 B:GLU217 3.5 5.6 1.0 CB B:ASP287 3.5 7.2 1.0 H12 B:EDO1203 3.5 32.4 1.0 HE1 B:HIS220 3.6 9.6 1.0 HB3 B:ASP245 3.7 6.8 1.0 O B:HOH1308 3.8 15.4 1.0 O B:HOH1513 4.0 20.1 1.0 CB B:ASP245 4.0 5.7 1.0 OE1 B:GLU217 4.0 9.8 1.0 HB2 B:ASP245 4.0 6.8 1.0 CE1 B:HIS220 4.1 8.0 1.0 CG B:GLU217 4.2 5.5 1.0 OD1 B:ASP287 4.2 8.9 1.0 CB B:GLU217 4.2 4.7 1.0 CG B:GLU181 4.3 8.8 1.0 HG3 B:GLU217 4.3 6.6 1.0 HG3 B:GLU181 4.5 10.5 1.0 OD1 B:ASP245 4.5 10.2 1.0 HG2 B:GLU181 4.5 10.5 1.0 HD21 B:ASN215 4.6 9.0 1.0 C2 B:EDO1203 4.6 19.8 1.0 HB3 B:GLU217 4.6 5.6 1.0 NE2 B:HIS220 4.6 9.7 1.0 HZ2 B:TRP16 4.6 8.4 1.0 H21 B:EDO1203 4.7 23.8 1.0 HD22 B:ASN215 4.8 9.0 1.0 ND1 B:HIS220 4.9 8.7 1.0 O B:HOH1579 4.9 18.7 1.0 MG B:MG1212 4.9 6.1 1.0 ND2 B:ASN215 5.0 7.5 1.0 H22 B:EDO1203 5.0 23.8 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Metal-Bound State of Glucose Isomerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Metal-Bound State of Glucose Isomerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1212 b:6.1 occ:1.00 OE1 B:GLU217 2.1 9.8 1.0 O B:HOH1513 2.2 20.1 1.0 OD1 B:ASP257 2.3 10.8 1.0 OD2 B:ASP255 2.4 14.6 1.0 OD1 B:ASP255 2.4 12.4 1.0 NE2 B:HIS220 2.6 9.7 1.0 CG B:ASP255 2.7 16.2 1.0 HD2 B:HIS220 3.1 8.0 1.0 CD B:GLU217 3.2 10.2 1.0 CD2 B:HIS220 3.2 6.7 1.0 CG B:ASP257 3.3 14.6 1.0 HD21 B:ASN247 3.4 8.2 1.0 OD2 B:ASP257 3.5 22.0 1.0 O B:HOH1579 3.5 18.7 1.0 OE2 B:GLU217 3.7 13.7 1.0 CE1 B:HIS220 3.7 8.0 1.0 HE3 B:LYS183 3.9 10.1 1.0 HD22 B:ASN247 3.9 8.2 1.0 HZ2 B:LYS183 4.0 13.1 1.0 ND2 B:ASN247 4.0 6.8 1.0 HE1 B:HIS220 4.0 9.6 1.0 O B:HOH1422 4.1 8.6 1.0 CB B:ASP255 4.2 10.5 1.0 HG2 B:GLU217 4.3 6.6 1.0 CG B:GLU217 4.4 5.5 1.0 CG B:HIS220 4.4 4.9 1.0 HZ1 B:LYS183 4.4 13.1 1.0 NZ B:LYS183 4.5 10.9 1.0 OD2 B:ASP287 4.5 12.4 1.0 HB2 B:ASP255 4.6 12.7 1.0 HB3 B:ASP255 4.6 12.7 1.0 CE B:LYS183 4.6 8.4 1.0 ND1 B:HIS220 4.6 8.7 1.0 HA B:ASP257 4.6 8.1 1.0 H B:ASP257 4.6 6.7 1.0 CB B:ASP257 4.7 7.3 1.0 O B:HOH1488 4.8 28.0 1.0 HD2 B:LYS183 4.9 7.4 1.0 MG B:MG1211 4.9 6.3 1.0 HG3 B:GLU217 5.0 6.6 1.0

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