Atomistry » Magnesium » PDB 9gch-9h4e » 9gre
Atomistry »
  Magnesium »
    PDB 9gch-9h4e »
      9gre »

Magnesium in PDB 9gre: Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site

Enzymatic activity of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site

All present enzymatic activity of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site:
5.3.1.5;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site (pdb code 9gre). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site, PDB code: 9gre:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 9gre

Go back to Magnesium Binding Sites List in 9gre
Magnesium binding site 1 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:54.7
occ:1.00
 OD2 A:ASP255 2.1 71.0 1.0
OE2 A:GLU217 2.3 69.5 1.0
NE2 A:HIS220 2.5 65.4 1.0
OD1 A:ASP257 2.6 75.7 1.0
CG A:ASP255 2.9 69.4 1.0
OD1 A:ASP255 3.0 71.6 1.0
OD2 A:ASP257 3.2 75.8 1.0
CG A:ASP257 3.2 73.7 1.0
CD2 A:HIS220 3.3 60.5 1.0
CE1 A:HIS220 3.3 63.9 1.0
CD A:GLU217 3.4 67.9 1.0
OE1 A:GLU217 3.9 71.1 1.0
ND2 A:ASN247 4.2 62.3 1.0
ND1 A:HIS220 4.2 62.0 1.0
CG A:HIS220 4.3 57.2 1.0
CB A:ASP255 4.3 64.8 1.0
CG A:GLU217 4.6 60.6 1.0
NZ A:LYS183 4.6 58.4 1.0
CB A:ASP257 4.7 66.0 1.0
OD2 A:ASP287 4.7 76.0 1.0
CE A:LYS183 4.8 52.1 1.0
MG A:MG402 4.8 70.7 1.0

Magnesium binding site 2 out of 8 in 9gre

Go back to Magnesium Binding Sites List in 9gre
Magnesium binding site 2 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:70.7
occ:1.00
 OE1 A:GLU217 2.1 71.1 1.0
OE2 A:GLU181 2.1 78.3 1.0
OD2 A:ASP287 2.1 76.0 1.0
OD2 A:ASP245 2.7 75.5 1.0
CD A:GLU181 3.1 74.9 1.0
CD A:GLU217 3.3 67.9 1.0
CG A:ASP287 3.3 73.3 1.0
OE1 A:GLU181 3.4 77.9 1.0
CG A:ASP245 3.8 69.6 1.0
O A:HOH501 3.9 30.0 1.0
OE2 A:GLU217 3.9 69.5 1.0
CB A:ASP287 4.0 66.4 1.0
CE1 A:HIS220 4.1 63.9 1.0
OD1 A:ASP287 4.2 73.5 1.0
CB A:ASP245 4.4 58.6 1.0
CG A:GLU217 4.4 60.6 1.0
CG A:GLU181 4.5 62.0 1.0
CB A:GLU217 4.6 55.0 1.0
ND1 A:HIS220 4.8 62.0 1.0
OD1 A:ASP245 4.8 71.5 1.0
MG A:MG401 4.8 54.7 1.0
NE2 A:HIS220 4.9 65.4 1.0

Magnesium binding site 3 out of 8 in 9gre

Go back to Magnesium Binding Sites List in 9gre
Magnesium binding site 3 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:54.7
occ:1.00
 OD2 B:ASP255 2.1 71.0 1.0
OE2 B:GLU217 2.3 69.5 1.0
NE2 B:HIS220 2.5 65.4 1.0
OD1 B:ASP257 2.6 75.7 1.0
CG B:ASP255 2.9 69.4 1.0
OD1 B:ASP255 3.0 71.6 1.0
OD2 B:ASP257 3.2 75.8 1.0
CG B:ASP257 3.2 73.7 1.0
CD2 B:HIS220 3.3 60.5 1.0
CE1 B:HIS220 3.3 63.9 1.0
CD B:GLU217 3.4 67.9 1.0
OE1 B:GLU217 3.9 71.1 1.0
ND2 B:ASN247 4.2 62.3 1.0
ND1 B:HIS220 4.2 62.0 1.0
CG B:HIS220 4.3 57.2 1.0
CB B:ASP255 4.3 64.8 1.0
CG B:GLU217 4.6 60.6 1.0
NZ B:LYS183 4.6 58.4 1.0
OD2 B:ASP287 4.7 76.0 1.0
CB B:ASP257 4.7 66.0 1.0
CE B:LYS183 4.8 52.1 1.0
MG B:MG402 4.8 70.7 1.0

Magnesium binding site 4 out of 8 in 9gre

Go back to Magnesium Binding Sites List in 9gre
Magnesium binding site 4 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:70.7
occ:1.00
 OE1 B:GLU217 2.1 71.1 1.0
OE2 B:GLU181 2.1 78.3 1.0
OD2 B:ASP287 2.1 76.0 1.0
OD2 B:ASP245 2.7 75.5 1.0
CD B:GLU181 3.1 74.9 1.0
CD B:GLU217 3.3 67.9 1.0
CG B:ASP287 3.3 73.3 1.0
OE1 B:GLU181 3.4 77.9 1.0
CG B:ASP245 3.8 69.6 1.0
O B:HOH501 3.9 30.0 1.0
OE2 B:GLU217 3.9 69.5 1.0
CB B:ASP287 4.0 66.4 1.0
CE1 B:HIS220 4.1 63.9 1.0
OD1 B:ASP287 4.2 73.5 1.0
CB B:ASP245 4.4 58.6 1.0
CG B:GLU217 4.4 60.6 1.0
CG B:GLU181 4.5 62.0 1.0
CB B:GLU217 4.6 55.0 1.0
ND1 B:HIS220 4.8 62.0 1.0
OD1 B:ASP245 4.8 71.5 1.0
MG B:MG401 4.8 54.7 1.0
NE2 B:HIS220 4.9 65.4 1.0

Magnesium binding site 5 out of 8 in 9gre

Go back to Magnesium Binding Sites List in 9gre
Magnesium binding site 5 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:54.7
occ:1.00
 OD2 C:ASP255 2.1 71.0 1.0
OE2 C:GLU217 2.3 69.5 1.0
NE2 C:HIS220 2.5 65.4 1.0
OD1 C:ASP257 2.6 75.7 1.0
CG C:ASP255 2.9 69.4 1.0
OD1 C:ASP255 3.0 71.6 1.0
OD2 C:ASP257 3.2 75.8 1.0
CG C:ASP257 3.2 73.7 1.0
CD2 C:HIS220 3.3 60.5 1.0
CE1 C:HIS220 3.3 63.9 1.0
CD C:GLU217 3.4 67.9 1.0
OE1 C:GLU217 3.9 71.1 1.0
ND2 C:ASN247 4.2 62.3 1.0
ND1 C:HIS220 4.2 62.0 1.0
CG C:HIS220 4.3 57.2 1.0
CB C:ASP255 4.3 64.8 1.0
CG C:GLU217 4.6 60.6 1.0
NZ C:LYS183 4.6 58.4 1.0
CB C:ASP257 4.7 66.0 1.0
OD2 C:ASP287 4.7 76.0 1.0
CE C:LYS183 4.8 52.1 1.0
MG C:MG402 4.8 70.7 1.0

Magnesium binding site 6 out of 8 in 9gre

Go back to Magnesium Binding Sites List in 9gre
Magnesium binding site 6 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:70.7
occ:1.00
 OE1 C:GLU217 2.1 71.1 1.0
OE2 C:GLU181 2.1 78.3 1.0
OD2 C:ASP287 2.1 76.0 1.0
OD2 C:ASP245 2.7 75.5 1.0
CD C:GLU181 3.1 74.9 1.0
CD C:GLU217 3.3 67.9 1.0
CG C:ASP287 3.3 73.3 1.0
OE1 C:GLU181 3.4 77.9 1.0
CG C:ASP245 3.8 69.6 1.0
O C:HOH501 3.9 30.0 1.0
OE2 C:GLU217 3.9 69.5 1.0
CB C:ASP287 4.0 66.4 1.0
CE1 C:HIS220 4.1 63.9 1.0
OD1 C:ASP287 4.2 73.5 1.0
CB C:ASP245 4.4 58.6 1.0
CG C:GLU217 4.4 60.6 1.0
CG C:GLU181 4.5 62.0 1.0
CB C:GLU217 4.6 55.0 1.0
ND1 C:HIS220 4.8 62.0 1.0
OD1 C:ASP245 4.8 71.5 1.0
MG C:MG401 4.8 54.7 1.0
NE2 C:HIS220 4.9 65.4 1.0

Magnesium binding site 7 out of 8 in 9gre

Go back to Magnesium Binding Sites List in 9gre
Magnesium binding site 7 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:54.7
occ:1.00
 OD2 D:ASP255 2.1 71.0 1.0
OE2 D:GLU217 2.3 69.5 1.0
NE2 D:HIS220 2.5 65.4 1.0
OD1 D:ASP257 2.6 75.7 1.0
CG D:ASP255 2.9 69.4 1.0
OD1 D:ASP255 3.0 71.6 1.0
OD2 D:ASP257 3.2 75.8 1.0
CG D:ASP257 3.2 73.7 1.0
CD2 D:HIS220 3.3 60.5 1.0
CE1 D:HIS220 3.3 63.9 1.0
CD D:GLU217 3.4 67.9 1.0
OE1 D:GLU217 3.9 71.1 1.0
ND2 D:ASN247 4.2 62.3 1.0
ND1 D:HIS220 4.2 62.0 1.0
CG D:HIS220 4.3 57.2 1.0
CB D:ASP255 4.3 64.8 1.0
CG D:GLU217 4.6 60.6 1.0
NZ D:LYS183 4.6 58.4 1.0
CB D:ASP257 4.7 66.0 1.0
OD2 D:ASP287 4.7 76.0 1.0
CE D:LYS183 4.8 52.1 1.0
MG D:MG402 4.8 70.7 1.0

Magnesium binding site 8 out of 8 in 9gre

Go back to Magnesium Binding Sites List in 9gre
Magnesium binding site 8 out of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:70.7
occ:1.00
 OE1 D:GLU217 2.1 71.1 1.0
OE2 D:GLU181 2.1 78.3 1.0
OD2 D:ASP287 2.1 76.0 1.0
OD2 D:ASP245 2.7 75.5 1.0
CD D:GLU181 3.1 74.9 1.0
CD D:GLU217 3.3 67.9 1.0
CG D:ASP287 3.3 73.3 1.0
OE1 D:GLU181 3.4 77.9 1.0
CG D:ASP245 3.8 69.6 1.0
OE2 D:GLU217 3.9 69.5 1.0
O D:HOH501 3.9 30.0 1.0
CB D:ASP287 4.0 66.4 1.0
CE1 D:HIS220 4.1 63.9 1.0
OD1 D:ASP287 4.2 73.5 1.0
CB D:ASP245 4.4 58.6 1.0
CG D:GLU217 4.4 60.6 1.0
CG D:GLU181 4.5 62.0 1.0
CB D:GLU217 4.6 55.0 1.0
ND1 D:HIS220 4.8 62.0 1.0
OD1 D:ASP245 4.8 71.5 1.0
MG D:MG401 4.8 54.7 1.0
NE2 D:HIS220 4.9 65.4 1.0

Reference:

J.Slawek, A.Klonecka, M.Rawski, M.Kozak. Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Magnesium Ions in the Active Site To Be Published.
Page generated: Sat Aug 16 03:05:52 2025

Last articles

Mg in 9LK4
Mg in 9LK5
Mg in 9KQQ
Mg in 9MF6
Mg in 9MED
Mg in 9MEC
Mg in 9MDY
Mg in 9MDW
Mg in 9M84
Mg in 9M7M
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy