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

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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

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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

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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

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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

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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

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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

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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

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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.
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