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: Thu Oct 31 22:33:34 2024
|