Cobalt in PDB 9grd: Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Enzymatic activity of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
All present enzymatic activity of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site:
5.3.1.5;
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
(pdb code 9grd). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the
Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site, PDB code: 9grd:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Cobalt binding site 1 out
of 8 in 9grd
Go back to
Cobalt Binding Sites List in 9grd
Cobalt binding site 1 out
of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co401
b:76.4
occ:1.00
|
OD2
|
A:ASP255
|
2.2
|
56.1
|
1.0
|
OD1
|
A:ASP257
|
2.2
|
64.9
|
1.0
|
NE2
|
A:HIS220
|
2.3
|
58.8
|
1.0
|
OD2
|
A:ASP257
|
2.8
|
60.8
|
1.0
|
CD2
|
A:HIS220
|
2.8
|
49.7
|
1.0
|
CG
|
A:ASP255
|
2.8
|
56.8
|
1.0
|
CG
|
A:ASP257
|
2.8
|
59.3
|
1.0
|
OD1
|
A:ASP255
|
2.9
|
61.6
|
1.0
|
OE2
|
A:GLU217
|
3.0
|
59.6
|
1.0
|
CE1
|
A:HIS220
|
3.3
|
58.9
|
1.0
|
CD
|
A:GLU217
|
3.5
|
57.7
|
1.0
|
ND2
|
A:ASN247
|
3.7
|
51.4
|
1.0
|
OE1
|
A:GLU217
|
3.8
|
64.0
|
1.0
|
CG
|
A:HIS220
|
4.0
|
49.0
|
1.0
|
ND1
|
A:HIS220
|
4.2
|
56.4
|
1.0
|
CB
|
A:ASP255
|
4.3
|
52.2
|
1.0
|
CB
|
A:ASP257
|
4.3
|
51.9
|
1.0
|
CG
|
A:GLU217
|
4.5
|
51.6
|
1.0
|
OD2
|
A:ASP287
|
4.5
|
68.4
|
1.0
|
CE
|
A:LYS183
|
4.8
|
46.5
|
1.0
|
CA
|
A:ASP257
|
5.0
|
50.0
|
1.0
|
NZ
|
A:LYS183
|
5.0
|
50.9
|
1.0
|
CG
|
A:ASN247
|
5.0
|
52.2
|
1.0
|
|
Cobalt binding site 2 out
of 8 in 9grd
Go back to
Cobalt Binding Sites List in 9grd
Cobalt binding site 2 out
of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co402
b:93.2
occ:1.00
|
OD2
|
A:ASP287
|
2.2
|
68.4
|
1.0
|
OE2
|
A:GLU181
|
2.2
|
66.8
|
1.0
|
OE1
|
A:GLU217
|
2.2
|
64.0
|
1.0
|
OD2
|
A:ASP245
|
2.4
|
67.1
|
1.0
|
CD
|
A:GLU217
|
3.1
|
57.7
|
1.0
|
CD
|
A:GLU181
|
3.1
|
60.2
|
1.0
|
CG
|
A:ASP287
|
3.1
|
63.4
|
1.0
|
O
|
A:HOH501
|
3.3
|
30.0
|
1.0
|
CG
|
A:ASP245
|
3.5
|
59.0
|
1.0
|
OE2
|
A:GLU217
|
3.5
|
59.6
|
1.0
|
OE1
|
A:GLU181
|
3.5
|
64.6
|
1.0
|
CB
|
A:ASP287
|
3.6
|
56.2
|
1.0
|
CB
|
A:ASP245
|
4.1
|
50.1
|
1.0
|
OD1
|
A:ASP287
|
4.2
|
63.5
|
1.0
|
CG
|
A:GLU217
|
4.3
|
51.6
|
1.0
|
CG
|
A:GLU181
|
4.3
|
51.0
|
1.0
|
CE1
|
A:HIS220
|
4.4
|
58.9
|
1.0
|
OD1
|
A:ASP245
|
4.5
|
56.8
|
1.0
|
CB
|
A:GLU217
|
4.6
|
47.2
|
1.0
|
ND1
|
A:HIS220
|
4.9
|
56.4
|
1.0
|
ND2
|
A:ASN215
|
5.0
|
47.7
|
1.0
|
NE2
|
A:HIS220
|
5.0
|
58.8
|
1.0
|
|
Cobalt binding site 3 out
of 8 in 9grd
Go back to
Cobalt Binding Sites List in 9grd
Cobalt binding site 3 out
of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co401
b:76.4
occ:1.00
|
OD2
|
B:ASP255
|
2.2
|
56.1
|
1.0
|
OD1
|
B:ASP257
|
2.2
|
64.9
|
1.0
|
NE2
|
B:HIS220
|
2.3
|
58.8
|
1.0
|
OD2
|
B:ASP257
|
2.8
|
60.8
|
1.0
|
CD2
|
B:HIS220
|
2.8
|
49.7
|
1.0
|
CG
|
B:ASP255
|
2.8
|
56.8
|
1.0
|
CG
|
B:ASP257
|
2.8
|
59.3
|
1.0
|
OD1
|
B:ASP255
|
2.9
|
61.6
|
1.0
|
OE2
|
B:GLU217
|
3.0
|
59.6
|
1.0
|
CE1
|
B:HIS220
|
3.3
|
58.9
|
1.0
|
CD
|
B:GLU217
|
3.5
|
57.7
|
1.0
|
ND2
|
B:ASN247
|
3.7
|
51.4
|
1.0
|
OE1
|
B:GLU217
|
3.8
|
64.0
|
1.0
|
CG
|
B:HIS220
|
4.0
|
49.0
|
1.0
|
ND1
|
B:HIS220
|
4.2
|
56.4
|
1.0
|
CB
|
B:ASP255
|
4.3
|
52.2
|
1.0
|
CB
|
B:ASP257
|
4.3
|
51.9
|
1.0
|
CG
|
B:GLU217
|
4.5
|
51.6
|
1.0
|
OD2
|
B:ASP287
|
4.5
|
68.4
|
1.0
|
CE
|
B:LYS183
|
4.8
|
46.5
|
1.0
|
CA
|
B:ASP257
|
5.0
|
50.0
|
1.0
|
NZ
|
B:LYS183
|
5.0
|
50.9
|
1.0
|
CG
|
B:ASN247
|
5.0
|
52.2
|
1.0
|
|
Cobalt binding site 4 out
of 8 in 9grd
Go back to
Cobalt Binding Sites List in 9grd
Cobalt binding site 4 out
of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co402
b:93.2
occ:1.00
|
OD2
|
B:ASP287
|
2.2
|
68.4
|
1.0
|
OE2
|
B:GLU181
|
2.2
|
66.8
|
1.0
|
OE1
|
B:GLU217
|
2.2
|
64.0
|
1.0
|
OD2
|
B:ASP245
|
2.4
|
67.1
|
1.0
|
CD
|
B:GLU217
|
3.1
|
57.7
|
1.0
|
CD
|
B:GLU181
|
3.1
|
60.2
|
1.0
|
CG
|
B:ASP287
|
3.1
|
63.4
|
1.0
|
O
|
B:HOH501
|
3.3
|
30.0
|
1.0
|
CG
|
B:ASP245
|
3.5
|
59.0
|
1.0
|
OE2
|
B:GLU217
|
3.5
|
59.6
|
1.0
|
OE1
|
B:GLU181
|
3.5
|
64.6
|
1.0
|
CB
|
B:ASP287
|
3.6
|
56.2
|
1.0
|
CB
|
B:ASP245
|
4.1
|
50.1
|
1.0
|
OD1
|
B:ASP287
|
4.2
|
63.5
|
1.0
|
CG
|
B:GLU217
|
4.3
|
51.6
|
1.0
|
CG
|
B:GLU181
|
4.3
|
51.0
|
1.0
|
CE1
|
B:HIS220
|
4.4
|
58.9
|
1.0
|
OD1
|
B:ASP245
|
4.5
|
56.8
|
1.0
|
CB
|
B:GLU217
|
4.6
|
47.2
|
1.0
|
ND1
|
B:HIS220
|
4.9
|
56.4
|
1.0
|
ND2
|
B:ASN215
|
5.0
|
47.7
|
1.0
|
NE2
|
B:HIS220
|
5.0
|
58.8
|
1.0
|
|
Cobalt binding site 5 out
of 8 in 9grd
Go back to
Cobalt Binding Sites List in 9grd
Cobalt binding site 5 out
of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co401
b:76.4
occ:1.00
|
OD2
|
C:ASP255
|
2.2
|
56.1
|
1.0
|
OD1
|
C:ASP257
|
2.2
|
64.9
|
1.0
|
NE2
|
C:HIS220
|
2.3
|
58.8
|
1.0
|
OD2
|
C:ASP257
|
2.8
|
60.8
|
1.0
|
CD2
|
C:HIS220
|
2.8
|
49.7
|
1.0
|
CG
|
C:ASP255
|
2.8
|
56.8
|
1.0
|
CG
|
C:ASP257
|
2.8
|
59.3
|
1.0
|
OD1
|
C:ASP255
|
2.9
|
61.6
|
1.0
|
OE2
|
C:GLU217
|
3.0
|
59.6
|
1.0
|
CE1
|
C:HIS220
|
3.3
|
58.9
|
1.0
|
CD
|
C:GLU217
|
3.5
|
57.7
|
1.0
|
ND2
|
C:ASN247
|
3.7
|
51.4
|
1.0
|
OE1
|
C:GLU217
|
3.8
|
64.0
|
1.0
|
CG
|
C:HIS220
|
4.0
|
49.0
|
1.0
|
ND1
|
C:HIS220
|
4.2
|
56.4
|
1.0
|
CB
|
C:ASP255
|
4.3
|
52.2
|
1.0
|
CB
|
C:ASP257
|
4.3
|
51.9
|
1.0
|
CG
|
C:GLU217
|
4.5
|
51.6
|
1.0
|
OD2
|
C:ASP287
|
4.5
|
68.4
|
1.0
|
CE
|
C:LYS183
|
4.8
|
46.5
|
1.0
|
CA
|
C:ASP257
|
5.0
|
50.0
|
1.0
|
NZ
|
C:LYS183
|
5.0
|
50.9
|
1.0
|
CG
|
C:ASN247
|
5.0
|
52.2
|
1.0
|
|
Cobalt binding site 6 out
of 8 in 9grd
Go back to
Cobalt Binding Sites List in 9grd
Cobalt binding site 6 out
of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co402
b:93.2
occ:1.00
|
OD2
|
C:ASP287
|
2.2
|
68.4
|
1.0
|
OE2
|
C:GLU181
|
2.2
|
66.8
|
1.0
|
OE1
|
C:GLU217
|
2.2
|
64.0
|
1.0
|
OD2
|
C:ASP245
|
2.4
|
67.1
|
1.0
|
CD
|
C:GLU217
|
3.1
|
57.7
|
1.0
|
CD
|
C:GLU181
|
3.1
|
60.2
|
1.0
|
CG
|
C:ASP287
|
3.1
|
63.4
|
1.0
|
O
|
C:HOH501
|
3.4
|
30.0
|
1.0
|
CG
|
C:ASP245
|
3.5
|
59.0
|
1.0
|
OE2
|
C:GLU217
|
3.5
|
59.6
|
1.0
|
OE1
|
C:GLU181
|
3.5
|
64.6
|
1.0
|
CB
|
C:ASP287
|
3.6
|
56.2
|
1.0
|
CB
|
C:ASP245
|
4.1
|
50.1
|
1.0
|
OD1
|
C:ASP287
|
4.2
|
63.5
|
1.0
|
CG
|
C:GLU217
|
4.3
|
51.6
|
1.0
|
CG
|
C:GLU181
|
4.3
|
51.0
|
1.0
|
CE1
|
C:HIS220
|
4.4
|
58.9
|
1.0
|
OD1
|
C:ASP245
|
4.5
|
56.8
|
1.0
|
CB
|
C:GLU217
|
4.6
|
47.2
|
1.0
|
ND1
|
C:HIS220
|
4.9
|
56.4
|
1.0
|
ND2
|
C:ASN215
|
5.0
|
47.7
|
1.0
|
NE2
|
C:HIS220
|
5.0
|
58.8
|
1.0
|
|
Cobalt binding site 7 out
of 8 in 9grd
Go back to
Cobalt Binding Sites List in 9grd
Cobalt binding site 7 out
of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co401
b:76.4
occ:1.00
|
OD2
|
D:ASP255
|
2.2
|
56.1
|
1.0
|
OD1
|
D:ASP257
|
2.2
|
64.9
|
1.0
|
NE2
|
D:HIS220
|
2.3
|
58.8
|
1.0
|
OD2
|
D:ASP257
|
2.8
|
60.8
|
1.0
|
CD2
|
D:HIS220
|
2.8
|
49.7
|
1.0
|
CG
|
D:ASP255
|
2.8
|
56.8
|
1.0
|
CG
|
D:ASP257
|
2.8
|
59.3
|
1.0
|
OD1
|
D:ASP255
|
2.9
|
61.6
|
1.0
|
OE2
|
D:GLU217
|
3.0
|
59.6
|
1.0
|
CE1
|
D:HIS220
|
3.3
|
58.9
|
1.0
|
CD
|
D:GLU217
|
3.5
|
57.7
|
1.0
|
ND2
|
D:ASN247
|
3.7
|
51.4
|
1.0
|
OE1
|
D:GLU217
|
3.8
|
64.0
|
1.0
|
CG
|
D:HIS220
|
4.0
|
49.0
|
1.0
|
ND1
|
D:HIS220
|
4.2
|
56.4
|
1.0
|
CB
|
D:ASP255
|
4.3
|
52.2
|
1.0
|
CB
|
D:ASP257
|
4.3
|
51.9
|
1.0
|
CG
|
D:GLU217
|
4.5
|
51.6
|
1.0
|
OD2
|
D:ASP287
|
4.5
|
68.4
|
1.0
|
CE
|
D:LYS183
|
4.8
|
46.5
|
1.0
|
CA
|
D:ASP257
|
5.0
|
50.0
|
1.0
|
NZ
|
D:LYS183
|
5.0
|
50.9
|
1.0
|
CG
|
D:ASN247
|
5.0
|
52.2
|
1.0
|
|
Cobalt binding site 8 out
of 8 in 9grd
Go back to
Cobalt Binding Sites List in 9grd
Cobalt binding site 8 out
of 8 in the Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 8 of Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co402
b:93.2
occ:1.00
|
OD2
|
D:ASP287
|
2.2
|
68.4
|
1.0
|
OE2
|
D:GLU181
|
2.2
|
66.8
|
1.0
|
OE1
|
D:GLU217
|
2.2
|
64.0
|
1.0
|
OD2
|
D:ASP245
|
2.4
|
67.1
|
1.0
|
CD
|
D:GLU217
|
3.1
|
57.7
|
1.0
|
CD
|
D:GLU181
|
3.1
|
60.2
|
1.0
|
CG
|
D:ASP287
|
3.1
|
63.4
|
1.0
|
O
|
D:HOH501
|
3.3
|
30.0
|
1.0
|
OE2
|
D:GLU217
|
3.5
|
59.6
|
1.0
|
CG
|
D:ASP245
|
3.5
|
59.0
|
1.0
|
OE1
|
D:GLU181
|
3.5
|
64.6
|
1.0
|
CB
|
D:ASP287
|
3.6
|
56.2
|
1.0
|
CB
|
D:ASP245
|
4.1
|
50.1
|
1.0
|
OD1
|
D:ASP287
|
4.2
|
63.5
|
1.0
|
CG
|
D:GLU217
|
4.3
|
51.6
|
1.0
|
CG
|
D:GLU181
|
4.3
|
51.0
|
1.0
|
CE1
|
D:HIS220
|
4.4
|
58.9
|
1.0
|
OD1
|
D:ASP245
|
4.5
|
56.8
|
1.0
|
CB
|
D:GLU217
|
4.6
|
47.2
|
1.0
|
ND1
|
D:HIS220
|
4.9
|
56.4
|
1.0
|
ND2
|
D:ASN215
|
5.0
|
47.7
|
1.0
|
NE2
|
D:HIS220
|
5.0
|
58.8
|
1.0
|
|
Reference:
J.Slawek,
A.Klonecka,
M.Kozak,
M.Rawski.
Cryo-Electron Microscopy Structure of Glucose/Xylose Isomerase From Streptomyces Rubiginosus with Cobalt Ions in the Active Site To Be Published.
Page generated: Thu Oct 31 18:23:00 2024
|