Magnesium in PDB 4hhm: Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
Enzymatic activity of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
All present enzymatic activity of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk:
5.3.1.5;
Protein crystallography data
The structure of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk, PDB code: 4hhm
was solved by
H.Ben Hlima,
J.Riguet,
R.Haser,
N.Aghajari,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.50 /
2.15
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.500,
137.400,
136.600,
90.00,
90.06,
90.00
|
R / Rfree (%)
|
19.7 /
25
|
Other elements in 4hhm:
The structure of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
(pdb code 4hhm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the
Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk, PDB code: 4hhm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Magnesium binding site 1 out
of 8 in 4hhm
Go back to
Magnesium Binding Sites List in 4hhm
Magnesium binding site 1 out
of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg2002
b:11.9
occ:1.00
|
OE2
|
A:GLU181
|
2.1
|
13.2
|
1.0
|
OD2
|
A:ASP287
|
2.2
|
20.0
|
1.0
|
OD2
|
A:ASP245
|
2.2
|
17.6
|
1.0
|
OE1
|
A:GLU217
|
2.3
|
23.7
|
1.0
|
O
|
A:HOH2259
|
2.5
|
21.0
|
1.0
|
O
|
A:HOH2260
|
2.6
|
16.2
|
1.0
|
CD
|
A:GLU181
|
2.9
|
15.7
|
1.0
|
OE1
|
A:GLU181
|
3.1
|
12.6
|
1.0
|
CD
|
A:GLU217
|
3.3
|
22.2
|
1.0
|
CG
|
A:ASP287
|
3.3
|
20.0
|
1.0
|
CG
|
A:ASP245
|
3.4
|
18.1
|
1.0
|
OE2
|
A:GLU217
|
3.8
|
23.6
|
1.0
|
CB
|
A:ASP287
|
3.8
|
20.1
|
1.0
|
CB
|
A:ASP245
|
3.9
|
18.0
|
1.0
|
O
|
A:HOH2109
|
4.0
|
17.5
|
1.0
|
CE1
|
A:HIS220
|
4.2
|
10.3
|
1.0
|
CB
|
A:GLU217
|
4.3
|
18.5
|
1.0
|
OD1
|
A:ASP287
|
4.3
|
22.0
|
1.0
|
CG
|
A:GLU217
|
4.3
|
19.9
|
1.0
|
CG
|
A:GLU181
|
4.3
|
15.5
|
1.0
|
OD1
|
A:ASP245
|
4.4
|
20.6
|
1.0
|
NE2
|
A:HIS220
|
4.4
|
15.1
|
1.0
|
ND2
|
A:ASN215
|
4.5
|
14.8
|
1.0
|
CO
|
A:CO2001
|
4.6
|
47.9
|
1.0
|
|
Magnesium binding site 2 out
of 8 in 4hhm
Go back to
Magnesium Binding Sites List in 4hhm
Magnesium binding site 2 out
of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2002
b:18.1
occ:1.00
|
OE1
|
B:GLU217
|
2.1
|
13.1
|
1.0
|
OD2
|
B:ASP245
|
2.3
|
17.6
|
1.0
|
OD2
|
B:ASP287
|
2.3
|
23.3
|
1.0
|
OE2
|
B:GLU181
|
2.4
|
23.9
|
1.0
|
O
|
B:HOH2337
|
2.5
|
27.0
|
1.0
|
O
|
B:HOH2161
|
2.7
|
20.6
|
1.0
|
CD
|
B:GLU181
|
2.9
|
22.1
|
1.0
|
OE1
|
B:GLU181
|
3.0
|
19.4
|
1.0
|
CD
|
B:GLU217
|
3.3
|
12.8
|
1.0
|
CG
|
B:ASP245
|
3.4
|
15.5
|
1.0
|
CG
|
B:ASP287
|
3.4
|
18.8
|
1.0
|
CE1
|
B:HIS220
|
3.7
|
13.0
|
1.0
|
O
|
B:HOH2190
|
3.8
|
50.8
|
1.0
|
CB
|
B:ASP245
|
4.0
|
14.0
|
1.0
|
CB
|
B:ASP287
|
4.1
|
18.2
|
1.0
|
NE2
|
B:HIS220
|
4.1
|
14.1
|
1.0
|
OE2
|
B:GLU217
|
4.1
|
10.1
|
1.0
|
CB
|
B:GLU217
|
4.2
|
15.6
|
1.0
|
CG
|
B:GLU217
|
4.3
|
14.3
|
1.0
|
CG
|
B:GLU181
|
4.3
|
21.5
|
1.0
|
O
|
B:HOH2160
|
4.3
|
14.5
|
1.0
|
OD1
|
B:ASP245
|
4.4
|
17.8
|
1.0
|
OD1
|
B:ASP287
|
4.4
|
20.1
|
1.0
|
ND1
|
B:HIS220
|
4.6
|
12.4
|
1.0
|
CO
|
B:CO2001
|
4.6
|
35.2
|
1.0
|
ND2
|
B:ASN215
|
4.8
|
16.0
|
1.0
|
O
|
B:HOH2251
|
5.0
|
12.5
|
1.0
|
|
Magnesium binding site 3 out
of 8 in 4hhm
Go back to
Magnesium Binding Sites List in 4hhm
Magnesium binding site 3 out
of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg2002
b:15.4
occ:1.00
|
OE2
|
C:GLU181
|
2.2
|
17.6
|
1.0
|
OD2
|
C:ASP287
|
2.2
|
18.0
|
1.0
|
OD2
|
C:ASP245
|
2.4
|
26.5
|
1.0
|
OE1
|
C:GLU217
|
2.4
|
21.9
|
1.0
|
O
|
C:HOH2313
|
2.6
|
30.2
|
1.0
|
O
|
C:HOH2314
|
2.7
|
32.7
|
1.0
|
CD
|
C:GLU181
|
2.9
|
19.2
|
1.0
|
OE1
|
C:GLU181
|
3.1
|
18.9
|
1.0
|
CG
|
C:ASP245
|
3.3
|
23.6
|
1.0
|
CG
|
C:ASP287
|
3.3
|
22.2
|
1.0
|
CD
|
C:GLU217
|
3.6
|
15.9
|
1.0
|
CB
|
C:ASP245
|
3.8
|
21.7
|
1.0
|
CB
|
C:ASP287
|
3.9
|
21.2
|
1.0
|
O
|
C:HOH2140
|
4.0
|
20.4
|
1.0
|
OD1
|
C:ASP245
|
4.2
|
23.9
|
1.0
|
CE1
|
C:HIS220
|
4.2
|
17.2
|
1.0
|
CG
|
C:GLU181
|
4.3
|
16.9
|
1.0
|
CB
|
C:GLU217
|
4.4
|
14.4
|
1.0
|
OD1
|
C:ASP287
|
4.4
|
24.0
|
1.0
|
NE2
|
C:HIS220
|
4.4
|
18.2
|
1.0
|
CG
|
C:GLU217
|
4.4
|
15.8
|
1.0
|
O
|
C:HOH2143
|
4.4
|
35.3
|
1.0
|
OE2
|
C:GLU217
|
4.5
|
15.4
|
1.0
|
ND2
|
C:ASN215
|
4.7
|
16.5
|
1.0
|
CO
|
C:CO2001
|
4.8
|
39.3
|
1.0
|
|
Magnesium binding site 4 out
of 8 in 4hhm
Go back to
Magnesium Binding Sites List in 4hhm
Magnesium binding site 4 out
of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
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 A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg2002
b:17.9
occ:1.00
|
OE2
|
D:GLU181
|
2.3
|
22.5
|
1.0
|
OD2
|
D:ASP245
|
2.3
|
20.3
|
1.0
|
OE1
|
D:GLU217
|
2.3
|
21.1
|
1.0
|
OD2
|
D:ASP287
|
2.4
|
17.7
|
1.0
|
O
|
D:HOH2254
|
2.8
|
27.9
|
1.0
|
OE1
|
D:GLU181
|
2.9
|
20.1
|
1.0
|
CD
|
D:GLU181
|
3.0
|
19.7
|
1.0
|
CG
|
D:ASP287
|
3.2
|
16.5
|
1.0
|
CG
|
D:ASP245
|
3.5
|
21.8
|
1.0
|
CD
|
D:GLU217
|
3.6
|
19.2
|
1.0
|
O
|
D:HOH2255
|
3.6
|
51.9
|
1.0
|
CB
|
D:ASP287
|
3.9
|
18.6
|
1.0
|
O
|
D:HOH2335
|
4.1
|
14.2
|
1.0
|
CB
|
D:ASP245
|
4.1
|
21.6
|
1.0
|
OD1
|
D:ASP287
|
4.1
|
19.9
|
1.0
|
CE1
|
D:HIS220
|
4.1
|
12.0
|
1.0
|
NE2
|
D:HIS220
|
4.3
|
14.4
|
1.0
|
CG
|
D:GLU217
|
4.3
|
19.9
|
1.0
|
CB
|
D:GLU217
|
4.4
|
18.1
|
1.0
|
OE2
|
D:GLU217
|
4.5
|
20.9
|
1.0
|
OD1
|
D:ASP245
|
4.5
|
23.6
|
1.0
|
CG
|
D:GLU181
|
4.5
|
20.1
|
1.0
|
CO
|
D:CO2001
|
4.5
|
40.8
|
1.0
|
ND2
|
D:ASN215
|
4.8
|
23.7
|
1.0
|
ND1
|
D:HIS220
|
4.9
|
12.5
|
1.0
|
|
Magnesium binding site 5 out
of 8 in 4hhm
Go back to
Magnesium Binding Sites List in 4hhm
Magnesium binding site 5 out
of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg2002
b:17.8
occ:1.00
|
OE2
|
E:GLU181
|
2.2
|
15.7
|
1.0
|
OD2
|
E:ASP287
|
2.2
|
21.6
|
1.0
|
OD2
|
E:ASP245
|
2.2
|
18.8
|
1.0
|
OE1
|
E:GLU217
|
2.3
|
16.8
|
1.0
|
O
|
E:HOH2261
|
2.6
|
30.4
|
1.0
|
O
|
E:HOH2151
|
2.6
|
16.5
|
1.0
|
CD
|
E:GLU181
|
3.1
|
17.4
|
1.0
|
CG
|
E:ASP287
|
3.2
|
23.2
|
1.0
|
OE1
|
E:GLU181
|
3.3
|
14.2
|
1.0
|
CG
|
E:ASP245
|
3.3
|
15.9
|
1.0
|
CD
|
E:GLU217
|
3.5
|
13.0
|
1.0
|
CB
|
E:ASP287
|
3.7
|
21.9
|
1.0
|
CB
|
E:ASP245
|
3.9
|
15.1
|
1.0
|
CE1
|
E:HIS220
|
4.1
|
16.3
|
1.0
|
OD1
|
E:ASP287
|
4.1
|
24.1
|
1.0
|
CO
|
E:CO2001
|
4.2
|
40.2
|
1.0
|
CB
|
E:GLU217
|
4.2
|
14.4
|
1.0
|
CG
|
E:GLU217
|
4.3
|
13.2
|
1.0
|
O
|
E:HOH2120
|
4.3
|
26.5
|
1.0
|
OD1
|
E:ASP245
|
4.4
|
17.1
|
1.0
|
OE2
|
E:GLU217
|
4.4
|
15.1
|
1.0
|
NE2
|
E:HIS220
|
4.4
|
16.9
|
1.0
|
CG
|
E:GLU181
|
4.5
|
16.7
|
1.0
|
O
|
E:HOH2359
|
4.6
|
36.5
|
1.0
|
ND2
|
E:ASN215
|
4.6
|
11.9
|
1.0
|
ND1
|
E:HIS220
|
4.9
|
16.9
|
1.0
|
|
Magnesium binding site 6 out
of 8 in 4hhm
Go back to
Magnesium Binding Sites List in 4hhm
Magnesium binding site 6 out
of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg2002
b:21.0
occ:1.00
|
OE2
|
F:GLU181
|
2.3
|
25.6
|
1.0
|
OD2
|
F:ASP287
|
2.3
|
19.9
|
1.0
|
OE1
|
F:GLU217
|
2.3
|
21.9
|
1.0
|
OD2
|
F:ASP245
|
2.4
|
25.4
|
1.0
|
O
|
F:HOH2210
|
2.5
|
16.0
|
1.0
|
O
|
F:HOH2141
|
2.6
|
26.2
|
1.0
|
OE1
|
F:GLU181
|
2.9
|
23.9
|
1.0
|
CD
|
F:GLU181
|
2.9
|
23.1
|
1.0
|
CG
|
F:ASP287
|
3.4
|
18.4
|
1.0
|
O
|
F:HOH2140
|
3.5
|
20.3
|
1.0
|
CG
|
F:ASP245
|
3.5
|
24.1
|
1.0
|
CD
|
F:GLU217
|
3.5
|
18.3
|
1.0
|
CB
|
F:ASP287
|
4.1
|
17.7
|
1.0
|
CB
|
F:ASP245
|
4.1
|
22.8
|
1.0
|
CG
|
F:GLU217
|
4.2
|
17.5
|
1.0
|
CE1
|
F:HIS220
|
4.3
|
16.8
|
1.0
|
CG
|
F:GLU181
|
4.3
|
20.6
|
1.0
|
OD1
|
F:ASP287
|
4.3
|
24.2
|
1.0
|
CB
|
F:GLU217
|
4.4
|
16.8
|
1.0
|
OE2
|
F:GLU217
|
4.5
|
17.8
|
1.0
|
NE2
|
F:HIS220
|
4.5
|
19.6
|
1.0
|
OD1
|
F:ASP245
|
4.5
|
22.6
|
1.0
|
ND2
|
F:ASN215
|
4.6
|
23.5
|
1.0
|
CO
|
F:CO2001
|
4.9
|
40.1
|
1.0
|
|
Magnesium binding site 7 out
of 8 in 4hhm
Go back to
Magnesium Binding Sites List in 4hhm
Magnesium binding site 7 out
of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Mg2002
b:13.0
occ:1.00
|
OD2
|
G:ASP287
|
2.2
|
20.0
|
1.0
|
OE2
|
G:GLU181
|
2.2
|
16.0
|
1.0
|
OD2
|
G:ASP245
|
2.4
|
16.2
|
1.0
|
OE1
|
G:GLU217
|
2.4
|
16.7
|
1.0
|
O
|
G:HOH2262
|
2.6
|
24.2
|
1.0
|
O
|
G:HOH2261
|
2.7
|
24.2
|
1.0
|
CD
|
G:GLU181
|
3.1
|
14.7
|
1.0
|
CG
|
G:ASP287
|
3.3
|
19.5
|
1.0
|
OE1
|
G:GLU181
|
3.3
|
13.8
|
1.0
|
CG
|
G:ASP245
|
3.5
|
15.4
|
1.0
|
CD
|
G:GLU217
|
3.6
|
19.7
|
1.0
|
CB
|
G:ASP287
|
3.9
|
19.1
|
1.0
|
CB
|
G:ASP245
|
4.0
|
14.3
|
1.0
|
CE1
|
G:HIS220
|
4.1
|
17.8
|
1.0
|
O
|
G:HOH2147
|
4.1
|
15.7
|
1.0
|
OD1
|
G:ASP287
|
4.3
|
20.2
|
1.0
|
CB
|
G:GLU217
|
4.3
|
18.2
|
1.0
|
NE2
|
G:HIS220
|
4.4
|
18.8
|
1.0
|
CO
|
G:CO2001
|
4.4
|
40.3
|
1.0
|
CG
|
G:GLU217
|
4.4
|
19.4
|
1.0
|
OE2
|
G:GLU217
|
4.5
|
24.4
|
1.0
|
CG
|
G:GLU181
|
4.5
|
14.2
|
1.0
|
OD1
|
G:ASP245
|
4.6
|
18.1
|
1.0
|
ND2
|
G:ASN215
|
4.8
|
15.7
|
1.0
|
|
Magnesium binding site 8 out
of 8 in 4hhm
Go back to
Magnesium Binding Sites List in 4hhm
Magnesium binding site 8 out
of 8 in the Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Mg2002
b:21.7
occ:1.00
|
OE2
|
H:GLU181
|
2.2
|
19.9
|
1.0
|
OD2
|
H:ASP287
|
2.3
|
15.3
|
1.0
|
OD2
|
H:ASP245
|
2.3
|
16.2
|
1.0
|
OE1
|
H:GLU217
|
2.4
|
16.6
|
1.0
|
O
|
H:HOH2276
|
2.5
|
16.8
|
1.0
|
O
|
H:HOH2387
|
2.6
|
30.6
|
1.0
|
CD
|
H:GLU181
|
2.9
|
18.5
|
1.0
|
OE1
|
H:GLU181
|
2.9
|
16.3
|
1.0
|
CG
|
H:ASP287
|
3.4
|
17.0
|
1.0
|
CG
|
H:ASP245
|
3.5
|
16.1
|
1.0
|
CD
|
H:GLU217
|
3.7
|
18.5
|
1.0
|
O
|
H:HOH2216
|
3.9
|
17.7
|
1.0
|
CB
|
H:ASP287
|
4.0
|
16.1
|
1.0
|
CE1
|
H:HIS220
|
4.0
|
11.0
|
1.0
|
CB
|
H:ASP245
|
4.1
|
15.1
|
1.0
|
CG
|
H:GLU181
|
4.3
|
17.9
|
1.0
|
NE2
|
H:HIS220
|
4.4
|
11.7
|
1.0
|
OD1
|
H:ASP287
|
4.4
|
17.3
|
1.0
|
CG
|
H:GLU217
|
4.5
|
16.6
|
1.0
|
OD1
|
H:ASP245
|
4.5
|
15.9
|
1.0
|
OE2
|
H:GLU217
|
4.6
|
20.8
|
1.0
|
CB
|
H:GLU217
|
4.6
|
14.8
|
1.0
|
CO
|
H:CO2001
|
4.6
|
37.6
|
1.0
|
O
|
H:HOH2236
|
4.6
|
28.3
|
1.0
|
ND2
|
H:ASN215
|
4.7
|
10.3
|
1.0
|
O
|
H:HOH2249
|
4.9
|
30.7
|
1.0
|
|
Reference:
H.Ben Hlima,
S.Bejar,
J.Riguet,
R.Haser,
N.Aghajari.
Identification of Critical Residues For the Activity and Thermostability of Streptomyces Sp. Sk Glucose Isomerase. Appl.Microbiol.Biotechnol. V. 97 9715 2013.
ISSN: ISSN 0175-7598
PubMed: 23463249
DOI: 10.1007/S00253-013-4784-2
Page generated: Fri Aug 16 16:18:32 2024
|