Cobalt 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:
Cobalt Binding Sites:
The binding sites of Cobalt 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 Cobalt atom.
In total 8 binding sites of Cobalt where determined in the
Crystal Structure of A Mutant, G219A, of Glucose Isomerase From Streptomyces Sp. Sk, PDB code: 4hhm:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Cobalt binding site 1 out
of 8 in 4hhm
Go back to
Cobalt Binding Sites List in 4hhm
Cobalt 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 Cobalt with other atoms in the Co 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:Co2001
b:47.9
occ:1.00
|
OE2
|
A:GLU217
|
2.0
|
23.6
|
1.0
|
OD2
|
A:ASP255
|
2.1
|
25.7
|
1.0
|
OD1
|
A:ASP257
|
2.2
|
21.9
|
1.0
|
CG
|
A:ASP255
|
3.0
|
27.5
|
1.0
|
CG
|
A:ASP257
|
3.1
|
21.4
|
1.0
|
OD1
|
A:ASP255
|
3.1
|
26.8
|
1.0
|
CD
|
A:GLU217
|
3.2
|
22.2
|
1.0
|
O
|
A:HOH2260
|
3.2
|
16.2
|
1.0
|
OD2
|
A:ASP257
|
3.3
|
25.0
|
1.0
|
NE2
|
A:HIS220
|
3.3
|
15.1
|
1.0
|
OE1
|
A:GLU217
|
3.7
|
23.7
|
1.0
|
CD2
|
A:HIS220
|
3.8
|
10.7
|
1.0
|
ND2
|
A:ASN247
|
4.0
|
16.0
|
1.0
|
CG
|
A:GLU217
|
4.4
|
19.9
|
1.0
|
OD2
|
A:ASP287
|
4.4
|
20.0
|
1.0
|
CB
|
A:ASP255
|
4.4
|
22.3
|
1.0
|
CE1
|
A:HIS220
|
4.4
|
10.3
|
1.0
|
CB
|
A:ASP257
|
4.5
|
19.3
|
1.0
|
OD1
|
A:ASP287
|
4.5
|
22.0
|
1.0
|
CG
|
A:ASP287
|
4.5
|
20.0
|
1.0
|
O
|
A:ASP287
|
4.5
|
21.6
|
1.0
|
MG
|
A:MG2002
|
4.6
|
11.9
|
1.0
|
CB
|
A:ALA219
|
4.9
|
10.3
|
1.0
|
NZ
|
A:LYS289
|
5.0
|
28.2
|
1.0
|
|
Cobalt binding site 2 out
of 8 in 4hhm
Go back to
Cobalt Binding Sites List in 4hhm
Cobalt 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 Cobalt with other atoms in the Co 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:Co2001
b:35.2
occ:1.00
|
OD2
|
B:ASP255
|
2.1
|
24.2
|
1.0
|
OE2
|
B:GLU217
|
2.2
|
10.1
|
1.0
|
OD1
|
B:ASP257
|
2.3
|
19.7
|
1.0
|
CG
|
B:ASP255
|
2.7
|
26.1
|
1.0
|
OD1
|
B:ASP255
|
2.8
|
27.1
|
1.0
|
O
|
B:HOH2251
|
3.0
|
12.5
|
1.0
|
CG
|
B:ASP257
|
3.1
|
17.4
|
1.0
|
OD2
|
B:ASP257
|
3.1
|
22.8
|
1.0
|
CD
|
B:GLU217
|
3.2
|
12.8
|
1.0
|
NE2
|
B:HIS220
|
3.2
|
14.1
|
1.0
|
OE1
|
B:GLU217
|
3.5
|
13.1
|
1.0
|
CD2
|
B:HIS220
|
3.7
|
13.8
|
1.0
|
O
|
B:HOH2337
|
4.0
|
27.0
|
1.0
|
ND2
|
B:ASN247
|
4.0
|
6.8
|
1.0
|
CB
|
B:ASP255
|
4.1
|
21.7
|
1.0
|
CE1
|
B:HIS220
|
4.3
|
13.0
|
1.0
|
OD2
|
B:ASP287
|
4.4
|
23.3
|
1.0
|
CB
|
B:ASP257
|
4.5
|
13.6
|
1.0
|
CG
|
B:GLU217
|
4.5
|
14.3
|
1.0
|
MG
|
B:MG2002
|
4.6
|
18.1
|
1.0
|
CB
|
B:ALA219
|
4.7
|
8.3
|
1.0
|
CG
|
B:ASP287
|
4.8
|
18.8
|
1.0
|
O
|
B:HOH2401
|
4.8
|
39.6
|
1.0
|
NZ
|
B:LYS183
|
4.9
|
17.3
|
1.0
|
O
|
B:ASP287
|
4.9
|
18.9
|
1.0
|
O
|
B:HOH2168
|
4.9
|
27.9
|
1.0
|
OD1
|
B:ASP287
|
4.9
|
20.1
|
1.0
|
CG
|
B:HIS220
|
5.0
|
14.4
|
1.0
|
|
Cobalt binding site 3 out
of 8 in 4hhm
Go back to
Cobalt Binding Sites List in 4hhm
Cobalt 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 Cobalt with other atoms in the Co 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:Co2001
b:39.3
occ:1.00
|
OD2
|
C:ASP255
|
2.1
|
26.8
|
1.0
|
OE2
|
C:GLU217
|
2.2
|
15.4
|
1.0
|
OD1
|
C:ASP257
|
2.4
|
27.9
|
1.0
|
OD2
|
C:ASP257
|
2.9
|
29.5
|
1.0
|
CG
|
C:ASP255
|
3.0
|
26.8
|
1.0
|
CG
|
C:ASP257
|
3.0
|
24.9
|
1.0
|
CD
|
C:GLU217
|
3.0
|
15.9
|
1.0
|
OE1
|
C:GLU217
|
3.1
|
21.9
|
1.0
|
O
|
C:HOH2314
|
3.2
|
32.7
|
1.0
|
OD1
|
C:ASP255
|
3.2
|
29.3
|
1.0
|
NE2
|
C:HIS220
|
3.5
|
18.2
|
1.0
|
ND2
|
C:ASN247
|
3.8
|
18.7
|
1.0
|
CD2
|
C:HIS220
|
3.9
|
15.0
|
1.0
|
O
|
C:HOH2315
|
4.1
|
29.5
|
1.0
|
OD2
|
C:ASP287
|
4.3
|
18.0
|
1.0
|
CB
|
C:ASP255
|
4.3
|
22.4
|
1.0
|
CG
|
C:GLU217
|
4.4
|
15.8
|
1.0
|
CB
|
C:ASP257
|
4.4
|
22.3
|
1.0
|
O
|
C:ASP287
|
4.5
|
22.6
|
1.0
|
CB
|
C:ALA219
|
4.6
|
15.4
|
1.0
|
CE1
|
C:HIS220
|
4.7
|
17.2
|
1.0
|
CG
|
C:ASP287
|
4.7
|
22.2
|
1.0
|
MG
|
C:MG2002
|
4.8
|
15.4
|
1.0
|
OD1
|
C:ASP287
|
4.9
|
24.0
|
1.0
|
CA
|
C:ASP257
|
4.9
|
19.4
|
1.0
|
|
Cobalt binding site 4 out
of 8 in 4hhm
Go back to
Cobalt Binding Sites List in 4hhm
Cobalt 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 Cobalt with other atoms in the Co 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:Co2001
b:40.8
occ:1.00
|
OD1
|
D:ASP257
|
2.1
|
19.1
|
1.0
|
OE2
|
D:GLU217
|
2.2
|
20.9
|
1.0
|
OD2
|
D:ASP255
|
2.2
|
25.7
|
1.0
|
CG
|
D:ASP255
|
2.9
|
25.1
|
1.0
|
CD
|
D:GLU217
|
3.0
|
19.2
|
1.0
|
CG
|
D:ASP257
|
3.0
|
17.6
|
1.0
|
OD1
|
D:ASP255
|
3.0
|
26.0
|
1.0
|
OE1
|
D:GLU217
|
3.0
|
21.1
|
1.0
|
NE2
|
D:HIS220
|
3.2
|
14.4
|
1.0
|
OD2
|
D:ASP257
|
3.2
|
21.7
|
1.0
|
CD2
|
D:HIS220
|
3.6
|
11.7
|
1.0
|
ND2
|
D:ASN247
|
3.9
|
17.4
|
1.0
|
O
|
D:HOH2255
|
3.9
|
51.9
|
1.0
|
OD1
|
D:ASP287
|
4.1
|
19.9
|
1.0
|
CE1
|
D:HIS220
|
4.3
|
12.0
|
1.0
|
CB
|
D:ASP255
|
4.4
|
20.4
|
1.0
|
CB
|
D:ASP257
|
4.4
|
16.2
|
1.0
|
CG
|
D:GLU217
|
4.4
|
19.9
|
1.0
|
CG
|
D:ASP287
|
4.5
|
16.5
|
1.0
|
MG
|
D:MG2002
|
4.5
|
17.9
|
1.0
|
O
|
D:ASP287
|
4.6
|
19.0
|
1.0
|
OD2
|
D:ASP287
|
4.7
|
17.7
|
1.0
|
CB
|
D:ALA219
|
4.7
|
12.2
|
1.0
|
NZ
|
D:LYS289
|
4.9
|
29.4
|
1.0
|
CG
|
D:HIS220
|
4.9
|
13.3
|
1.0
|
CA
|
D:ASP257
|
4.9
|
16.2
|
1.0
|
|
Cobalt binding site 5 out
of 8 in 4hhm
Go back to
Cobalt Binding Sites List in 4hhm
Cobalt 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 Cobalt with other atoms in the Co 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:Co2001
b:40.2
occ:1.00
|
OD2
|
E:ASP255
|
2.2
|
24.0
|
1.0
|
OE2
|
E:GLU217
|
2.2
|
15.1
|
1.0
|
OD1
|
E:ASP257
|
2.3
|
21.4
|
1.0
|
OE1
|
E:GLU217
|
2.7
|
16.8
|
1.0
|
O
|
E:HOH2359
|
2.7
|
36.5
|
1.0
|
CD
|
E:GLU217
|
2.8
|
13.0
|
1.0
|
NE2
|
E:HIS220
|
3.1
|
16.9
|
1.0
|
CG
|
E:ASP255
|
3.1
|
25.3
|
1.0
|
CG
|
E:ASP257
|
3.3
|
21.0
|
1.0
|
OD1
|
E:ASP255
|
3.4
|
22.1
|
1.0
|
OD2
|
E:ASP257
|
3.5
|
27.5
|
1.0
|
CD2
|
E:HIS220
|
3.6
|
14.4
|
1.0
|
O
|
E:HOH2261
|
3.7
|
30.4
|
1.0
|
ND2
|
E:ASN247
|
3.9
|
11.5
|
1.0
|
CE1
|
E:HIS220
|
4.0
|
16.3
|
1.0
|
MG
|
E:MG2002
|
4.2
|
17.8
|
1.0
|
CG
|
E:GLU217
|
4.3
|
13.2
|
1.0
|
OD2
|
E:ASP287
|
4.5
|
21.6
|
1.0
|
CB
|
E:ASP255
|
4.5
|
18.1
|
1.0
|
OD1
|
E:ASP287
|
4.5
|
24.1
|
1.0
|
CG
|
E:ASP287
|
4.6
|
23.2
|
1.0
|
O
|
E:ASP287
|
4.7
|
19.0
|
1.0
|
CB
|
E:ASP257
|
4.7
|
16.2
|
1.0
|
CG
|
E:HIS220
|
4.8
|
16.3
|
1.0
|
ND1
|
E:HIS220
|
5.0
|
16.9
|
1.0
|
CB
|
E:ALA219
|
5.0
|
8.9
|
1.0
|
|
Cobalt binding site 6 out
of 8 in 4hhm
Go back to
Cobalt Binding Sites List in 4hhm
Cobalt 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 Cobalt with other atoms in the Co 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:Co2001
b:40.1
occ:1.00
|
OE2
|
F:GLU217
|
2.0
|
17.8
|
1.0
|
OD1
|
F:ASP257
|
2.1
|
24.1
|
1.0
|
OD2
|
F:ASP255
|
2.1
|
21.2
|
1.0
|
CG
|
F:ASP255
|
2.9
|
25.1
|
1.0
|
CD
|
F:GLU217
|
2.9
|
18.3
|
1.0
|
OD1
|
F:ASP255
|
3.0
|
24.8
|
1.0
|
CG
|
F:ASP257
|
3.0
|
26.0
|
1.0
|
OE1
|
F:GLU217
|
3.1
|
21.9
|
1.0
|
OD2
|
F:ASP257
|
3.3
|
29.6
|
1.0
|
NE2
|
F:HIS220
|
3.5
|
19.6
|
1.0
|
ND2
|
F:ASN247
|
3.8
|
11.4
|
1.0
|
CD2
|
F:HIS220
|
3.9
|
16.6
|
1.0
|
O
|
F:HOH2210
|
4.3
|
16.0
|
1.0
|
CG
|
F:GLU217
|
4.3
|
17.5
|
1.0
|
CB
|
F:ASP257
|
4.4
|
24.6
|
1.0
|
CB
|
F:ASP255
|
4.4
|
21.9
|
1.0
|
O
|
F:ASP287
|
4.5
|
21.8
|
1.0
|
CB
|
F:ALA219
|
4.5
|
15.0
|
1.0
|
OD1
|
F:ASP287
|
4.6
|
24.2
|
1.0
|
CE1
|
F:HIS220
|
4.6
|
16.8
|
1.0
|
OD2
|
F:ASP287
|
4.7
|
19.9
|
1.0
|
CG
|
F:ASP287
|
4.7
|
18.4
|
1.0
|
CA
|
F:ASP257
|
4.8
|
21.2
|
1.0
|
MG
|
F:MG2002
|
4.9
|
21.0
|
1.0
|
|
Cobalt binding site 7 out
of 8 in 4hhm
Go back to
Cobalt Binding Sites List in 4hhm
Cobalt 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 Cobalt with other atoms in the Co 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:Co2001
b:40.3
occ:1.00
|
OD1
|
G:ASP257
|
2.1
|
22.5
|
1.0
|
OD2
|
G:ASP255
|
2.2
|
20.1
|
1.0
|
OE2
|
G:GLU217
|
2.3
|
24.4
|
1.0
|
CD
|
G:GLU217
|
3.0
|
19.7
|
1.0
|
OE1
|
G:GLU217
|
3.0
|
16.7
|
1.0
|
CG
|
G:ASP255
|
3.0
|
25.2
|
1.0
|
CG
|
G:ASP257
|
3.1
|
22.9
|
1.0
|
OD1
|
G:ASP255
|
3.2
|
23.8
|
1.0
|
NE2
|
G:HIS220
|
3.3
|
18.8
|
1.0
|
OD2
|
G:ASP257
|
3.4
|
24.3
|
1.0
|
ND2
|
G:ASN247
|
3.8
|
19.6
|
1.0
|
CD2
|
G:HIS220
|
3.8
|
18.1
|
1.0
|
O
|
G:HOH2262
|
3.9
|
24.2
|
1.0
|
OD2
|
G:ASP287
|
4.2
|
20.0
|
1.0
|
MG
|
G:MG2002
|
4.4
|
13.0
|
1.0
|
CE1
|
G:HIS220
|
4.4
|
17.8
|
1.0
|
CG
|
G:GLU217
|
4.4
|
19.4
|
1.0
|
CB
|
G:ASP257
|
4.4
|
19.9
|
1.0
|
CB
|
G:ASP255
|
4.5
|
19.3
|
1.0
|
CG
|
G:ASP287
|
4.5
|
19.5
|
1.0
|
O
|
G:ASP287
|
4.5
|
21.2
|
1.0
|
OD1
|
G:ASP287
|
4.5
|
20.2
|
1.0
|
CB
|
G:ALA219
|
4.7
|
9.1
|
1.0
|
CA
|
G:ASP257
|
4.9
|
20.6
|
1.0
|
|
Cobalt binding site 8 out
of 8 in 4hhm
Go back to
Cobalt Binding Sites List in 4hhm
Cobalt 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 Cobalt with other atoms in the Co 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:Co2001
b:37.6
occ:1.00
|
OD2
|
H:ASP255
|
2.1
|
17.7
|
1.0
|
OE2
|
H:GLU217
|
2.3
|
20.8
|
1.0
|
OD1
|
H:ASP257
|
2.3
|
24.6
|
1.0
|
O
|
H:HOH2387
|
2.8
|
30.6
|
1.0
|
CD
|
H:GLU217
|
3.0
|
18.5
|
1.0
|
OE1
|
H:GLU217
|
3.0
|
16.6
|
1.0
|
CG
|
H:ASP255
|
3.0
|
21.9
|
1.0
|
CG
|
H:ASP257
|
3.1
|
21.8
|
1.0
|
O
|
H:HOH2277
|
3.2
|
34.6
|
1.0
|
OD2
|
H:ASP257
|
3.2
|
25.6
|
1.0
|
OD1
|
H:ASP255
|
3.2
|
22.2
|
1.0
|
NE2
|
H:HIS220
|
3.4
|
11.7
|
1.0
|
ND2
|
H:ASN247
|
3.8
|
11.1
|
1.0
|
CD2
|
H:HIS220
|
3.9
|
11.7
|
1.0
|
OD2
|
H:ASP287
|
4.0
|
15.3
|
1.0
|
CB
|
H:ASP255
|
4.4
|
16.6
|
1.0
|
CE1
|
H:HIS220
|
4.4
|
11.0
|
1.0
|
CG
|
H:GLU217
|
4.4
|
16.6
|
1.0
|
CB
|
H:ASP257
|
4.5
|
17.4
|
1.0
|
CG
|
H:ASP287
|
4.6
|
17.0
|
1.0
|
MG
|
H:MG2002
|
4.6
|
21.7
|
1.0
|
O
|
H:ASP287
|
4.6
|
17.9
|
1.0
|
O
|
H:HOH2249
|
4.7
|
30.7
|
1.0
|
CB
|
H:ALA219
|
4.8
|
7.0
|
1.0
|
OD1
|
H:ASP287
|
4.9
|
17.3
|
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: Tue Jul 30 17:09:38 2024
|