Manganese in PDB 6quk: Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel
Enzymatic activity of Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel
All present enzymatic activity of Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel:
5.3.1.5;
Protein crystallography data
The structure of Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel, PDB code: 6quk
was solved by
B.D.Belviso,
R.Caliandro,
R.Caliandro,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
62.98 /
1.58
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
85.900,
92.598,
99.111,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.7 /
19.4
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel
(pdb code 6quk). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the
Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel, PDB code: 6quk:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 6quk
Go back to
Manganese Binding Sites List in 6quk
Manganese binding site 1 out
of 4 in the Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn401
b:8.1
occ:0.56
|
OE2
|
A:GLU181
|
2.0
|
16.1
|
1.0
|
OE1
|
A:GLU217
|
2.0
|
13.6
|
1.0
|
OD2
|
A:ASP287
|
2.0
|
10.7
|
1.0
|
OD2
|
A:ASP245
|
2.2
|
11.9
|
1.0
|
O2
|
A:GOL403
|
2.3
|
18.4
|
1.0
|
O1
|
A:GOL403
|
2.6
|
27.7
|
1.0
|
HO2
|
A:GOL403
|
2.9
|
18.1
|
0.0
|
CD
|
A:GLU181
|
2.9
|
14.1
|
1.0
|
CG
|
A:ASP287
|
3.1
|
9.4
|
1.0
|
HO1
|
A:GOL403
|
3.1
|
27.8
|
0.0
|
CD
|
A:GLU217
|
3.2
|
10.6
|
1.0
|
OE1
|
A:GLU181
|
3.3
|
13.5
|
1.0
|
C2
|
A:GOL403
|
3.3
|
19.5
|
1.0
|
HB3
|
A:ASP287
|
3.3
|
8.5
|
1.0
|
CG
|
A:ASP245
|
3.3
|
9.4
|
1.0
|
C1
|
A:GOL403
|
3.4
|
25.0
|
1.0
|
HB2
|
A:GLU217
|
3.4
|
7.9
|
1.0
|
HB2
|
A:ASP287
|
3.5
|
8.5
|
1.0
|
CB
|
A:ASP287
|
3.6
|
8.5
|
1.0
|
H12
|
A:GOL403
|
3.6
|
23.9
|
1.0
|
HE1
|
A:HIS220
|
3.7
|
10.2
|
1.0
|
HB3
|
A:ASP245
|
3.7
|
8.1
|
1.0
|
H2
|
A:GOL403
|
3.7
|
19.6
|
1.0
|
O
|
A:HOH520
|
3.7
|
17.0
|
1.0
|
O
|
A:HOH730
|
3.9
|
13.9
|
1.0
|
CB
|
A:ASP245
|
3.9
|
7.8
|
1.0
|
HB2
|
A:ASP245
|
3.9
|
8.1
|
1.0
|
CG
|
A:GLU217
|
4.1
|
8.6
|
1.0
|
CE1
|
A:HIS220
|
4.1
|
10.6
|
1.0
|
OE2
|
A:GLU217
|
4.1
|
13.6
|
1.0
|
CB
|
A:GLU217
|
4.1
|
8.0
|
1.0
|
HG3
|
A:GLU217
|
4.2
|
8.9
|
1.0
|
OD1
|
A:ASP287
|
4.2
|
9.4
|
1.0
|
H11
|
A:GOL403
|
4.2
|
24.0
|
1.0
|
CG
|
A:GLU181
|
4.3
|
11.8
|
1.0
|
OD1
|
A:ASP245
|
4.4
|
9.3
|
1.0
|
HB3
|
A:GLU217
|
4.4
|
7.9
|
1.0
|
HE2
|
A:HIS220
|
4.5
|
10.5
|
0.0
|
HG2
|
A:GLU181
|
4.5
|
11.9
|
1.0
|
NE2
|
A:HIS220
|
4.5
|
10.2
|
1.0
|
HG3
|
A:GLU181
|
4.5
|
11.9
|
1.0
|
HZ2
|
A:TRP16
|
4.6
|
7.5
|
1.0
|
HD21
|
A:ASN215
|
4.6
|
7.8
|
0.0
|
C3
|
A:GOL403
|
4.6
|
16.8
|
1.0
|
H31
|
A:GOL403
|
4.6
|
17.1
|
1.0
|
HD22
|
A:ASN215
|
4.8
|
7.8
|
0.0
|
ND1
|
A:HIS220
|
4.8
|
9.6
|
1.0
|
MN
|
A:MN402
|
4.9
|
7.3
|
0.5
|
H32
|
A:GOL403
|
4.9
|
17.1
|
1.0
|
ND2
|
A:ASN215
|
5.0
|
7.6
|
1.0
|
HG2
|
A:GLU217
|
5.0
|
8.9
|
1.0
|
|
Manganese binding site 2 out
of 4 in 6quk
Go back to
Manganese Binding Sites List in 6quk
Manganese binding site 2 out
of 4 in the Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn402
b:7.3
occ:0.51
|
OD2
|
A:ASP255
|
2.0
|
17.1
|
1.0
|
O
|
A:HOH730
|
2.0
|
13.9
|
1.0
|
OE2
|
A:GLU217
|
2.0
|
13.6
|
1.0
|
HE2
|
A:HIS220
|
2.1
|
10.5
|
0.0
|
OD1
|
A:ASP257
|
2.2
|
12.9
|
1.0
|
OD1
|
A:ASP255
|
2.5
|
19.8
|
1.0
|
CG
|
A:ASP255
|
2.5
|
14.7
|
1.0
|
NE2
|
A:HIS220
|
2.8
|
10.2
|
1.0
|
CD
|
A:GLU217
|
3.0
|
10.6
|
1.0
|
CG
|
A:ASP257
|
3.1
|
11.8
|
1.0
|
HD2
|
A:HIS220
|
3.1
|
9.7
|
1.0
|
HD21
|
A:ASN247
|
3.2
|
8.0
|
0.0
|
CD2
|
A:HIS220
|
3.3
|
10.0
|
1.0
|
OD2
|
A:ASP257
|
3.3
|
16.5
|
1.0
|
OE1
|
A:GLU217
|
3.4
|
13.6
|
1.0
|
O
|
A:HOH770
|
3.6
|
30.0
|
1.0
|
HD22
|
A:ASN247
|
3.7
|
8.0
|
0.0
|
ND2
|
A:ASN247
|
3.8
|
7.8
|
1.0
|
CE1
|
A:HIS220
|
3.9
|
10.6
|
1.0
|
HE3
|
A:LYS183
|
3.9
|
8.7
|
1.0
|
CB
|
A:ASP255
|
4.0
|
11.3
|
1.0
|
O
|
A:HOH565
|
4.1
|
11.2
|
1.0
|
HO1
|
A:GOL403
|
4.2
|
27.8
|
0.0
|
HE1
|
A:HIS220
|
4.3
|
10.2
|
1.0
|
HB3
|
A:ASP255
|
4.3
|
11.5
|
1.0
|
HB2
|
A:ASP255
|
4.4
|
11.5
|
1.0
|
CG
|
A:GLU217
|
4.4
|
8.6
|
1.0
|
HG2
|
A:GLU217
|
4.4
|
8.9
|
1.0
|
HA
|
A:ASP257
|
4.5
|
9.0
|
1.0
|
CG
|
A:HIS220
|
4.5
|
8.9
|
1.0
|
CB
|
A:ASP257
|
4.5
|
10.5
|
1.0
|
O1
|
A:GOL403
|
4.6
|
27.7
|
1.0
|
HZ1
|
A:LYS183
|
4.6
|
9.6
|
1.0
|
OD2
|
A:ASP287
|
4.6
|
10.7
|
1.0
|
H
|
A:ASP257
|
4.6
|
8.8
|
1.0
|
O
|
A:HOH552
|
4.7
|
35.6
|
1.0
|
HA3
|
A:GLY219
|
4.8
|
5.7
|
1.0
|
ND1
|
A:HIS220
|
4.8
|
9.6
|
1.0
|
HZ2
|
A:LYS183
|
4.8
|
9.6
|
1.0
|
CE
|
A:LYS183
|
4.8
|
8.7
|
1.0
|
MN
|
A:MN401
|
4.9
|
8.1
|
0.6
|
CA
|
A:ASP257
|
4.9
|
8.9
|
1.0
|
HG3
|
A:GLU217
|
4.9
|
8.9
|
1.0
|
NZ
|
A:LYS183
|
5.0
|
10.1
|
1.0
|
O
|
A:ASP287
|
5.0
|
7.4
|
1.0
|
HA
|
A:ASP255
|
5.0
|
9.4
|
1.0
|
N
|
A:ASP257
|
5.0
|
8.7
|
1.0
|
|
Manganese binding site 3 out
of 4 in 6quk
Go back to
Manganese Binding Sites List in 6quk
Manganese binding site 3 out
of 4 in the Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn401
b:7.1
occ:0.51
|
OE2
|
B:GLU217
|
2.0
|
11.1
|
1.0
|
O
|
B:HOH707
|
2.0
|
17.1
|
1.0
|
HE2
|
B:HIS220
|
2.0
|
10.9
|
0.0
|
OD2
|
B:ASP255
|
2.0
|
17.0
|
1.0
|
OD1
|
B:ASP257
|
2.2
|
14.9
|
1.0
|
OD1
|
B:ASP255
|
2.4
|
17.4
|
1.0
|
CG
|
B:ASP255
|
2.5
|
14.1
|
1.0
|
NE2
|
B:HIS220
|
2.7
|
10.1
|
1.0
|
HD2
|
B:HIS220
|
3.0
|
9.0
|
1.0
|
CD
|
B:GLU217
|
3.0
|
10.1
|
1.0
|
CG
|
B:ASP257
|
3.1
|
12.9
|
1.0
|
CD2
|
B:HIS220
|
3.2
|
9.0
|
1.0
|
HD21
|
B:ASN247
|
3.3
|
8.0
|
0.0
|
OD2
|
B:ASP257
|
3.3
|
19.1
|
1.0
|
OE1
|
B:GLU217
|
3.5
|
14.9
|
1.0
|
O
|
B:HOH706
|
3.6
|
28.5
|
1.0
|
CE1
|
B:HIS220
|
3.8
|
9.7
|
1.0
|
HD22
|
B:ASN247
|
3.8
|
8.0
|
0.0
|
ND2
|
B:ASN247
|
3.9
|
8.1
|
1.0
|
CB
|
B:ASP255
|
4.0
|
11.3
|
1.0
|
HE3
|
B:LYS183
|
4.1
|
9.6
|
1.0
|
O
|
B:HOH562
|
4.1
|
11.3
|
1.0
|
HE1
|
B:HIS220
|
4.2
|
9.5
|
1.0
|
HZ1
|
B:LYS183
|
4.2
|
10.5
|
1.0
|
HG2
|
B:GLU217
|
4.3
|
8.2
|
1.0
|
CG
|
B:GLU217
|
4.3
|
7.9
|
1.0
|
HB3
|
B:ASP255
|
4.4
|
11.5
|
1.0
|
HB2
|
B:ASP255
|
4.4
|
11.5
|
1.0
|
CG
|
B:HIS220
|
4.4
|
8.0
|
1.0
|
OD2
|
B:ASP287
|
4.5
|
11.9
|
1.0
|
CB
|
B:ASP257
|
4.5
|
11.1
|
1.0
|
HA
|
B:ASP257
|
4.5
|
9.7
|
1.0
|
H
|
B:ASP257
|
4.6
|
9.4
|
1.0
|
HZ2
|
B:LYS183
|
4.6
|
10.5
|
1.0
|
ND1
|
B:HIS220
|
4.7
|
8.6
|
1.0
|
O3
|
B:GOL403
|
4.7
|
30.4
|
1.0
|
NZ
|
B:LYS183
|
4.7
|
10.9
|
1.0
|
O
|
B:HOH549
|
4.7
|
31.7
|
1.0
|
HA3
|
B:GLY219
|
4.8
|
5.6
|
1.0
|
CE
|
B:LYS183
|
4.8
|
9.6
|
1.0
|
MN
|
B:MN402
|
4.9
|
5.6
|
0.5
|
HG3
|
B:GLU217
|
4.9
|
8.2
|
1.0
|
HO3
|
B:GOL403
|
4.9
|
29.8
|
1.0
|
CA
|
B:ASP257
|
4.9
|
9.5
|
1.0
|
HD2
|
B:LYS183
|
5.0
|
8.7
|
1.0
|
HZ3
|
B:LYS289
|
5.0
|
19.9
|
1.0
|
|
Manganese binding site 4 out
of 4 in 6quk
Go back to
Manganese Binding Sites List in 6quk
Manganese binding site 4 out
of 4 in the Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Protein Crystallization By Ionic Liquid Hydrogel Support: Glucose Isomerase Grown By Using Ionic Liquid Hydrogel within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn402
b:5.6
occ:0.50
|
OE1
|
B:GLU217
|
1.9
|
14.9
|
1.0
|
HO2
|
B:GOL403
|
1.9
|
21.7
|
0.0
|
OD2
|
B:ASP287
|
2.0
|
11.9
|
1.0
|
OE2
|
B:GLU181
|
2.0
|
14.2
|
1.0
|
OD2
|
B:ASP245
|
2.2
|
10.3
|
1.0
|
O2
|
B:GOL403
|
2.3
|
22.4
|
1.0
|
HO3
|
B:GOL403
|
2.6
|
29.8
|
1.0
|
O3
|
B:GOL403
|
2.7
|
30.4
|
1.0
|
CD
|
B:GLU181
|
2.9
|
12.7
|
1.0
|
CG
|
B:ASP287
|
3.1
|
9.1
|
1.0
|
CD
|
B:GLU217
|
3.2
|
10.1
|
1.0
|
C2
|
B:GOL403
|
3.2
|
24.0
|
1.0
|
OE1
|
B:GLU181
|
3.2
|
12.3
|
1.0
|
H2
|
B:GOL403
|
3.3
|
23.5
|
1.0
|
HB3
|
B:ASP287
|
3.3
|
8.4
|
1.0
|
CG
|
B:ASP245
|
3.3
|
8.6
|
1.0
|
C3
|
B:GOL403
|
3.4
|
29.9
|
1.0
|
HB2
|
B:GLU217
|
3.4
|
7.5
|
1.0
|
HB2
|
B:ASP287
|
3.5
|
8.4
|
1.0
|
CB
|
B:ASP287
|
3.5
|
8.5
|
1.0
|
H32
|
B:GOL403
|
3.6
|
28.4
|
1.0
|
HE1
|
B:HIS220
|
3.7
|
9.5
|
1.0
|
HB3
|
B:ASP245
|
3.7
|
7.8
|
1.0
|
O
|
B:HOH515
|
3.8
|
16.0
|
1.0
|
O
|
B:HOH707
|
3.9
|
17.1
|
1.0
|
HB2
|
B:ASP245
|
3.9
|
7.8
|
1.0
|
CB
|
B:ASP245
|
3.9
|
7.7
|
1.0
|
OE2
|
B:GLU217
|
4.0
|
11.1
|
1.0
|
CE1
|
B:HIS220
|
4.0
|
9.7
|
1.0
|
CG
|
B:GLU217
|
4.1
|
7.9
|
1.0
|
CB
|
B:GLU217
|
4.1
|
7.5
|
1.0
|
OD1
|
B:ASP287
|
4.2
|
9.0
|
1.0
|
HG3
|
B:GLU217
|
4.2
|
8.2
|
1.0
|
H31
|
B:GOL403
|
4.3
|
28.3
|
1.0
|
CG
|
B:GLU181
|
4.3
|
10.5
|
1.0
|
OD1
|
B:ASP245
|
4.4
|
8.8
|
1.0
|
HB3
|
B:GLU217
|
4.4
|
7.5
|
1.0
|
HE2
|
B:HIS220
|
4.5
|
10.9
|
0.0
|
NE2
|
B:HIS220
|
4.5
|
10.1
|
1.0
|
HG3
|
B:GLU181
|
4.5
|
10.8
|
1.0
|
HD21
|
B:ASN215
|
4.5
|
8.4
|
0.0
|
HG2
|
B:GLU181
|
4.6
|
10.8
|
1.0
|
C1
|
B:GOL403
|
4.6
|
19.0
|
1.0
|
HZ2
|
B:TRP16
|
4.6
|
8.1
|
1.0
|
HD22
|
B:ASN215
|
4.7
|
8.4
|
0.0
|
H11
|
B:GOL403
|
4.8
|
19.2
|
1.0
|
ND1
|
B:HIS220
|
4.8
|
8.6
|
1.0
|
MN
|
B:MN401
|
4.9
|
7.1
|
0.5
|
O
|
B:HOH706
|
4.9
|
28.5
|
1.0
|
H12
|
B:GOL403
|
4.9
|
19.2
|
1.0
|
HG2
|
B:GLU217
|
4.9
|
8.2
|
1.0
|
HD1
|
B:HIS220
|
4.9
|
8.7
|
0.0
|
ND2
|
B:ASN215
|
5.0
|
8.4
|
1.0
|
|
Reference:
B.D.Belviso,
R.Caliandro,
S.M.Salehi,
G.Di Profio,
R.Caliandro.
Protein Crystallization in Ionic-Liquid Hydrogel Composite Membranes Crystals 2019.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST9050253
Page generated: Sun Oct 6 06:08:56 2024
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