Iodine in PDB 1xc6: Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
Enzymatic activity of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
All present enzymatic activity of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose:
3.2.1.23;
Protein crystallography data
The structure of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose, PDB code: 1xc6
was solved by
A.L.Rojas,
R.A.P.Nagem,
K.N.Neustroev,
M.Arand,
M.Adamska,
E.V.Eneyskaya,
A.A.Kulminskaya,
R.C.Garratt,
A.M.Golubev,
I.Polikarpov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
23.40 /
2.10
|
Space group
|
P 43
|
Cell size a, b, c (Å), α, β, γ (°)
|
110.960,
110.960,
161.050,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.1 /
18.6
|
Other elements in 1xc6:
The structure of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose also contains other interesting chemical elements:
Iodine Binding Sites:
Iodine binding site 1 out
of 52 in 1xc6
Go back to
Iodine Binding Sites List in 1xc6
Iodine binding site 1 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_01.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9021
b:28.0
occ:0.70
|
O
|
A:HOH9811
|
2.9
|
44.9
|
1.0
|
O
|
A:HOH9097
|
3.6
|
9.6
|
1.0
|
O
|
A:HOH9197
|
3.7
|
18.4
|
1.0
|
OH
|
A:TYR360
|
3.8
|
11.1
|
1.0
|
N
|
A:PHE313
|
3.9
|
12.8
|
1.0
|
O
|
A:HOH9417
|
4.0
|
16.6
|
1.0
|
CE2
|
A:TYR360
|
4.1
|
8.7
|
1.0
|
CA
|
A:GLY312
|
4.2
|
12.5
|
1.0
|
CD2
|
A:PHE313
|
4.3
|
10.5
|
1.0
|
C8
|
A:NAG1992
|
4.4
|
24.4
|
1.0
|
CZ
|
A:TYR360
|
4.5
|
8.6
|
1.0
|
CB
|
A:GLN946
|
4.5
|
10.9
|
1.0
|
CA
|
A:GLN946
|
4.6
|
11.3
|
1.0
|
C
|
A:GLY312
|
4.6
|
12.8
|
1.0
|
CG
|
A:GLN946
|
4.6
|
9.4
|
1.0
|
CB
|
A:PHE313
|
4.7
|
12.5
|
1.0
|
O
|
A:HOH9925
|
4.9
|
45.7
|
1.0
|
CA
|
A:PHE313
|
4.9
|
13.8
|
1.0
|
OG
|
A:SER362
|
4.9
|
10.4
|
1.0
|
CB
|
A:SER362
|
4.9
|
7.8
|
1.0
|
CG
|
A:PHE313
|
4.9
|
11.7
|
1.0
|
CD
|
A:GLN946
|
5.0
|
10.4
|
1.0
|
|
Iodine binding site 2 out
of 52 in 1xc6
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Iodine Binding Sites List in 1xc6
Iodine binding site 2 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_02.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9022
b:27.7
occ:0.30
|
O
|
A:HOH9353
|
2.9
|
23.8
|
1.0
|
N
|
A:LYS379
|
3.3
|
13.2
|
1.0
|
CB
|
A:ASN321
|
3.6
|
14.3
|
1.0
|
N
|
A:HIS322
|
3.7
|
13.2
|
1.0
|
CB
|
A:LYS379
|
3.7
|
13.3
|
1.0
|
O
|
A:HOH9610
|
3.7
|
31.4
|
1.0
|
N
|
A:GLU378
|
3.8
|
13.5
|
1.0
|
CA
|
A:ASN321
|
3.9
|
14.4
|
1.0
|
CG
|
A:LYS379
|
3.9
|
13.1
|
1.0
|
CA
|
A:LYS379
|
4.0
|
12.9
|
1.0
|
CB
|
A:GLU378
|
4.1
|
14.6
|
1.0
|
CD2
|
A:HIS322
|
4.1
|
13.9
|
1.0
|
C
|
A:GLU378
|
4.2
|
14.3
|
1.0
|
I
|
A:IOD9023
|
4.2
|
28.7
|
0.7
|
CA
|
A:GLU378
|
4.2
|
13.1
|
1.0
|
C
|
A:ASN321
|
4.2
|
13.5
|
1.0
|
CD
|
A:LYS379
|
4.4
|
13.9
|
1.0
|
O
|
A:ALA317
|
4.4
|
13.7
|
1.0
|
CB
|
A:ARG377
|
4.5
|
14.3
|
1.0
|
C
|
A:ARG377
|
4.5
|
13.0
|
1.0
|
CB
|
A:HIS322
|
4.5
|
14.0
|
1.0
|
CG
|
A:HIS322
|
4.7
|
14.9
|
1.0
|
CA
|
A:HIS322
|
4.7
|
13.0
|
1.0
|
CA
|
A:ARG377
|
4.8
|
13.4
|
1.0
|
CG
|
A:ASN321
|
4.9
|
16.2
|
1.0
|
|
Iodine binding site 3 out
of 52 in 1xc6
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Iodine Binding Sites List in 1xc6
Iodine binding site 3 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_03.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9023
b:28.7
occ:0.70
|
O
|
A:HOH9610
|
3.1
|
31.4
|
1.0
|
I
|
A:IOD9057
|
3.7
|
69.0
|
0.5
|
O2
|
A:BMA3004
|
3.8
|
48.6
|
1.0
|
O
|
A:HOH9353
|
3.8
|
23.8
|
1.0
|
N
|
A:GLU378
|
3.9
|
13.5
|
1.0
|
CA
|
A:ARG377
|
3.9
|
13.4
|
1.0
|
O6
|
A:NAG3002
|
3.9
|
32.6
|
1.0
|
C2
|
A:BMA3003
|
4.0
|
22.9
|
1.0
|
O4
|
A:NAG3002
|
4.0
|
17.9
|
1.0
|
I
|
A:IOD9022
|
4.2
|
27.7
|
0.3
|
O2
|
A:BMA3003
|
4.3
|
18.7
|
1.0
|
CG
|
A:ARG377
|
4.4
|
13.4
|
1.0
|
CB
|
A:ARG377
|
4.4
|
14.3
|
1.0
|
C6
|
A:NAG3002
|
4.4
|
24.4
|
1.0
|
C
|
A:ARG377
|
4.4
|
13.0
|
1.0
|
C1
|
A:BMA3003
|
4.5
|
20.6
|
1.0
|
C5
|
A:NAG3002
|
4.5
|
21.3
|
1.0
|
CB
|
A:GLU378
|
4.8
|
14.6
|
1.0
|
O
|
A:THR376
|
4.9
|
16.2
|
1.0
|
C4
|
A:NAG3002
|
4.9
|
18.7
|
1.0
|
N
|
A:ARG377
|
4.9
|
14.6
|
1.0
|
CA
|
A:GLU378
|
5.0
|
13.1
|
1.0
|
|
Iodine binding site 4 out
of 52 in 1xc6
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Iodine Binding Sites List in 1xc6
Iodine binding site 4 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_04.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9024
b:29.1
occ:0.50
|
O
|
A:HOH9486
|
3.2
|
22.9
|
1.0
|
N
|
A:ASN244
|
3.5
|
16.2
|
1.0
|
CA
|
A:HIS243
|
4.0
|
17.4
|
1.0
|
CG
|
A:PRO212
|
4.1
|
21.3
|
1.0
|
C
|
A:HIS243
|
4.3
|
17.1
|
1.0
|
CB
|
A:THR248
|
4.3
|
20.5
|
1.0
|
CG2
|
A:THR248
|
4.4
|
21.2
|
1.0
|
O
|
A:HOH7027
|
4.4
|
41.2
|
1.0
|
CD2
|
A:HIS243
|
4.4
|
16.9
|
1.0
|
CB
|
A:PRO212
|
4.4
|
21.4
|
1.0
|
O
|
A:HOH9239
|
4.4
|
14.9
|
1.0
|
CA
|
A:ASN244
|
4.4
|
16.1
|
1.0
|
O
|
A:HOH9884
|
4.5
|
47.3
|
1.0
|
O
|
A:GLY242
|
4.6
|
18.1
|
1.0
|
OG1
|
A:THR248
|
4.6
|
19.1
|
1.0
|
CB
|
A:HIS243
|
4.7
|
17.4
|
1.0
|
ND2
|
A:ASN244
|
4.8
|
16.5
|
1.0
|
CG
|
A:HIS243
|
4.9
|
17.3
|
1.0
|
N
|
A:HIS243
|
5.0
|
17.2
|
1.0
|
|
Iodine binding site 5 out
of 52 in 1xc6
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Iodine Binding Sites List in 1xc6
Iodine binding site 5 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_05.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9025
b:32.9
occ:0.30
|
O
|
A:HOH9424
|
3.0
|
25.6
|
1.0
|
N
|
A:LEU713
|
3.4
|
18.9
|
1.0
|
CB
|
A:LEU713
|
3.9
|
20.2
|
1.0
|
CA
|
A:SER712
|
4.0
|
20.9
|
1.0
|
CG
|
A:LEU713
|
4.1
|
21.2
|
1.0
|
CB
|
A:SER712
|
4.1
|
22.0
|
1.0
|
CG2
|
A:THR706
|
4.2
|
12.4
|
1.0
|
C
|
A:SER712
|
4.2
|
19.8
|
1.0
|
CA
|
A:LEU713
|
4.2
|
19.2
|
1.0
|
CD1
|
A:LEU713
|
4.6
|
18.8
|
1.0
|
O
|
A:LEU713
|
4.8
|
17.8
|
1.0
|
N
|
A:THR706
|
4.9
|
17.9
|
1.0
|
O
|
A:HOH9463
|
5.0
|
26.6
|
1.0
|
|
Iodine binding site 6 out
of 52 in 1xc6
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Iodine Binding Sites List in 1xc6
Iodine binding site 6 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_06.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9026
b:32.2
occ:0.50
|
OG
|
A:SER260
|
3.3
|
15.6
|
1.0
|
O
|
A:HOH9522
|
3.5
|
32.3
|
1.0
|
O
|
A:HOH9301
|
3.8
|
21.7
|
1.0
|
O
|
A:HOH9864
|
4.1
|
48.6
|
1.0
|
CA
|
A:PRO262
|
4.1
|
18.1
|
1.0
|
N
|
A:PRO262
|
4.1
|
17.5
|
1.0
|
CB
|
A:SER260
|
4.2
|
14.5
|
1.0
|
CB
|
A:PRO262
|
4.3
|
19.3
|
1.0
|
N
|
A:TYR261
|
4.4
|
13.2
|
1.0
|
CZ
|
A:PHE282
|
4.4
|
17.2
|
1.0
|
CD
|
A:PRO262
|
4.4
|
19.1
|
1.0
|
CA
|
A:SER260
|
4.5
|
13.3
|
1.0
|
C
|
A:TYR261
|
4.6
|
15.0
|
1.0
|
C
|
A:SER260
|
4.8
|
13.5
|
1.0
|
CB
|
A:PRO279
|
4.9
|
21.7
|
1.0
|
OH
|
A:TYR281
|
4.9
|
25.5
|
1.0
|
CG
|
A:PRO279
|
4.9
|
22.3
|
1.0
|
O
|
A:TYR261
|
5.0
|
14.1
|
1.0
|
CG
|
A:PRO262
|
5.0
|
20.0
|
1.0
|
|
Iodine binding site 7 out
of 52 in 1xc6
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Iodine Binding Sites List in 1xc6
Iodine binding site 7 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_07.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9027
b:37.8
occ:0.65
|
OG
|
A:SER465
|
3.1
|
36.0
|
1.0
|
ND2
|
A:ASN411
|
3.5
|
28.1
|
1.0
|
CB
|
A:SER465
|
4.0
|
28.7
|
1.0
|
CA
|
A:TYR446
|
4.0
|
22.8
|
1.0
|
N
|
A:TYR446
|
4.1
|
23.1
|
1.0
|
CG
|
A:LYS447
|
4.1
|
28.6
|
1.0
|
C
|
A:TYR446
|
4.1
|
22.8
|
1.0
|
C
|
A:GLU445
|
4.4
|
25.3
|
1.0
|
O
|
A:TYR446
|
4.4
|
24.7
|
1.0
|
CE
|
A:LYS447
|
4.4
|
34.7
|
1.0
|
CB
|
A:GLU445
|
4.5
|
32.3
|
1.0
|
O
|
A:GLU445
|
4.5
|
24.4
|
1.0
|
CG
|
A:ASN411
|
4.5
|
29.4
|
1.0
|
N
|
A:LYS447
|
4.5
|
23.2
|
1.0
|
OD1
|
A:ASN411
|
4.6
|
28.6
|
1.0
|
CD
|
A:LYS447
|
4.7
|
32.3
|
1.0
|
|
Iodine binding site 8 out
of 52 in 1xc6
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Iodine Binding Sites List in 1xc6
Iodine binding site 8 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_08.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9028
b:47.9
occ:0.30
|
OG1
|
A:THR692
|
3.3
|
30.9
|
1.0
|
O
|
A:HOH9585
|
3.6
|
35.2
|
1.0
|
N
|
A:TYR693
|
4.0
|
25.1
|
1.0
|
O
|
A:HOH9532
|
4.0
|
28.9
|
1.0
|
CA
|
A:TYR693
|
4.0
|
23.3
|
1.0
|
C
|
A:THR692
|
4.1
|
27.6
|
1.0
|
O
|
A:THR692
|
4.2
|
27.6
|
1.0
|
CB
|
A:THR692
|
4.3
|
30.2
|
1.0
|
CD1
|
A:TYR693
|
4.3
|
18.7
|
1.0
|
CD
|
A:LYS690
|
4.3
|
40.1
|
1.0
|
O
|
A:PRO687
|
4.4
|
16.5
|
1.0
|
CB
|
A:PRO687
|
4.4
|
17.0
|
1.0
|
CB
|
A:TYR693
|
4.4
|
21.0
|
1.0
|
CB
|
A:LYS690
|
4.7
|
31.4
|
1.0
|
CA
|
A:THR692
|
4.8
|
28.5
|
1.0
|
CG
|
A:TYR693
|
4.9
|
20.4
|
1.0
|
|
Iodine binding site 9 out
of 52 in 1xc6
Go back to
Iodine Binding Sites List in 1xc6
Iodine binding site 9 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_09.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 9 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9029
b:29.5
occ:0.39
|
I
|
A:IOD9065
|
3.6
|
56.8
|
0.3
|
N
|
A:THR888
|
3.7
|
17.8
|
1.0
|
CA
|
A:LEU887
|
3.8
|
19.8
|
1.0
|
OG1
|
A:THR888
|
4.0
|
20.6
|
1.0
|
CB
|
A:LEU887
|
4.0
|
21.3
|
1.0
|
C
|
A:LEU887
|
4.3
|
19.0
|
1.0
|
CE
|
A:LYS889
|
4.3
|
36.6
|
1.0
|
CG
|
A:LYS889
|
4.4
|
27.4
|
1.0
|
CG
|
A:LEU887
|
4.4
|
23.8
|
1.0
|
NZ
|
A:LYS889
|
4.4
|
42.2
|
1.0
|
O
|
A:GLY886
|
4.7
|
18.7
|
1.0
|
CD
|
A:ARG893
|
4.7
|
24.3
|
1.0
|
CA
|
A:THR888
|
4.8
|
19.2
|
1.0
|
O
|
A:HOH9831
|
4.8
|
66.3
|
1.0
|
N
|
A:LYS889
|
4.8
|
17.6
|
1.0
|
CD
|
A:LYS889
|
4.9
|
32.3
|
1.0
|
CB
|
A:THR888
|
4.9
|
21.4
|
1.0
|
CD2
|
A:LEU887
|
5.0
|
25.2
|
1.0
|
|
Iodine binding site 10 out
of 52 in 1xc6
Go back to
Iodine Binding Sites List in 1xc6
Iodine binding site 10 out
of 52 in the Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose
![](/pictures/I/pdb/xc/1xc6-I-sphere_10.jpg) Mono view
![](/pictures/I/pdb/xc/1xc6-I-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 10 of Native Structure of Beta-Galactosidase From Penicillium Sp. in Complex with Galactose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I9030
b:38.5
occ:0.65
|
O
|
A:HOH9370
|
3.4
|
33.2
|
1.0
|
O
|
A:VAL551
|
3.9
|
19.8
|
1.0
|
N
|
A:GLY513
|
4.0
|
23.5
|
1.0
|
CA
|
A:PRO512
|
4.0
|
23.3
|
1.0
|
CA
|
A:SER552
|
4.1
|
20.8
|
1.0
|
CG1
|
A:VAL551
|
4.3
|
19.0
|
1.0
|
C
|
A:VAL551
|
4.3
|
19.9
|
1.0
|
N
|
A:THR553
|
4.3
|
20.4
|
1.0
|
CB
|
A:PRO512
|
4.3
|
24.8
|
1.0
|
CG2
|
A:THR553
|
4.4
|
24.6
|
1.0
|
C
|
A:SER552
|
4.4
|
20.3
|
1.0
|
N
|
A:SER552
|
4.5
|
20.1
|
1.0
|
C
|
A:PRO512
|
4.6
|
23.6
|
1.0
|
CB
|
A:VAL551
|
4.9
|
19.6
|
1.0
|
O
|
A:HOH9783
|
5.0
|
44.2
|
1.0
|
O
|
A:HOH9527
|
5.0
|
32.2
|
1.0
|
|
Reference:
A.L.Rojas,
R.A.P.Nagem,
K.N.Neustroev,
M.Arand,
M.Adamska,
E.V.Eneyskaya,
A.A.Kulminskaya,
R.C.Garratt,
A.M.Golubev,
I.Polikarpov.
Crystal Structures of Beta-Galactosidase From Penicillium Sp. and Its Complex with Galactose J.Mol.Biol. V. 343 1281 2004.
ISSN: ISSN 0022-2836
PubMed: 15491613
DOI: 10.1016/J.JMB.2004.09.012
Page generated: Sun Aug 11 13:03:05 2024
|