Iodine in PDB 4j3t: Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Enzymatic activity of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
All present enzymatic activity of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose:
3.2.1.41;
Protein crystallography data
The structure of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose, PDB code: 4j3t
was solved by
L.Sim,
M.S.Windahl,
M.S.Moeller,
A.Henriksen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.70 /
1.60
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
175.090,
86.230,
61.510,
90.00,
95.58,
90.00
|
R / Rfree (%)
|
13.3 /
17.7
|
Other elements in 4j3t:
The structure of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
(pdb code 4j3t). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the
Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose, PDB code: 4j3t:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iodine binding site 1 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 1 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I908
b:23.7
occ:1.00
|
O
|
A:HOH1812
|
3.0
|
45.5
|
1.0
|
O
|
A:HOH1247
|
3.4
|
19.1
|
1.0
|
CA
|
A:GLY423
|
3.8
|
12.0
|
1.0
|
NE
|
A:ARG428
|
3.8
|
13.8
|
1.0
|
CZ
|
A:ARG428
|
3.9
|
12.4
|
1.0
|
N
|
A:GLY423
|
4.0
|
10.8
|
1.0
|
NH2
|
A:ARG428
|
4.1
|
16.2
|
1.0
|
CG
|
A:PRO198
|
4.2
|
19.1
|
1.0
|
CB
|
A:PRO198
|
4.3
|
20.9
|
1.0
|
CD
|
A:ARG428
|
4.3
|
14.6
|
1.0
|
CG2
|
A:THR199
|
4.3
|
19.5
|
1.0
|
NH1
|
A:ARG428
|
4.4
|
13.4
|
1.0
|
O
|
A:GLY432
|
4.4
|
15.4
|
1.0
|
O
|
A:HOH1258
|
4.5
|
18.9
|
1.0
|
CD
|
A:PRO198
|
4.5
|
18.6
|
1.0
|
CG1
|
A:ILE434
|
4.7
|
15.2
|
1.0
|
O
|
A:HOH1261
|
4.7
|
28.4
|
1.0
|
O
|
A:HOH1226
|
4.7
|
23.5
|
1.0
|
CD1
|
A:ILE434
|
4.8
|
14.4
|
1.0
|
C
|
A:PRO422
|
4.9
|
11.6
|
1.0
|
CG
|
A:ARG428
|
4.9
|
12.9
|
1.0
|
|
Iodine binding site 2 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 2 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I909
b:18.1
occ:1.00
|
O
|
A:HOH1168
|
3.6
|
12.0
|
1.0
|
O
|
A:HOH1065
|
3.6
|
14.6
|
1.0
|
CD
|
A:ARG452
|
3.8
|
9.2
|
1.0
|
CG
|
A:ARG452
|
4.0
|
9.3
|
1.0
|
CG2
|
A:THR127
|
4.0
|
11.2
|
1.0
|
CB
|
A:THR127
|
4.0
|
11.0
|
1.0
|
NE
|
A:ARG452
|
4.0
|
9.4
|
1.0
|
CA
|
A:THR127
|
4.1
|
10.8
|
1.0
|
CZ
|
A:ARG452
|
4.5
|
10.5
|
1.0
|
O
|
A:THR127
|
4.5
|
14.0
|
1.0
|
NH1
|
A:ARG452
|
4.7
|
12.0
|
1.0
|
C
|
A:THR127
|
4.8
|
11.4
|
1.0
|
NH1
|
A:ARG485
|
4.8
|
10.9
|
1.0
|
CB
|
A:ARG452
|
4.8
|
9.8
|
1.0
|
O
|
A:TYR126
|
4.8
|
10.6
|
1.0
|
NH2
|
A:ARG485
|
4.9
|
10.7
|
1.0
|
|
Iodine binding site 3 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 3 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I910
b:23.6
occ:1.00
|
O
|
A:HOH1386
|
3.5
|
24.7
|
1.0
|
NE2
|
A:GLN850
|
3.6
|
14.1
|
1.0
|
CG1
|
A:ILE761
|
3.6
|
20.5
|
1.0
|
CE1
|
A:HIS668
|
3.7
|
14.9
|
1.0
|
NE2
|
A:HIS668
|
3.8
|
17.6
|
1.0
|
CD1
|
A:ILE761
|
3.8
|
21.4
|
1.0
|
O
|
A:HOH1062
|
4.1
|
16.3
|
1.0
|
O
|
A:HOH1105
|
4.1
|
16.2
|
1.0
|
CG
|
A:GLN850
|
4.2
|
13.1
|
1.0
|
O
|
A:SER757
|
4.2
|
10.6
|
0.4
|
O
|
A:SER757
|
4.3
|
11.0
|
0.6
|
CB
|
A:ASP760
|
4.3
|
11.3
|
1.0
|
CD
|
A:GLN850
|
4.4
|
12.9
|
1.0
|
CB
|
A:SER757
|
4.6
|
13.2
|
0.6
|
N
|
A:ILE761
|
4.7
|
11.9
|
1.0
|
CD1
|
A:ILE764
|
4.8
|
14.0
|
1.0
|
CA
|
A:SER757
|
4.8
|
12.4
|
0.6
|
ND1
|
A:HIS668
|
4.9
|
16.8
|
1.0
|
CB
|
A:ILE761
|
4.9
|
14.4
|
1.0
|
CA
|
A:SER757
|
4.9
|
10.8
|
0.4
|
C
|
A:SER757
|
5.0
|
11.5
|
0.6
|
|
Iodine binding site 4 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 4 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I911
b:30.4
occ:1.00
|
OG
|
A:SER414
|
2.9
|
32.9
|
1.0
|
O
|
A:HOH1169
|
3.5
|
14.2
|
1.0
|
O
|
A:HOH1230
|
3.6
|
16.6
|
1.0
|
O
|
A:HOH1493
|
3.6
|
22.5
|
1.0
|
O
|
A:HOH1727
|
3.8
|
30.0
|
1.0
|
O
|
A:ASN219
|
3.9
|
12.2
|
1.0
|
CB
|
A:SER414
|
4.0
|
20.3
|
1.0
|
CB
|
A:ALA313
|
4.1
|
9.4
|
1.0
|
CG2
|
A:ILE413
|
4.2
|
29.2
|
1.0
|
CE1
|
A:HIS311
|
4.2
|
11.1
|
1.0
|
CA
|
A:ALA313
|
4.2
|
8.6
|
1.0
|
NE2
|
A:HIS311
|
4.2
|
11.2
|
1.0
|
CA
|
A:SER414
|
4.3
|
17.5
|
1.0
|
CG2
|
A:VAL360
|
4.5
|
9.7
|
1.0
|
N
|
A:SER414
|
4.6
|
19.1
|
1.0
|
CG1
|
A:ILE413
|
4.7
|
30.5
|
1.0
|
O
|
A:ILE413
|
4.7
|
21.5
|
1.0
|
C
|
A:ILE413
|
4.7
|
21.4
|
1.0
|
C
|
A:ASN219
|
4.7
|
10.6
|
1.0
|
CB
|
A:ASN219
|
4.7
|
11.8
|
1.0
|
N
|
A:ALA313
|
4.9
|
9.2
|
1.0
|
CA
|
A:ASN219
|
4.9
|
11.2
|
1.0
|
|
Iodine binding site 5 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 5 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I912
b:47.2
occ:1.00
|
O
|
A:HOH1264
|
3.2
|
29.4
|
1.0
|
O
|
A:HOH1885
|
3.2
|
39.5
|
1.0
|
O
|
A:HOH1349
|
3.5
|
30.0
|
1.0
|
OG
|
A:SER53
|
3.8
|
25.8
|
1.0
|
CB
|
A:SER53
|
3.9
|
23.8
|
1.0
|
CB
|
A:VAL55
|
4.1
|
24.9
|
1.0
|
CG2
|
A:VAL87
|
4.1
|
23.7
|
1.0
|
CG1
|
A:VAL55
|
4.2
|
25.3
|
1.0
|
CD1
|
A:LEU92
|
4.4
|
26.8
|
1.0
|
O
|
A:LYS54
|
4.6
|
27.2
|
1.0
|
CG1
|
A:VAL87
|
4.7
|
24.2
|
1.0
|
CD2
|
A:LEU92
|
4.7
|
27.1
|
1.0
|
C
|
A:LYS54
|
4.7
|
25.1
|
1.0
|
CA
|
A:VAL87
|
4.7
|
24.9
|
1.0
|
CB
|
A:VAL87
|
4.8
|
23.0
|
1.0
|
CG
|
A:LEU92
|
4.9
|
25.6
|
1.0
|
N
|
A:VAL55
|
4.9
|
22.6
|
1.0
|
N
|
A:LYS54
|
5.0
|
23.8
|
1.0
|
|
Iodine binding site 6 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 6 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I913
b:50.2
occ:1.00
|
NH1
|
A:ARG581
|
3.7
|
14.5
|
1.0
|
CD
|
A:ARG581
|
3.9
|
17.2
|
1.0
|
CE1
|
A:PHE566
|
4.1
|
14.4
|
1.0
|
CG
|
A:GLU577
|
4.1
|
35.1
|
1.0
|
CZ
|
A:PHE566
|
4.3
|
14.3
|
1.0
|
CB
|
A:GLU577
|
4.4
|
29.8
|
1.0
|
O
|
A:GLU577
|
4.4
|
23.0
|
1.0
|
C
|
A:GLU577
|
4.5
|
23.7
|
1.0
|
CZ
|
A:ARG581
|
4.6
|
14.4
|
1.0
|
N
|
A:ALA578
|
4.6
|
22.5
|
1.0
|
NE
|
A:ARG581
|
4.6
|
14.9
|
1.0
|
CB
|
A:ARG581
|
4.6
|
14.5
|
1.0
|
CA
|
A:ALA578
|
4.7
|
24.9
|
1.0
|
CG
|
A:ARG581
|
4.8
|
15.1
|
1.0
|
|
Iodine binding site 7 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 7 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I914
b:36.6
occ:0.50
|
I
|
A:IOD914
|
0.0
|
36.6
|
0.5
|
I
|
A:IOD914
|
2.4
|
25.2
|
0.5
|
O
|
A:HOH1597
|
3.5
|
25.6
|
1.0
|
CG
|
A:MET484
|
4.0
|
12.4
|
1.0
|
CA
|
A:ARG481
|
4.0
|
10.5
|
1.0
|
O
|
A:HOH1114
|
4.1
|
16.6
|
1.0
|
CB
|
A:MET484
|
4.2
|
11.3
|
1.0
|
CG
|
A:LYS480
|
4.3
|
10.5
|
1.0
|
N
|
A:ARG481
|
4.4
|
9.8
|
1.0
|
CB
|
A:ARG481
|
4.4
|
11.4
|
1.0
|
CE
|
A:LYS480
|
4.5
|
12.9
|
1.0
|
O
|
A:LYS480
|
4.5
|
9.4
|
1.0
|
C
|
A:LYS480
|
4.6
|
9.8
|
1.0
|
CD
|
A:LYS480
|
4.7
|
12.3
|
1.0
|
O
|
A:HOH1574
|
4.9
|
30.9
|
1.0
|
|
Iodine binding site 8 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 8 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I914
b:25.2
occ:0.50
|
I
|
A:IOD914
|
0.0
|
25.2
|
0.5
|
I
|
A:IOD914
|
2.4
|
36.6
|
0.5
|
O
|
A:HOH1231
|
3.9
|
12.0
|
1.0
|
O
|
A:HOH1574
|
3.9
|
30.9
|
1.0
|
CG
|
A:LYS480
|
3.9
|
10.5
|
1.0
|
CD
|
A:LYS480
|
4.0
|
12.3
|
1.0
|
N
|
A:ARG481
|
4.0
|
9.8
|
1.0
|
CB
|
A:LYS480
|
4.1
|
10.1
|
1.0
|
CA
|
A:ARG481
|
4.2
|
10.5
|
1.0
|
CB
|
A:ARG481
|
4.2
|
11.4
|
1.0
|
O
|
A:HOH1691
|
4.2
|
26.8
|
1.0
|
C
|
A:LYS480
|
4.4
|
9.8
|
1.0
|
CE
|
A:LYS480
|
4.4
|
12.9
|
1.0
|
CD1
|
A:ILE524
|
4.6
|
16.1
|
1.0
|
CB
|
A:ILE524
|
4.7
|
11.8
|
1.0
|
CG2
|
A:ILE524
|
4.9
|
11.8
|
1.0
|
CA
|
A:LYS480
|
4.9
|
9.9
|
1.0
|
O
|
A:LYS480
|
5.0
|
9.4
|
1.0
|
|
Iodine binding site 9 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 9 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 9 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I915
b:47.2
occ:1.00
|
O
|
A:HOH1804
|
3.8
|
30.7
|
1.0
|
CA
|
A:PRO162
|
3.9
|
15.1
|
1.0
|
O
|
A:HOH1913
|
4.1
|
35.0
|
1.0
|
N
|
A:PRO162
|
4.2
|
18.2
|
1.0
|
CB
|
A:PRO162
|
4.3
|
17.2
|
1.0
|
O
|
A:GLY161
|
4.3
|
18.5
|
1.0
|
O
|
A:ALA160
|
4.4
|
24.5
|
1.0
|
C
|
A:GLY161
|
4.4
|
19.9
|
1.0
|
NH2
|
A:ARG222
|
4.7
|
15.5
|
1.0
|
CD
|
A:PRO162
|
4.9
|
18.6
|
1.0
|
|
Iodine binding site 10 out
of 10 in 4j3t
Go back to
Iodine Binding Sites List in 4j3t
Iodine binding site 10 out
of 10 in the Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 10 of Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I916
b:48.2
occ:1.00
|
O
|
A:HOH1670
|
3.2
|
34.1
|
1.0
|
O
|
A:HOH1956
|
3.7
|
47.6
|
1.0
|
CE1
|
A:HIS847
|
3.7
|
13.3
|
1.0
|
O
|
A:HOH1873
|
4.1
|
32.9
|
1.0
|
CB
|
A:SER767
|
4.3
|
12.2
|
1.0
|
NE2
|
A:HIS847
|
4.4
|
11.9
|
1.0
|
CG
|
A:PRO848
|
4.5
|
17.0
|
1.0
|
CB
|
A:PRO848
|
4.5
|
16.8
|
1.0
|
CZ
|
A:PHE818
|
4.6
|
17.3
|
1.0
|
ND1
|
A:HIS847
|
4.6
|
12.7
|
1.0
|
CG2
|
A:VAL849
|
4.7
|
14.1
|
1.0
|
CD
|
A:PRO848
|
4.7
|
14.3
|
1.0
|
OG
|
A:SER767
|
4.9
|
12.2
|
1.0
|
|
Reference:
L.Sim,
M.S.Windahl,
M.S.Moeller,
A.Henriksen.
Crystal Structure of Barley Limit Dextrinase Co-Crystallized with 25MM Maltotetraose To Be Published.
Page generated: Sun Aug 11 18:13:32 2024
|