Iodine in PDB 4ljj: Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
Enzymatic activity of Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
All present enzymatic activity of Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution:
1.11.1.7;
Protein crystallography data
The structure of Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution, PDB code: 4ljj
was solved by
M.Kumar,
R.P.Singh,
A.K.Singh,
M.Sinha,
P.Kaur,
S.Sharma,
T.P.Singh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
74.22 /
1.98
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.052,
80.342,
76.121,
90.00,
102.82,
90.00
|
R / Rfree (%)
|
19 /
24.2
|
Other elements in 4ljj:
The structure of Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution also contains other interesting chemical elements:
Iodine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
13;
Binding sites:
The binding sites of Iodine atom in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
(pdb code 4ljj). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the
Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution, PDB code: 4ljj:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iodine binding site 1 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 1 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I607
b:49.8
occ:0.66
|
O
|
A:HOH926
|
3.7
|
45.1
|
1.0
|
N
|
A:PHE229
|
3.8
|
34.7
|
1.0
|
N
|
A:GLN217
|
3.8
|
38.2
|
1.0
|
CG
|
A:ASN216
|
4.0
|
35.3
|
1.0
|
CG
|
A:GLU218
|
4.1
|
59.1
|
1.0
|
CA
|
A:ASN216
|
4.1
|
35.2
|
1.0
|
ND2
|
A:ASN216
|
4.1
|
30.6
|
1.0
|
OD1
|
A:ASN216
|
4.1
|
35.8
|
1.0
|
CD2
|
A:PHE229
|
4.1
|
44.7
|
1.0
|
CA
|
A:PRO228
|
4.2
|
35.6
|
1.0
|
CB
|
A:PHE229
|
4.4
|
38.6
|
1.0
|
C
|
A:ASN216
|
4.5
|
36.5
|
1.0
|
C
|
A:PRO228
|
4.5
|
34.1
|
1.0
|
CB
|
A:PRO228
|
4.5
|
36.0
|
1.0
|
CG
|
A:PHE229
|
4.6
|
41.0
|
1.0
|
CD
|
A:GLU218
|
4.7
|
65.5
|
1.0
|
CB
|
A:ASN216
|
4.7
|
34.4
|
1.0
|
CA
|
A:PHE229
|
4.7
|
35.3
|
1.0
|
N
|
A:GLU218
|
4.7
|
44.3
|
1.0
|
O
|
A:VAL215
|
4.8
|
39.8
|
1.0
|
CA
|
A:GLN217
|
4.8
|
45.0
|
1.0
|
CB
|
A:GLN217
|
4.9
|
42.6
|
1.0
|
CE2
|
A:PHE229
|
5.0
|
45.4
|
1.0
|
|
Iodine binding site 2 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 2 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I608
b:35.9
occ:0.60
|
NE
|
A:ARG397
|
3.5
|
39.0
|
1.0
|
N
|
A:THR560
|
3.6
|
39.2
|
1.0
|
OG1
|
A:THR560
|
3.8
|
41.2
|
1.0
|
N
|
A:LYS561
|
3.9
|
37.4
|
1.0
|
O
|
A:GLU363
|
4.0
|
39.4
|
1.0
|
CG2
|
A:ILE559
|
4.0
|
36.1
|
1.0
|
NH2
|
A:ARG397
|
4.0
|
39.7
|
1.0
|
CA
|
A:ILE559
|
4.0
|
35.4
|
1.0
|
CG
|
A:LYS561
|
4.1
|
51.5
|
1.0
|
CA
|
A:GLU363
|
4.1
|
46.8
|
1.0
|
CZ
|
A:ARG397
|
4.2
|
35.8
|
1.0
|
CB
|
A:LYS561
|
4.2
|
42.1
|
1.0
|
CD
|
A:ARG397
|
4.3
|
38.2
|
1.0
|
C
|
A:ILE559
|
4.3
|
37.3
|
1.0
|
CE2
|
A:TYR365
|
4.4
|
35.5
|
1.0
|
CB
|
A:GLU363
|
4.4
|
53.0
|
1.0
|
C
|
A:GLU363
|
4.5
|
39.4
|
1.0
|
CA
|
A:THR560
|
4.5
|
39.0
|
1.0
|
CB
|
A:ILE559
|
4.6
|
35.8
|
1.0
|
CA
|
A:LYS561
|
4.6
|
36.5
|
1.0
|
O
|
A:HIS558
|
4.6
|
43.6
|
1.0
|
C
|
A:THR560
|
4.7
|
36.0
|
1.0
|
O
|
A:LYS561
|
4.7
|
33.2
|
1.0
|
CB
|
A:THR560
|
4.7
|
41.4
|
1.0
|
CG
|
A:ARG397
|
4.9
|
36.4
|
1.0
|
CD1
|
A:ILE559
|
5.0
|
37.5
|
1.0
|
|
Iodine binding site 3 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 3 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I609
b:38.7
occ:0.70
|
ND2
|
A:ASN80
|
3.5
|
26.4
|
1.0
|
CG
|
A:PRO145
|
3.8
|
29.1
|
1.0
|
CB
|
A:ASN80
|
3.8
|
28.7
|
1.0
|
CG
|
A:ASN80
|
4.2
|
30.1
|
1.0
|
O
|
A:LYS146
|
4.2
|
56.5
|
1.0
|
CB
|
A:PRO145
|
4.3
|
31.5
|
1.0
|
CE
|
A:LYS81
|
4.3
|
40.0
|
1.0
|
CG
|
A:GLU77
|
4.3
|
27.3
|
1.0
|
O
|
A:HOH825
|
4.5
|
61.2
|
1.0
|
CG
|
A:LYS81
|
4.5
|
33.9
|
1.0
|
CD
|
A:LYS81
|
4.6
|
37.1
|
1.0
|
CA
|
A:GLU77
|
4.6
|
22.7
|
1.0
|
CB
|
A:GLU77
|
4.8
|
24.2
|
1.0
|
O
|
A:GLU77
|
4.8
|
27.5
|
1.0
|
CD
|
A:GLU77
|
4.9
|
32.4
|
1.0
|
|
Iodine binding site 4 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 4 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I610
b:57.3
occ:0.54
|
NH1
|
A:ARG96
|
3.5
|
31.7
|
1.0
|
NH2
|
A:ARG96
|
3.6
|
32.4
|
1.0
|
O
|
A:HOH910
|
3.7
|
38.3
|
1.0
|
O5
|
A:NAG601
|
4.0
|
59.2
|
1.0
|
CZ
|
A:ARG96
|
4.0
|
33.0
|
1.0
|
NH1
|
A:ARG506
|
4.0
|
28.4
|
1.0
|
ND2
|
A:ASN95
|
4.1
|
42.9
|
1.0
|
CA
|
A:ARG504
|
4.1
|
34.2
|
1.0
|
NH2
|
A:ARG506
|
4.3
|
27.4
|
1.0
|
O
|
A:ARG504
|
4.3
|
29.8
|
1.0
|
C
|
A:ARG504
|
4.4
|
30.6
|
1.0
|
C2
|
A:NAG601
|
4.4
|
60.7
|
1.0
|
C1
|
A:NAG601
|
4.5
|
57.5
|
1.0
|
O7
|
A:NAG601
|
4.6
|
63.3
|
1.0
|
CZ
|
A:ARG506
|
4.6
|
27.7
|
1.0
|
CB
|
A:ARG504
|
4.6
|
38.3
|
1.0
|
C5
|
A:NAG601
|
4.8
|
61.4
|
1.0
|
C4
|
A:NAG601
|
4.8
|
61.8
|
1.0
|
C6
|
A:NAG601
|
4.8
|
62.1
|
1.0
|
|
Iodine binding site 5 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 5 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I611
b:31.3
occ:0.70
|
CB
|
A:PHE309
|
3.8
|
28.2
|
1.0
|
NE1
|
A:TRP530
|
3.8
|
28.1
|
1.0
|
CZ2
|
A:TRP530
|
3.9
|
32.3
|
1.0
|
O
|
A:HOH848
|
3.9
|
43.5
|
1.0
|
CE2
|
A:TRP530
|
4.2
|
29.4
|
1.0
|
N
|
A:ARG310
|
4.2
|
29.3
|
1.0
|
CA
|
A:ILE306
|
4.4
|
26.0
|
1.0
|
CZ2
|
A:TRP529
|
4.4
|
30.2
|
1.0
|
CB
|
A:ARG310
|
4.5
|
32.7
|
1.0
|
C
|
A:PHE309
|
4.6
|
24.9
|
1.0
|
CG1
|
A:ILE306
|
4.6
|
32.8
|
1.0
|
CA
|
A:PHE309
|
4.7
|
24.7
|
1.0
|
O
|
A:ILE306
|
4.7
|
29.2
|
1.0
|
CA
|
A:ARG310
|
4.8
|
30.7
|
1.0
|
O
|
A:GLN305
|
4.8
|
22.7
|
1.0
|
OE1
|
A:GLU531
|
4.8
|
46.5
|
1.0
|
CB
|
A:ILE306
|
4.9
|
29.6
|
1.0
|
CG
|
A:PHE309
|
4.9
|
24.5
|
1.0
|
|
Iodine binding site 6 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 6 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I612
b:55.9
occ:0.67
|
N
|
A:LYS462
|
3.6
|
37.2
|
1.0
|
OG1
|
A:THR463
|
3.7
|
34.1
|
1.0
|
N
|
A:THR463
|
4.0
|
36.3
|
1.0
|
CA
|
A:GLY466
|
4.0
|
33.5
|
1.0
|
CA
|
A:PRO461
|
4.2
|
35.7
|
1.0
|
CG2
|
A:THR463
|
4.3
|
32.5
|
1.0
|
CA
|
A:LYS462
|
4.4
|
36.0
|
1.0
|
C
|
A:PRO461
|
4.4
|
37.3
|
1.0
|
CB
|
A:LYS462
|
4.5
|
39.1
|
1.0
|
CB
|
A:THR463
|
4.5
|
34.9
|
1.0
|
N
|
A:GLY466
|
4.5
|
30.1
|
1.0
|
C
|
A:LYS462
|
4.7
|
36.8
|
1.0
|
CA
|
A:THR463
|
4.8
|
34.6
|
1.0
|
CB
|
A:PRO461
|
4.9
|
35.6
|
1.0
|
CG
|
A:LYS462
|
4.9
|
42.6
|
1.0
|
|
Iodine binding site 7 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 7 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I613
b:62.7
occ:0.63
|
O
|
A:HOH981
|
2.7
|
35.2
|
1.0
|
N
|
A:PHE567
|
3.4
|
28.4
|
1.0
|
C
|
A:HIS565
|
3.5
|
28.3
|
1.0
|
CD2
|
A:PHE567
|
3.5
|
38.9
|
1.0
|
CA
|
A:HIS565
|
3.6
|
32.5
|
1.0
|
N
|
A:ALA566
|
3.6
|
26.5
|
1.0
|
CB
|
A:PHE567
|
3.6
|
32.7
|
1.0
|
CB
|
A:HIS565
|
3.8
|
31.6
|
1.0
|
O
|
A:HOH824
|
3.8
|
39.9
|
1.0
|
O
|
A:HIS565
|
3.9
|
29.7
|
1.0
|
CA
|
A:PHE567
|
4.0
|
32.3
|
1.0
|
CG
|
A:PHE567
|
4.1
|
35.6
|
1.0
|
O
|
A:HOH832
|
4.1
|
36.2
|
1.0
|
N
|
A:GLN568
|
4.4
|
30.8
|
1.0
|
C
|
A:ALA566
|
4.4
|
27.2
|
1.0
|
CB
|
A:ASP311
|
4.5
|
25.4
|
1.0
|
CA
|
A:ALA566
|
4.5
|
28.1
|
1.0
|
ND1
|
A:HIS565
|
4.6
|
35.9
|
1.0
|
C
|
A:PHE567
|
4.6
|
33.1
|
1.0
|
CG
|
A:ASP311
|
4.6
|
32.3
|
1.0
|
CE2
|
A:PHE567
|
4.6
|
41.2
|
1.0
|
OD1
|
A:ASP311
|
4.6
|
31.4
|
1.0
|
CG
|
A:HIS565
|
4.7
|
36.3
|
1.0
|
O
|
A:HOH768
|
4.9
|
30.8
|
1.0
|
|
Iodine binding site 8 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 8 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I614
b:56.2
occ:0.42
|
O
|
A:HOH718
|
2.6
|
36.0
|
1.0
|
N
|
A:ALA225
|
3.5
|
39.4
|
1.0
|
CB
|
A:ALA225
|
3.9
|
41.5
|
1.0
|
CG
|
A:ARG271
|
4.0
|
34.1
|
1.0
|
CA
|
A:LEU224
|
4.0
|
46.6
|
1.0
|
CB
|
A:LEU224
|
4.1
|
51.0
|
1.0
|
CD2
|
A:LEU224
|
4.1
|
53.4
|
1.0
|
O
|
A:HOH797
|
4.2
|
52.6
|
1.0
|
CD
|
A:ARG271
|
4.3
|
32.2
|
1.0
|
C
|
A:LEU224
|
4.3
|
41.2
|
1.0
|
CA
|
A:ALA225
|
4.3
|
38.3
|
1.0
|
NH1
|
A:ARG278
|
4.4
|
55.1
|
1.0
|
CB
|
A:ARG271
|
4.4
|
32.1
|
1.0
|
NE
|
A:ARG271
|
4.6
|
32.8
|
1.0
|
CA
|
A:ARG271
|
4.7
|
35.3
|
1.0
|
CG
|
A:LEU224
|
4.7
|
55.7
|
1.0
|
O
|
A:ARG271
|
4.9
|
37.5
|
1.0
|
NH2
|
A:ARG278
|
4.9
|
50.8
|
1.0
|
O
|
A:GLY223
|
5.0
|
50.8
|
1.0
|
|
Iodine binding site 9 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 9 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I615
b:50.0
occ:0.47
|
O
|
A:GLU373
|
3.4
|
31.7
|
1.0
|
CG
|
A:GLU373
|
3.7
|
34.9
|
1.0
|
C
|
A:GLU373
|
3.9
|
30.8
|
1.0
|
CD
|
A:PRO375
|
4.0
|
23.8
|
1.0
|
CA
|
A:LEU374
|
4.2
|
23.7
|
1.0
|
N
|
A:PRO375
|
4.2
|
23.2
|
1.0
|
N
|
A:LEU374
|
4.2
|
25.1
|
1.0
|
CB
|
A:GLU373
|
4.2
|
31.6
|
1.0
|
C
|
A:LEU374
|
4.2
|
25.0
|
1.0
|
CG
|
A:PRO375
|
4.3
|
25.8
|
1.0
|
CG2
|
A:THR357
|
4.5
|
24.7
|
1.0
|
CD
|
A:GLU373
|
4.5
|
37.6
|
1.0
|
CA
|
A:GLU373
|
4.7
|
30.0
|
1.0
|
O
|
A:LEU374
|
4.8
|
23.4
|
1.0
|
OE2
|
A:GLU373
|
4.8
|
44.0
|
1.0
|
CA
|
A:PRO375
|
4.9
|
23.9
|
1.0
|
|
Iodine binding site 10 out
of 13 in 4ljj
Go back to
Iodine Binding Sites List in 4ljj
Iodine binding site 10 out
of 13 in the Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution
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 the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I616
b:54.0
occ:0.78
|
N
|
A:THR425
|
3.4
|
54.2
|
1.0
|
CA
|
A:PRO236
|
3.6
|
35.6
|
1.0
|
CB
|
A:PRO236
|
3.8
|
39.2
|
1.0
|
N
|
A:PRO236
|
3.9
|
37.1
|
1.0
|
CA
|
A:THR425
|
4.0
|
58.8
|
1.0
|
CB
|
A:PHE239
|
4.1
|
37.4
|
1.0
|
C
|
A:SER235
|
4.2
|
44.5
|
1.0
|
O
|
A:SER235
|
4.2
|
38.6
|
1.0
|
CG
|
A:PHE239
|
4.4
|
37.7
|
1.0
|
C
|
A:PRO424
|
4.4
|
42.6
|
1.0
|
CD
|
A:PRO236
|
4.4
|
38.3
|
1.0
|
CA
|
A:PRO424
|
4.5
|
40.5
|
1.0
|
CD1
|
A:PHE239
|
4.6
|
42.7
|
1.0
|
CB
|
A:PRO234
|
4.7
|
66.0
|
1.0
|
CG
|
A:PRO236
|
4.7
|
39.4
|
1.0
|
O
|
A:PRO234
|
4.7
|
52.2
|
1.0
|
CG
|
A:PRO234
|
4.8
|
67.4
|
1.0
|
C
|
A:PRO234
|
4.8
|
58.1
|
1.0
|
CB
|
A:PRO424
|
4.8
|
41.2
|
1.0
|
OG1
|
A:THR425
|
4.8
|
58.9
|
1.0
|
N
|
A:SER235
|
4.9
|
54.5
|
1.0
|
C
|
A:PRO236
|
5.0
|
30.1
|
1.0
|
|
Reference:
M.Kumar,
R.P.Singh,
A.K.Singh,
M.Sinha,
P.Kaur,
S.Sharma,
T.P.Singh.
Crystal Structure of the Complex of Goat Lactoperoxidase with Acrylonitrile at 1.98 A Resolution To Be Published.
Page generated: Sun Dec 13 19:34:31 2020
|