Iodine in PDB 3gc1: Crystal Structure of Bovine Lactoperoxidase
Enzymatic activity of Crystal Structure of Bovine Lactoperoxidase
All present enzymatic activity of Crystal Structure of Bovine Lactoperoxidase:
1.11.1.7;
Protein crystallography data
The structure of Crystal Structure of Bovine Lactoperoxidase, PDB code: 3gc1
was solved by
A.K.Singh,
N.Singh,
M.Sinha,
P.Kaur,
A.Srinivasan,
S.Sharma,
T.P.Singh,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.97 /
2.50
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
53.650,
80.710,
75.680,
90.00,
101.75,
90.00
|
R / Rfree (%)
|
24.7 /
26.8
|
Other elements in 3gc1:
The structure of Crystal Structure of Bovine Lactoperoxidase also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of Bovine Lactoperoxidase
(pdb code 3gc1). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the
Crystal Structure of Bovine Lactoperoxidase, PDB code: 3gc1:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
Iodine binding site 1 out
of 7 in 3gc1
Go back to
Iodine Binding Sites List in 3gc1
Iodine binding site 1 out
of 7 in the Crystal Structure of Bovine Lactoperoxidase
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 Bovine Lactoperoxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I608
b:43.2
occ:1.00
|
N
|
A:TRP46
|
3.4
|
35.7
|
1.0
|
CG1
|
A:VAL342
|
3.5
|
29.6
|
1.0
|
CH2
|
A:TRP452
|
3.5
|
32.7
|
1.0
|
N
|
A:VAL342
|
3.6
|
31.1
|
1.0
|
CA
|
A:ARG45
|
3.8
|
36.0
|
1.0
|
CZ2
|
A:TRP452
|
3.9
|
31.1
|
1.0
|
O
|
A:ALA44
|
3.9
|
32.8
|
1.0
|
CB
|
A:ASN341
|
3.9
|
31.0
|
1.0
|
CB
|
A:VAL342
|
4.0
|
29.5
|
1.0
|
N
|
A:ASN341
|
4.1
|
32.9
|
1.0
|
C
|
A:ARG45
|
4.1
|
35.4
|
1.0
|
N
|
A:LEU47
|
4.2
|
29.7
|
1.0
|
CB
|
A:TRP46
|
4.3
|
34.1
|
1.0
|
CA
|
A:TRP46
|
4.3
|
32.9
|
1.0
|
CA
|
A:ASN341
|
4.3
|
32.2
|
1.0
|
CE
|
A:MET446
|
4.4
|
33.2
|
1.0
|
CD
|
A:ARG45
|
4.4
|
40.4
|
1.0
|
C
|
A:ASN341
|
4.4
|
32.3
|
1.0
|
CA
|
A:VAL342
|
4.4
|
29.8
|
1.0
|
O
|
A:LEU47
|
4.5
|
29.5
|
1.0
|
OG
|
A:SER340
|
4.7
|
36.0
|
1.0
|
CB
|
A:ARG45
|
4.7
|
37.1
|
1.0
|
CZ3
|
A:TRP452
|
4.7
|
32.5
|
1.0
|
C
|
A:ALA44
|
4.7
|
34.4
|
1.0
|
CB
|
A:SER340
|
4.7
|
35.2
|
1.0
|
CG
|
A:TRP46
|
4.8
|
34.5
|
1.0
|
C
|
A:TRP46
|
4.8
|
31.0
|
1.0
|
N
|
A:ARG45
|
4.8
|
35.2
|
1.0
|
NH1
|
A:ARG45
|
4.8
|
44.1
|
1.0
|
SD
|
A:MET446
|
5.0
|
35.9
|
1.0
|
C
|
A:SER340
|
5.0
|
32.9
|
1.0
|
CG
|
A:ARG45
|
5.0
|
38.3
|
1.0
|
|
Iodine binding site 2 out
of 7 in 3gc1
Go back to
Iodine Binding Sites List in 3gc1
Iodine binding site 2 out
of 7 in the Crystal Structure of Bovine Lactoperoxidase
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 Bovine Lactoperoxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I609
b:60.1
occ:1.00
|
ND2
|
A:ASN80
|
3.6
|
43.6
|
1.0
|
CB
|
A:PRO145
|
3.7
|
47.5
|
1.0
|
CG
|
A:PRO145
|
3.8
|
45.9
|
1.0
|
CB
|
A:ASN80
|
3.9
|
43.2
|
1.0
|
O
|
A:LYS146
|
4.1
|
47.8
|
1.0
|
CG
|
A:GLU77
|
4.1
|
48.2
|
1.0
|
CG
|
A:ASN80
|
4.3
|
43.2
|
1.0
|
CE
|
A:LYS81
|
4.5
|
44.8
|
1.0
|
O
|
A:HOH809
|
4.5
|
55.2
|
1.0
|
CB
|
A:ASN147
|
4.6
|
46.1
|
1.0
|
CG
|
A:LYS81
|
4.6
|
43.5
|
1.0
|
CA
|
A:GLU77
|
4.7
|
44.1
|
1.0
|
CD
|
A:LYS81
|
4.8
|
46.0
|
1.0
|
N
|
A:ASP148
|
4.9
|
48.5
|
1.0
|
CB
|
A:GLU77
|
4.9
|
46.3
|
1.0
|
C
|
A:ASN147
|
4.9
|
47.7
|
1.0
|
CD
|
A:GLU77
|
4.9
|
50.8
|
1.0
|
|
Iodine binding site 3 out
of 7 in 3gc1
Go back to
Iodine Binding Sites List in 3gc1
Iodine binding site 3 out
of 7 in the Crystal Structure of Bovine Lactoperoxidase
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 Bovine Lactoperoxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I610
b:56.9
occ:1.00
|
O
|
A:PRO424
|
2.6
|
50.3
|
1.0
|
O
|
A:HOH717
|
2.9
|
60.6
|
1.0
|
O
|
A:HOH782
|
3.5
|
52.4
|
1.0
|
C
|
A:PRO424
|
3.8
|
48.6
|
1.0
|
CA
|
A:PRO236
|
3.9
|
45.6
|
1.0
|
CB
|
A:PRO236
|
4.0
|
44.6
|
1.0
|
N
|
A:PRO236
|
4.0
|
47.8
|
1.0
|
CG
|
A:PRO236
|
4.1
|
45.3
|
1.0
|
CB
|
A:PHE239
|
4.3
|
43.1
|
1.0
|
CD1
|
A:PHE239
|
4.4
|
41.7
|
1.0
|
CG
|
A:PHE239
|
4.4
|
42.8
|
1.0
|
CA
|
A:THR425
|
4.4
|
50.0
|
1.0
|
C
|
A:SER235
|
4.5
|
50.2
|
1.0
|
CB
|
A:PRO234
|
4.5
|
56.0
|
1.0
|
CA
|
A:PRO424
|
4.6
|
47.8
|
1.0
|
CD
|
A:PRO236
|
4.7
|
45.6
|
1.0
|
OG1
|
A:THR425
|
4.7
|
49.1
|
1.0
|
N
|
A:THR425
|
4.7
|
49.3
|
1.0
|
O
|
A:SER235
|
4.8
|
51.4
|
1.0
|
CZ
|
A:PHE422
|
4.8
|
41.7
|
1.0
|
C
|
A:PRO234
|
4.9
|
54.5
|
1.0
|
|
Iodine binding site 4 out
of 7 in 3gc1
Go back to
Iodine Binding Sites List in 3gc1
Iodine binding site 4 out
of 7 in the Crystal Structure of Bovine Lactoperoxidase
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 Bovine Lactoperoxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I611
b:57.5
occ:1.00
|
CZ2
|
A:TRP530
|
3.8
|
56.7
|
1.0
|
NE1
|
A:TRP530
|
3.8
|
56.1
|
1.0
|
O
|
A:HOH818
|
3.9
|
50.2
|
1.0
|
CB
|
A:PHE309
|
4.0
|
43.9
|
1.0
|
CE2
|
A:TRP530
|
4.2
|
57.2
|
1.0
|
CZ2
|
A:TRP529
|
4.2
|
62.6
|
1.0
|
CG1
|
A:ILE306
|
4.2
|
42.5
|
1.0
|
CA
|
A:ILE306
|
4.3
|
42.6
|
1.0
|
CB
|
A:ARG310
|
4.4
|
47.6
|
1.0
|
N
|
A:ARG310
|
4.5
|
46.6
|
1.0
|
C
|
A:PHE309
|
4.6
|
46.2
|
1.0
|
O
|
A:GLN305
|
4.7
|
45.1
|
1.0
|
CB
|
A:ILE306
|
4.7
|
42.9
|
1.0
|
CG2
|
A:ILE306
|
4.7
|
41.8
|
1.0
|
CA
|
A:ARG310
|
4.8
|
47.8
|
1.0
|
OE1
|
A:GLU531
|
4.8
|
59.8
|
1.0
|
O
|
A:ILE306
|
4.8
|
42.6
|
1.0
|
CH2
|
A:TRP529
|
4.8
|
63.0
|
1.0
|
CA
|
A:PHE309
|
4.9
|
45.2
|
1.0
|
O
|
A:PHE309
|
5.0
|
47.9
|
1.0
|
CG
|
A:ARG310
|
5.0
|
46.9
|
1.0
|
N
|
A:ILE306
|
5.0
|
43.7
|
1.0
|
|
Iodine binding site 5 out
of 7 in 3gc1
Go back to
Iodine Binding Sites List in 3gc1
Iodine binding site 5 out
of 7 in the Crystal Structure of Bovine Lactoperoxidase
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 Bovine Lactoperoxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I612
b:75.4
occ:1.00
|
N
|
A:THR560
|
3.5
|
60.9
|
1.0
|
N
|
A:LYS561
|
4.0
|
62.2
|
1.0
|
CA
|
A:ILE559
|
4.0
|
60.8
|
1.0
|
CG2
|
A:ILE559
|
4.0
|
62.3
|
1.0
|
OE1
|
A:GLU363
|
4.1
|
52.5
|
1.0
|
C
|
A:ILE559
|
4.1
|
60.8
|
1.0
|
CB
|
A:LYS561
|
4.2
|
64.8
|
1.0
|
O
|
A:GLU363
|
4.2
|
52.8
|
1.0
|
CG
|
A:LYS561
|
4.3
|
65.8
|
1.0
|
NE
|
A:ARG397
|
4.4
|
40.5
|
1.0
|
CA
|
A:GLU363
|
4.4
|
53.7
|
1.0
|
CE2
|
A:TYR365
|
4.4
|
49.9
|
1.0
|
CA
|
A:THR560
|
4.5
|
60.8
|
1.0
|
O
|
A:HIS558
|
4.5
|
60.6
|
1.0
|
C
|
A:THR560
|
4.5
|
61.5
|
1.0
|
CB
|
A:ILE559
|
4.6
|
61.6
|
1.0
|
CA
|
A:LYS561
|
4.7
|
63.2
|
1.0
|
CB
|
A:GLU363
|
4.7
|
53.8
|
1.0
|
OG1
|
A:THR560
|
4.7
|
60.8
|
1.0
|
NH2
|
A:ARG397
|
4.8
|
41.2
|
1.0
|
C
|
A:GLU363
|
4.9
|
52.6
|
1.0
|
CZ
|
A:ARG397
|
4.9
|
41.0
|
1.0
|
OH
|
A:TYR365
|
5.0
|
50.8
|
1.0
|
|
Iodine binding site 6 out
of 7 in 3gc1
Go back to
Iodine Binding Sites List in 3gc1
Iodine binding site 6 out
of 7 in the Crystal Structure of Bovine Lactoperoxidase
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 Bovine Lactoperoxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I613
b:85.5
occ:1.00
|
CD2
|
A:PHE229
|
3.4
|
61.5
|
1.0
|
N
|
A:PHE229
|
3.5
|
55.9
|
1.0
|
CB
|
A:PHE229
|
3.7
|
59.2
|
1.0
|
OD1
|
A:ASN216
|
3.8
|
60.5
|
1.0
|
CG
|
A:PHE229
|
3.9
|
60.5
|
1.0
|
CG
|
A:ASN216
|
3.9
|
59.3
|
1.0
|
ND2
|
A:ASN216
|
4.0
|
59.1
|
1.0
|
N
|
A:GLN217
|
4.1
|
59.0
|
1.0
|
CA
|
A:PHE229
|
4.2
|
58.1
|
1.0
|
OE2
|
A:GLU218
|
4.3
|
63.5
|
1.0
|
CE2
|
A:PHE229
|
4.4
|
60.8
|
1.0
|
CA
|
A:ASN216
|
4.4
|
59.7
|
1.0
|
C
|
A:PRO228
|
4.4
|
54.1
|
1.0
|
CA
|
A:PRO228
|
4.5
|
52.8
|
1.0
|
N
|
A:GLU218
|
4.6
|
60.5
|
1.0
|
C
|
A:ASN216
|
4.8
|
59.6
|
1.0
|
CB
|
A:ASN216
|
4.8
|
59.0
|
1.0
|
CB
|
A:GLU218
|
4.9
|
61.6
|
1.0
|
CD
|
A:GLU218
|
5.0
|
64.3
|
1.0
|
|
Iodine binding site 7 out
of 7 in 3gc1
Go back to
Iodine Binding Sites List in 3gc1
Iodine binding site 7 out
of 7 in the Crystal Structure of Bovine Lactoperoxidase
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 Bovine Lactoperoxidase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I614
b:54.5
occ:1.00
|
NE2
|
A:HIS377
|
3.5
|
50.8
|
1.0
|
CD2
|
A:HIS377
|
3.5
|
49.2
|
1.0
|
ND1
|
A:HIS429
|
3.9
|
38.3
|
1.0
|
CG
|
A:HIS429
|
4.0
|
36.4
|
1.0
|
CE1
|
A:HIS429
|
4.2
|
35.9
|
1.0
|
CG2
|
A:THR378
|
4.2
|
43.2
|
1.0
|
CD2
|
A:HIS429
|
4.3
|
36.4
|
1.0
|
O
|
A:HIS377
|
4.4
|
46.7
|
1.0
|
NE2
|
A:HIS429
|
4.4
|
36.6
|
1.0
|
CB
|
A:HIS429
|
4.5
|
37.3
|
1.0
|
CE1
|
A:HIS377
|
4.8
|
48.6
|
1.0
|
CG
|
A:HIS377
|
4.8
|
48.4
|
1.0
|
|
Reference:
A.K.Singh,
R.P.Kumar,
N.Pandey,
N.Singh,
M.Sinha,
A.Bhushan,
P.Kaur,
S.Sharma,
T.P.Singh.
Mode of Binding of the Tuberculosis Prodrug Isoniazid to Heme Peroxidases: Binding Studies and Crystal Structure of Bovine Lactoperoxidase with Isoniazid at 2.7 A Resolution. J.Biol.Chem. V. 285 1569 2010.
ISSN: ISSN 0021-9258
PubMed: 19907057
DOI: 10.1074/JBC.M109.060327
Page generated: Sun Aug 11 15:13:29 2024
|