Iodine in PDB 2ciw: Chloroperoxidase Iodide Complex
Enzymatic activity of Chloroperoxidase Iodide Complex
All present enzymatic activity of Chloroperoxidase Iodide Complex:
1.11.1.10;
Protein crystallography data
The structure of Chloroperoxidase Iodide Complex, PDB code: 2ciw
was solved by
K.Kuhnel,
W.Blankenfeldt,
J.Terner,
I.Schlichting,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.46 /
1.15
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
57.650,
151.400,
100.740,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.9 /
17.1
|
Other elements in 2ciw:
The structure of Chloroperoxidase Iodide Complex also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the Chloroperoxidase Iodide Complex
(pdb code 2ciw). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the
Chloroperoxidase Iodide Complex, PDB code: 2ciw:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
Iodine binding site 1 out
of 7 in 2ciw
Go back to
Iodine Binding Sites List in 2ciw
Iodine binding site 1 out
of 7 in the Chloroperoxidase Iodide Complex
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Chloroperoxidase Iodide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1319
b:21.0
occ:0.30
|
O
|
A:HOH2108
|
3.1
|
40.4
|
1.0
|
O
|
A:HOH2413
|
3.2
|
23.5
|
1.0
|
O
|
A:HOH2231
|
3.3
|
42.2
|
1.0
|
N
|
A:ALA265
|
3.4
|
15.7
|
1.0
|
O
|
A:HOH2405
|
3.5
|
17.9
|
1.0
|
CA
|
A:GLY264
|
3.8
|
16.4
|
1.0
|
CD
|
A:PRO178
|
3.9
|
12.6
|
1.0
|
CG
|
A:PRO178
|
4.0
|
13.6
|
1.0
|
CB
|
A:LYS177
|
4.1
|
13.7
|
1.0
|
CB
|
A:ALA265
|
4.1
|
16.7
|
1.0
|
C
|
A:GLY264
|
4.1
|
15.8
|
1.0
|
CD
|
A:LYS177
|
4.4
|
15.4
|
1.0
|
CA
|
A:ALA265
|
4.4
|
16.2
|
1.0
|
CE
|
A:LYS177
|
4.5
|
15.1
|
1.0
|
O
|
A:HOH2497
|
4.5
|
30.3
|
1.0
|
O
|
A:HOH2109
|
4.5
|
43.3
|
1.0
|
O
|
A:PRO263
|
4.6
|
18.9
|
1.0
|
O
|
A:HOH2225
|
4.6
|
39.0
|
1.0
|
O
|
A:HOH2406
|
4.7
|
24.2
|
1.0
|
N
|
A:PRO178
|
4.8
|
11.9
|
1.0
|
CG
|
A:LYS177
|
4.8
|
14.6
|
1.0
|
NZ
|
A:LYS177
|
4.8
|
17.1
|
1.0
|
|
Iodine binding site 2 out
of 7 in 2ciw
Go back to
Iodine Binding Sites List in 2ciw
Iodine binding site 2 out
of 7 in the Chloroperoxidase Iodide Complex
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Chloroperoxidase Iodide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1320
b:26.6
occ:0.20
|
O
|
A:HOH2506
|
2.7
|
24.9
|
1.0
|
O
|
A:HOH2500
|
2.8
|
27.2
|
1.0
|
O
|
A:HOH2162
|
3.0
|
47.5
|
1.0
|
N
|
A:VAL268
|
3.8
|
16.3
|
1.0
|
O
|
A:HOH2411
|
3.9
|
21.5
|
1.0
|
CG1
|
A:ILE179
|
4.1
|
14.1
|
1.0
|
CG2
|
A:VAL268
|
4.1
|
20.6
|
1.0
|
CA
|
A:ALA267
|
4.1
|
15.8
|
1.0
|
CB
|
A:PRO178
|
4.1
|
12.9
|
1.0
|
O
|
A:VAL268
|
4.2
|
15.8
|
1.0
|
CD1
|
A:ILE179
|
4.3
|
16.5
|
1.0
|
O
|
A:HOH2227
|
4.5
|
38.2
|
1.0
|
C
|
A:ALA267
|
4.5
|
16.1
|
1.0
|
CG
|
A:PRO178
|
4.6
|
13.6
|
1.0
|
CB
|
A:ALA267
|
4.6
|
16.3
|
1.0
|
O
|
A:GLU266
|
4.7
|
17.8
|
1.0
|
CD2
|
A:LEU270
|
4.8
|
19.3
|
1.0
|
CA
|
A:VAL268
|
4.8
|
17.2
|
1.0
|
C
|
A:VAL268
|
4.9
|
16.0
|
1.0
|
O
|
A:HOH2306
|
4.9
|
46.8
|
1.0
|
|
Iodine binding site 3 out
of 7 in 2ciw
Go back to
Iodine Binding Sites List in 2ciw
Iodine binding site 3 out
of 7 in the Chloroperoxidase Iodide Complex
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Chloroperoxidase Iodide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1321
b:16.8
occ:0.40
|
O
|
A:HOH2239
|
2.8
|
22.1
|
1.0
|
O
|
A:HOH2126
|
2.9
|
26.3
|
1.0
|
O
|
A:HOH2506
|
3.6
|
24.9
|
1.0
|
ND2
|
A:ASN74
|
3.7
|
16.7
|
1.0
|
CD2
|
A:LEU70
|
3.9
|
17.0
|
1.0
|
CE1
|
A:PHE103
|
4.0
|
14.4
|
1.0
|
CG
|
A:LEU70
|
4.1
|
14.4
|
1.0
|
CB
|
A:ALA267
|
4.1
|
16.3
|
1.0
|
CG1
|
A:ILE179
|
4.2
|
14.1
|
1.0
|
CZ
|
A:PHE103
|
4.3
|
13.1
|
1.0
|
CG2
|
A:ILE179
|
4.5
|
11.8
|
1.0
|
CD1
|
A:PHE103
|
4.8
|
12.7
|
1.0
|
CB
|
A:ILE179
|
4.8
|
11.6
|
1.0
|
O
|
A:HOH2122
|
4.8
|
27.9
|
1.0
|
CG
|
A:ASN74
|
4.8
|
13.3
|
1.0
|
CB
|
A:LEU70
|
4.8
|
12.9
|
1.0
|
CD1
|
A:ILE179
|
4.9
|
16.5
|
1.0
|
CA
|
A:ILE179
|
5.0
|
11.0
|
1.0
|
|
Iodine binding site 4 out
of 7 in 2ciw
Go back to
Iodine Binding Sites List in 2ciw
Iodine binding site 4 out
of 7 in the Chloroperoxidase Iodide Complex
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Chloroperoxidase Iodide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1322
b:18.8
occ:0.80
|
O
|
A:HOH2163
|
3.5
|
41.9
|
1.0
|
O
|
A:HOH2356
|
3.6
|
23.1
|
1.0
|
NE2
|
A:GLN116
|
3.8
|
15.2
|
1.0
|
CA
|
A:GLY117
|
4.1
|
15.0
|
1.0
|
CG
|
A:GLN116
|
4.2
|
13.4
|
1.0
|
CD1
|
A:LEU167
|
4.3
|
14.9
|
1.0
|
CD2
|
A:LEU167
|
4.3
|
15.2
|
1.0
|
CD
|
A:GLN116
|
4.5
|
13.7
|
1.0
|
N
|
A:GLY117
|
4.5
|
14.1
|
1.0
|
CB
|
A:LEU167
|
4.6
|
13.5
|
1.0
|
CG
|
A:LEU167
|
4.6
|
13.9
|
1.0
|
O
|
A:HOH2328
|
4.8
|
27.2
|
1.0
|
C
|
A:GLN116
|
4.8
|
13.8
|
1.0
|
O
|
A:GLN116
|
4.9
|
14.5
|
1.0
|
O
|
A:HOH2332
|
5.0
|
21.2
|
1.0
|
|
Iodine binding site 5 out
of 7 in 2ciw
Go back to
Iodine Binding Sites List in 2ciw
Iodine binding site 5 out
of 7 in the Chloroperoxidase Iodide Complex
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Chloroperoxidase Iodide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1323
b:29.9
occ:0.30
|
O
|
A:HOH2572
|
2.5
|
20.2
|
1.0
|
CB
|
A:HIS222
|
3.7
|
14.1
|
1.0
|
CD2
|
A:LEU223
|
3.8
|
15.0
|
1.0
|
CE2
|
A:TYR212
|
4.0
|
11.3
|
1.0
|
CG
|
A:LEU223
|
4.0
|
12.6
|
1.0
|
O
|
A:HOH2012
|
4.1
|
38.9
|
1.0
|
C4
|
A:NAG1305
|
4.2
|
13.2
|
1.0
|
O6
|
A:NAG1305
|
4.4
|
15.3
|
1.0
|
CD2
|
A:TYR212
|
4.4
|
11.2
|
1.0
|
O3
|
A:NAG1305
|
4.5
|
14.9
|
1.0
|
CD2
|
A:HIS222
|
4.5
|
17.1
|
1.0
|
CG
|
A:HIS222
|
4.5
|
16.2
|
1.0
|
O4
|
A:NAG1305
|
4.6
|
17.0
|
1.0
|
CD1
|
A:LEU223
|
4.7
|
12.6
|
1.0
|
C
|
A:HIS222
|
4.7
|
12.8
|
1.0
|
O
|
A:HOH2252
|
4.8
|
21.5
|
1.0
|
O
|
A:HIS222
|
4.9
|
15.0
|
1.0
|
C3
|
A:NAG1305
|
4.9
|
12.7
|
1.0
|
CA
|
A:HIS222
|
4.9
|
12.4
|
1.0
|
N
|
A:LEU223
|
4.9
|
11.7
|
1.0
|
|
Iodine binding site 6 out
of 7 in 2ciw
Go back to
Iodine Binding Sites List in 2ciw
Iodine binding site 6 out
of 7 in the Chloroperoxidase Iodide Complex
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Chloroperoxidase Iodide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1324
b:19.6
occ:0.30
|
O
|
A:HOH2562
|
3.2
|
25.5
|
1.0
|
O
|
A:HOH2559
|
3.2
|
21.2
|
1.0
|
NE
|
A:ARG46
|
3.3
|
13.7
|
1.0
|
ND2
|
A:ASN93
|
3.3
|
12.0
|
1.0
|
O7
|
A:NAG1302
|
3.4
|
14.6
|
1.0
|
CD
|
A:ARG46
|
3.6
|
12.9
|
1.0
|
CB
|
A:ASN93
|
4.0
|
10.4
|
1.0
|
CG1
|
A:VAL92
|
4.0
|
13.6
|
1.0
|
CG
|
A:ASN93
|
4.1
|
10.9
|
1.0
|
C1
|
A:NAG1302
|
4.1
|
12.4
|
1.0
|
CG
|
A:ARG46
|
4.2
|
11.7
|
1.0
|
O
|
A:VAL92
|
4.2
|
10.9
|
1.0
|
O5
|
A:NAG1302
|
4.2
|
13.2
|
1.0
|
C2
|
A:NAG1302
|
4.2
|
13.0
|
1.0
|
CZ
|
A:ARG46
|
4.4
|
12.8
|
1.0
|
C7
|
A:NAG1302
|
4.5
|
13.5
|
1.0
|
O
|
A:HOH2308
|
4.6
|
22.6
|
1.0
|
NH2
|
A:ARG46
|
4.6
|
13.9
|
1.0
|
O
|
A:HOH2096
|
4.7
|
45.9
|
1.0
|
C
|
A:VAL92
|
4.8
|
10.8
|
1.0
|
O
|
A:HOH2010
|
4.8
|
36.4
|
1.0
|
N2
|
A:NAG1302
|
4.8
|
13.1
|
1.0
|
O
|
A:HOH2568
|
4.8
|
41.4
|
1.0
|
O
|
A:HOH2155
|
4.9
|
31.4
|
1.0
|
|
Iodine binding site 7 out
of 7 in 2ciw
Go back to
Iodine Binding Sites List in 2ciw
Iodine binding site 7 out
of 7 in the Chloroperoxidase Iodide Complex
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Chloroperoxidase Iodide Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I1325
b:32.6
occ:0.30
|
O
|
A:HOH2397
|
2.4
|
33.5
|
1.0
|
O
|
A:HOH2085
|
3.2
|
44.2
|
1.0
|
N
|
A:TRP172
|
4.1
|
14.9
|
1.0
|
CE3
|
A:TRP172
|
4.1
|
13.8
|
1.0
|
CD
|
A:LYS115
|
4.1
|
15.6
|
1.0
|
CA
|
A:TRP172
|
4.2
|
14.4
|
1.0
|
CB
|
A:TRP172
|
4.2
|
13.9
|
1.0
|
CE
|
A:LYS115
|
4.3
|
17.3
|
1.0
|
C
|
A:GLY171
|
4.3
|
15.8
|
1.0
|
O
|
A:PRO170
|
4.4
|
19.3
|
1.0
|
CD2
|
A:PHE169
|
4.5
|
19.2
|
1.0
|
O
|
A:GLY171
|
4.6
|
17.8
|
1.0
|
O
|
A:HOH2400
|
4.8
|
27.5
|
1.0
|
CD2
|
A:TRP172
|
4.9
|
13.2
|
1.0
|
CA
|
A:GLY171
|
4.9
|
16.3
|
1.0
|
O
|
A:SER121
|
5.0
|
27.2
|
1.0
|
CZ3
|
A:TRP172
|
5.0
|
14.0
|
1.0
|
|
Reference:
K.Kuhnel,
W.Blankenfeldt,
J.Terner,
I.Schlichting.
Crystal Structures of Chloroperoxidase with Its Bound Substrates and Complexed with Formate, Acetate, and Nitrate. J.Biol.Chem. V. 281 23990 2006.
ISSN: ISSN 0021-9258
PubMed: 16790441
DOI: 10.1074/JBC.M603166200
Page generated: Sun Aug 11 13:36:18 2024
|