Iodine in PDB 3gt4: Structure of Proteinase K with the Magic Triangle I3C
Enzymatic activity of Structure of Proteinase K with the Magic Triangle I3C
All present enzymatic activity of Structure of Proteinase K with the Magic Triangle I3C:
3.4.21.64;
Protein crystallography data
The structure of Structure of Proteinase K with the Magic Triangle I3C, PDB code: 3gt4
was solved by
T.Beck,
T.Gruene,
G.M.Sheldrick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.90 /
1.76
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.784,
67.784,
101.845,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14 /
19.1
|
Iodine Binding Sites:
The binding sites of Iodine atom in the Structure of Proteinase K with the Magic Triangle I3C
(pdb code 3gt4). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 9 binding sites of Iodine where determined in the
Structure of Proteinase K with the Magic Triangle I3C, PDB code: 3gt4:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Iodine binding site 1 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 1 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I301
b:15.8
occ:0.74
|
I3
|
A:I3C301
|
0.0
|
15.8
|
0.7
|
C6
|
A:I3C301
|
2.1
|
15.8
|
1.0
|
C1
|
A:I3C301
|
3.1
|
15.8
|
1.0
|
C5
|
A:I3C301
|
3.1
|
15.8
|
1.0
|
C7
|
A:I3C301
|
3.2
|
15.8
|
1.0
|
N13
|
A:I3C301
|
3.3
|
15.8
|
1.0
|
O8
|
A:I3C301
|
3.5
|
15.8
|
1.0
|
O9
|
A:I3C301
|
3.6
|
15.8
|
1.0
|
N
|
A:GLY259
|
3.6
|
6.3
|
1.0
|
CA
|
A:GLY259
|
3.8
|
9.6
|
1.0
|
O
|
A:HOH607
|
3.8
|
20.6
|
1.0
|
O
|
A:HOH539
|
3.9
|
11.3
|
1.0
|
O
|
A:HOH694
|
4.1
|
26.3
|
1.0
|
O
|
A:ASN270
|
4.1
|
7.0
|
1.0
|
CB
|
A:LYS258
|
4.1
|
12.2
|
1.0
|
C
|
A:LYS258
|
4.1
|
9.6
|
1.0
|
O
|
A:HOH601
|
4.2
|
27.6
|
1.0
|
C2
|
A:I3C301
|
4.4
|
15.8
|
1.0
|
C4
|
A:I3C301
|
4.4
|
15.8
|
1.0
|
CB
|
A:ASN270
|
4.5
|
3.2
|
1.0
|
CA
|
A:LYS258
|
4.5
|
9.5
|
1.0
|
O
|
A:HOH656
|
4.5
|
33.1
|
1.0
|
O
|
A:LYS258
|
4.8
|
8.4
|
1.0
|
C3
|
A:I3C301
|
4.9
|
15.8
|
1.0
|
C
|
A:ASN270
|
5.0
|
7.3
|
1.0
|
|
Iodine binding site 2 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 2 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I301
b:15.8
occ:0.83
|
I2
|
A:I3C301
|
0.0
|
15.8
|
0.8
|
C4
|
A:I3C301
|
2.1
|
15.8
|
1.0
|
C3
|
A:I3C301
|
3.0
|
15.8
|
1.0
|
C5
|
A:I3C301
|
3.1
|
15.8
|
1.0
|
C10
|
A:I3C301
|
3.2
|
15.8
|
1.0
|
N13
|
A:I3C301
|
3.2
|
15.8
|
1.0
|
O12
|
A:I3C301
|
3.3
|
15.8
|
1.0
|
O11
|
A:I3C301
|
3.9
|
15.8
|
1.0
|
C2
|
A:I3C301
|
4.3
|
15.8
|
1.0
|
C6
|
A:I3C301
|
4.4
|
15.8
|
1.0
|
O
|
A:HOH514
|
4.4
|
30.7
|
1.0
|
C1
|
A:I3C301
|
4.9
|
15.8
|
1.0
|
|
Iodine binding site 3 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 3 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I301
b:15.8
occ:0.82
|
I1
|
A:I3C301
|
0.0
|
15.8
|
0.8
|
C2
|
A:I3C301
|
2.1
|
15.8
|
1.0
|
C3
|
A:I3C301
|
3.0
|
15.8
|
1.0
|
C1
|
A:I3C301
|
3.1
|
15.8
|
1.0
|
C10
|
A:I3C301
|
3.2
|
15.8
|
1.0
|
C7
|
A:I3C301
|
3.4
|
15.8
|
1.0
|
O11
|
A:I3C301
|
3.4
|
15.8
|
1.0
|
O8
|
A:I3C301
|
3.7
|
15.8
|
1.0
|
O9
|
A:I3C301
|
3.9
|
15.8
|
1.0
|
O12
|
A:I3C301
|
3.9
|
15.8
|
1.0
|
C4
|
A:I3C301
|
4.3
|
15.8
|
1.0
|
C6
|
A:I3C301
|
4.4
|
15.8
|
1.0
|
O
|
A:HOH694
|
4.4
|
26.3
|
1.0
|
O
|
A:HOH603
|
4.5
|
18.1
|
1.0
|
C5
|
A:I3C301
|
4.9
|
15.8
|
1.0
|
O
|
A:HOH703
|
4.9
|
31.2
|
1.0
|
|
Iodine binding site 4 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 4 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I302
b:15.8
occ:0.12
|
I3
|
A:I3C302
|
0.0
|
15.8
|
0.1
|
C6
|
A:I3C302
|
2.1
|
15.8
|
0.4
|
C5
|
A:I3C302
|
3.0
|
15.8
|
0.4
|
C1
|
A:I3C302
|
3.0
|
15.8
|
0.4
|
C7
|
A:I3C302
|
3.2
|
15.8
|
0.4
|
N13
|
A:I3C302
|
3.2
|
15.8
|
0.4
|
O9
|
A:I3C302
|
3.3
|
15.8
|
0.4
|
O8
|
A:I3C302
|
3.8
|
15.8
|
0.4
|
C4
|
A:I3C302
|
4.3
|
15.8
|
0.4
|
C2
|
A:I3C302
|
4.4
|
15.8
|
0.4
|
O
|
A:HOH731
|
4.7
|
42.0
|
1.0
|
O
|
A:HOH645
|
4.8
|
17.1
|
1.0
|
C3
|
A:I3C302
|
4.9
|
15.8
|
0.4
|
|
Iodine binding site 5 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 5 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I302
b:15.8
occ:0.19
|
I2
|
A:I3C302
|
0.0
|
15.8
|
0.2
|
C4
|
A:I3C302
|
2.1
|
15.8
|
0.4
|
C5
|
A:I3C302
|
3.0
|
15.8
|
0.4
|
N13
|
A:I3C302
|
3.1
|
15.8
|
0.4
|
C3
|
A:I3C302
|
3.1
|
15.8
|
0.4
|
C10
|
A:I3C302
|
3.4
|
15.8
|
0.4
|
O11
|
A:I3C302
|
3.6
|
15.8
|
0.4
|
O
|
A:HOH645
|
3.7
|
17.1
|
1.0
|
CB
|
A:ALA158
|
4.0
|
6.4
|
1.0
|
OG
|
A:SER224
|
4.0
|
10.5
|
1.0
|
C
|
A:LEU133
|
4.0
|
6.6
|
1.0
|
O12
|
A:I3C302
|
4.1
|
15.8
|
0.4
|
OG1
|
A:THR223
|
4.1
|
6.8
|
1.0
|
CA
|
A:LEU133
|
4.1
|
4.6
|
1.0
|
CA
|
A:GLY160
|
4.2
|
6.1
|
1.0
|
N
|
A:LEU133
|
4.2
|
10.6
|
1.0
|
C6
|
A:I3C302
|
4.3
|
15.8
|
0.4
|
O
|
A:LEU133
|
4.3
|
5.6
|
1.0
|
N
|
A:GLY134
|
4.3
|
13.4
|
1.0
|
C2
|
A:I3C302
|
4.4
|
15.8
|
0.4
|
O
|
A:HOH584
|
4.5
|
9.0
|
1.0
|
C
|
A:SER132
|
4.5
|
9.0
|
1.0
|
O
|
A:SER132
|
4.6
|
8.6
|
1.0
|
O
|
A:HOH687
|
4.6
|
25.5
|
1.0
|
O
|
A:HOH631
|
4.6
|
29.6
|
1.0
|
N
|
A:GLY160
|
4.7
|
5.8
|
1.0
|
O
|
A:HOH303
|
4.8
|
12.7
|
0.6
|
C1
|
A:I3C302
|
4.9
|
15.8
|
0.4
|
N
|
A:ASN161
|
4.9
|
5.9
|
1.0
|
C
|
A:GLY160
|
5.0
|
6.9
|
1.0
|
|
Iodine binding site 6 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 6 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I302
b:15.8
occ:0.11
|
I1
|
A:I3C302
|
0.0
|
15.8
|
0.1
|
C2
|
A:I3C302
|
2.1
|
15.8
|
0.4
|
O
|
A:HOH628
|
2.9
|
32.4
|
1.0
|
C3
|
A:I3C302
|
3.0
|
15.8
|
0.4
|
C1
|
A:I3C302
|
3.1
|
15.8
|
0.4
|
O
|
A:HOH304
|
3.1
|
28.7
|
0.6
|
C10
|
A:I3C302
|
3.1
|
15.8
|
0.4
|
O12
|
A:I3C302
|
3.4
|
15.8
|
0.4
|
C7
|
A:I3C302
|
3.4
|
15.8
|
0.4
|
O8
|
A:I3C302
|
3.4
|
15.8
|
0.4
|
O
|
A:HOH716
|
3.6
|
45.0
|
1.0
|
O11
|
A:I3C302
|
3.7
|
15.8
|
0.4
|
O
|
A:SER221
|
3.8
|
8.0
|
1.0
|
O
|
A:HOH621
|
3.9
|
39.1
|
1.0
|
CB
|
A:ASN161
|
3.9
|
20.6
|
1.0
|
CA
|
A:GLY222
|
4.1
|
4.6
|
1.0
|
O9
|
A:I3C302
|
4.2
|
15.8
|
0.4
|
O
|
A:HOH303
|
4.3
|
12.7
|
0.6
|
C4
|
A:I3C302
|
4.4
|
15.8
|
0.4
|
C6
|
A:I3C302
|
4.4
|
15.8
|
0.4
|
C
|
A:SER221
|
4.7
|
11.2
|
1.0
|
C5
|
A:I3C302
|
4.9
|
15.8
|
0.4
|
N
|
A:GLY222
|
4.9
|
8.1
|
1.0
|
|
Iodine binding site 7 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 7 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I305
b:15.8
occ:0.21
|
I3
|
A:I3C305
|
0.0
|
15.8
|
0.2
|
C6
|
A:I3C305
|
2.1
|
15.8
|
0.4
|
C5
|
A:I3C305
|
3.0
|
15.8
|
0.4
|
C1
|
A:I3C305
|
3.1
|
15.8
|
0.4
|
N13
|
A:I3C305
|
3.2
|
15.8
|
0.4
|
C7
|
A:I3C305
|
3.3
|
15.8
|
0.4
|
O8
|
A:I3C305
|
3.4
|
15.8
|
0.4
|
OH
|
A:TYR195
|
3.7
|
20.1
|
1.0
|
CZ
|
A:TYR195
|
3.8
|
13.5
|
1.0
|
CE2
|
A:TYR195
|
3.9
|
9.5
|
1.0
|
O9
|
A:I3C305
|
4.1
|
15.8
|
0.4
|
O
|
A:HOH633
|
4.1
|
32.5
|
1.0
|
NH2
|
A:ARG189
|
4.2
|
11.4
|
1.0
|
CG
|
A:PRO265
|
4.2
|
19.7
|
1.0
|
C4
|
A:I3C305
|
4.3
|
15.8
|
0.4
|
CE1
|
A:TYR195
|
4.4
|
10.7
|
1.0
|
C2
|
A:I3C305
|
4.4
|
15.8
|
0.4
|
CB
|
A:PRO265
|
4.5
|
14.8
|
1.0
|
CD2
|
A:TYR195
|
4.6
|
6.4
|
1.0
|
OD1
|
A:ASN163
|
4.9
|
9.0
|
1.0
|
C3
|
A:I3C305
|
4.9
|
15.8
|
0.4
|
|
Iodine binding site 8 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 8 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I305
b:15.8
occ:0.17
|
I2
|
A:I3C305
|
0.0
|
15.8
|
0.2
|
C4
|
A:I3C305
|
2.1
|
15.8
|
0.4
|
O
|
A:HOH308
|
2.3
|
14.9
|
0.6
|
O
|
A:HOH635
|
2.8
|
40.0
|
1.0
|
C5
|
A:I3C305
|
3.0
|
15.8
|
0.4
|
C3
|
A:I3C305
|
3.0
|
15.8
|
0.4
|
N13
|
A:I3C305
|
3.1
|
15.8
|
0.4
|
C10
|
A:I3C305
|
3.3
|
15.8
|
0.4
|
O11
|
A:I3C305
|
3.6
|
15.8
|
0.4
|
O12
|
A:I3C305
|
3.8
|
15.8
|
0.4
|
O
|
A:HOH723
|
4.1
|
34.2
|
1.0
|
C6
|
A:I3C305
|
4.3
|
15.8
|
0.4
|
C2
|
A:I3C305
|
4.3
|
15.8
|
0.4
|
CB
|
A:PHE266
|
4.4
|
13.4
|
1.0
|
N
|
A:PHE266
|
4.5
|
9.6
|
1.0
|
C1
|
A:I3C305
|
4.8
|
15.8
|
0.4
|
O
|
A:PHE266
|
4.9
|
13.0
|
1.0
|
CB
|
A:PRO265
|
4.9
|
14.8
|
1.0
|
|
Iodine binding site 9 out
of 9 in 3gt4
Go back to
Iodine Binding Sites List in 3gt4
Iodine binding site 9 out
of 9 in the Structure of Proteinase K with the Magic Triangle I3C
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 9 of Structure of Proteinase K with the Magic Triangle I3C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I305
b:15.8
occ:0.18
|
I1
|
A:I3C305
|
0.0
|
15.8
|
0.2
|
O
|
A:HOH306
|
2.1
|
14.1
|
0.6
|
C2
|
A:I3C305
|
2.1
|
15.8
|
0.4
|
O
|
A:HOH307
|
2.4
|
18.8
|
0.6
|
C3
|
A:I3C305
|
3.1
|
15.8
|
0.4
|
C1
|
A:I3C305
|
3.1
|
15.8
|
0.4
|
C7
|
A:I3C305
|
3.2
|
15.8
|
0.4
|
C10
|
A:I3C305
|
3.3
|
15.8
|
0.4
|
O9
|
A:I3C305
|
3.3
|
15.8
|
0.4
|
ND2
|
A:ASN263
|
3.6
|
5.6
|
1.0
|
O12
|
A:I3C305
|
3.6
|
15.8
|
0.4
|
O11
|
A:I3C305
|
3.8
|
15.8
|
0.4
|
O8
|
A:I3C305
|
3.8
|
15.8
|
0.4
|
O
|
A:ILE264
|
4.1
|
5.4
|
1.0
|
CA
|
A:PRO265
|
4.2
|
9.2
|
1.0
|
C4
|
A:I3C305
|
4.4
|
15.8
|
0.4
|
C
|
A:ILE264
|
4.4
|
7.5
|
1.0
|
C6
|
A:I3C305
|
4.4
|
15.8
|
0.4
|
CA
|
A:ASN263
|
4.5
|
9.4
|
1.0
|
N
|
A:PRO265
|
4.5
|
6.3
|
1.0
|
C
|
A:ASN263
|
4.5
|
2.6
|
1.0
|
CG
|
A:ASN263
|
4.6
|
7.1
|
1.0
|
N
|
A:ILE264
|
4.7
|
5.8
|
1.0
|
O
|
A:ASN263
|
4.8
|
6.9
|
1.0
|
CB
|
A:PRO265
|
4.9
|
14.8
|
1.0
|
C5
|
A:I3C305
|
4.9
|
15.8
|
0.4
|
|
Reference:
T.Beck,
T.Gruene,
G.M.Sheldrick.
The Magic Triangle Goes Mad: Experimental Phasing with A Bromine Derivative Acta Crystallogr.,Sect.D V. 66 374 2010.
ISSN: ISSN 0907-4449
PubMed: 20382990
DOI: 10.1107/S0907444909051609
Page generated: Sun Aug 11 15:16:43 2024
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