Iodine in PDB 5myq: Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
Protein crystallography data
The structure of Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative, PDB code: 5myq
was solved by
P.Strzelczyk,
G.Bujacz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
71.60 /
1.89
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
43.933,
82.081,
74.601,
90.00,
106.29,
90.00
|
R / Rfree (%)
|
18.6 /
23.2
|
Other elements in 5myq:
The structure of Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative also contains other interesting chemical elements:
Iodine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
21;
Binding sites:
The binding sites of Iodine atom in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
(pdb code 5myq). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 21 binding sites of Iodine where determined in the
Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative, PDB code: 5myq:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iodine binding site 1 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 1 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I303
b:32.9
occ:0.70
|
N
|
A:SER102
|
3.6
|
23.6
|
1.0
|
O
|
A:HOH411
|
3.9
|
26.9
|
1.0
|
C16
|
A:HBF301
|
3.9
|
29.1
|
1.0
|
C15
|
A:HBF301
|
4.1
|
27.0
|
1.0
|
N
|
A:SER75
|
4.1
|
21.1
|
1.0
|
OG
|
A:SER73
|
4.1
|
26.2
|
1.0
|
CB
|
A:SER75
|
4.2
|
18.9
|
1.0
|
CB
|
A:SER101
|
4.2
|
24.9
|
1.0
|
CA
|
A:SER101
|
4.2
|
21.9
|
1.0
|
CB
|
A:SER102
|
4.2
|
25.5
|
0.5
|
N
|
A:GLU74
|
4.4
|
22.6
|
1.0
|
CB
|
A:GLU74
|
4.4
|
26.3
|
1.0
|
C
|
A:SER101
|
4.4
|
21.6
|
1.0
|
O
|
A:SER102
|
4.5
|
27.9
|
1.0
|
CA
|
A:SER102
|
4.5
|
24.2
|
1.0
|
OG
|
A:SER101
|
4.5
|
26.3
|
1.0
|
C
|
A:GLU74
|
4.6
|
22.1
|
1.0
|
CA
|
A:SER75
|
4.6
|
19.1
|
1.0
|
CA
|
A:GLU74
|
4.7
|
23.8
|
1.0
|
OG
|
A:SER75
|
4.9
|
19.6
|
1.0
|
C
|
A:SER102
|
5.0
|
26.7
|
1.0
|
|
Iodine binding site 2 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 2 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I304
b:59.4
occ:0.70
|
OE1
|
A:GLU91
|
3.3
|
57.2
|
1.0
|
CD
|
A:ARG122
|
3.5
|
47.0
|
1.0
|
NE
|
A:ARG122
|
3.6
|
49.3
|
1.0
|
N
|
A:GLU91
|
3.6
|
48.0
|
1.0
|
O
|
A:GLY89
|
3.7
|
61.3
|
1.0
|
CA
|
A:LYS90
|
3.9
|
55.8
|
1.0
|
CG
|
A:ARG122
|
4.1
|
43.4
|
1.0
|
CD
|
A:GLU91
|
4.2
|
52.9
|
1.0
|
CG
|
A:GLU91
|
4.2
|
50.3
|
1.0
|
C
|
A:LYS90
|
4.3
|
50.9
|
1.0
|
CB
|
A:GLU91
|
4.3
|
45.3
|
1.0
|
O
|
A:HOH424
|
4.4
|
39.0
|
1.0
|
CB
|
A:ARG122
|
4.5
|
41.8
|
1.0
|
CA
|
A:GLU91
|
4.6
|
44.1
|
1.0
|
CB
|
A:LYS90
|
4.7
|
58.2
|
1.0
|
C
|
A:GLY89
|
4.7
|
61.4
|
1.0
|
CG
|
A:LYS90
|
4.8
|
56.9
|
1.0
|
N
|
A:LYS90
|
4.8
|
59.8
|
1.0
|
CZ
|
A:ARG122
|
4.8
|
46.6
|
1.0
|
|
Iodine binding site 3 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 3 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I305
b:40.8
occ:0.50
|
N
|
A:LYS9
|
3.7
|
31.1
|
1.0
|
NH1
|
A:ARG122
|
3.9
|
51.9
|
1.0
|
CD
|
A:ARG122
|
4.0
|
47.0
|
1.0
|
O
|
A:LYS9
|
4.1
|
31.4
|
1.0
|
CA
|
A:GLY8
|
4.2
|
32.0
|
1.0
|
C
|
A:GLY8
|
4.5
|
30.1
|
1.0
|
CA
|
A:LYS9
|
4.5
|
31.7
|
1.0
|
CB
|
A:LYS9
|
4.5
|
35.9
|
1.0
|
CZ
|
A:ARG122
|
4.5
|
46.6
|
1.0
|
NE
|
A:ARG122
|
4.6
|
49.3
|
1.0
|
CG
|
A:ARG122
|
4.7
|
43.4
|
1.0
|
C
|
A:LYS9
|
4.8
|
30.5
|
1.0
|
CB
|
A:ARG122
|
4.9
|
41.8
|
1.0
|
|
Iodine binding site 4 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 4 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I306
b:47.4
occ:0.50
|
N
|
A:PRO48
|
3.6
|
24.5
|
1.0
|
OE2
|
A:GLU46
|
3.6
|
38.4
|
1.0
|
C
|
A:SER47
|
3.7
|
23.6
|
1.0
|
CD
|
A:PRO48
|
3.8
|
26.6
|
1.0
|
CG2
|
A:THR32
|
3.9
|
24.3
|
1.0
|
O
|
A:HOH449
|
3.9
|
40.5
|
1.0
|
CA
|
A:PRO48
|
4.0
|
23.8
|
1.0
|
CG
|
A:GLU46
|
4.0
|
31.0
|
1.0
|
O
|
A:SER47
|
4.1
|
22.7
|
1.0
|
O
|
A:HOH483
|
4.1
|
44.7
|
1.0
|
CA
|
A:SER47
|
4.2
|
23.6
|
1.0
|
O
|
A:GLU46
|
4.2
|
25.5
|
1.0
|
N
|
A:SER47
|
4.2
|
24.4
|
1.0
|
CB
|
A:THR32
|
4.2
|
23.1
|
1.0
|
CB
|
A:PRO48
|
4.3
|
26.4
|
1.0
|
CD
|
A:GLU46
|
4.3
|
37.0
|
1.0
|
C
|
A:GLU46
|
4.3
|
25.1
|
1.0
|
CG
|
A:PRO48
|
4.5
|
26.6
|
1.0
|
CA
|
A:THR32
|
4.8
|
20.6
|
1.0
|
CB
|
A:GLU46
|
4.9
|
30.4
|
1.0
|
O
|
A:GLY31
|
4.9
|
19.2
|
1.0
|
|
Iodine binding site 5 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 5 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I203
b:37.7
occ:1.00
|
NH1
|
B:ARG2
|
3.6
|
38.9
|
1.0
|
N
|
B:GLU91
|
3.6
|
31.5
|
1.0
|
CG
|
B:ARG122
|
4.0
|
32.6
|
1.0
|
CA
|
B:LYS90
|
4.1
|
32.6
|
1.0
|
O
|
B:HOH308
|
4.3
|
33.5
|
1.0
|
CB
|
B:GLU91
|
4.4
|
32.4
|
1.0
|
NE
|
B:ARG122
|
4.4
|
38.1
|
1.0
|
C
|
B:LYS90
|
4.4
|
30.8
|
1.0
|
NZ
|
B:LYS90
|
4.4
|
40.7
|
1.0
|
CA
|
B:GLU91
|
4.6
|
30.2
|
1.0
|
OE1
|
B:GLU91
|
4.6
|
48.5
|
1.0
|
CG
|
B:GLU91
|
4.6
|
36.2
|
1.0
|
CD
|
B:GLU91
|
4.6
|
40.5
|
1.0
|
CD
|
B:LYS90
|
4.6
|
38.2
|
1.0
|
CB
|
B:LYS90
|
4.7
|
32.5
|
1.0
|
O
|
B:GLY89
|
4.7
|
34.7
|
1.0
|
CD
|
B:ARG122
|
4.8
|
34.9
|
1.0
|
CB
|
B:ARG122
|
4.8
|
33.0
|
1.0
|
CZ
|
B:ARG2
|
4.9
|
36.0
|
1.0
|
CE
|
B:LYS90
|
4.9
|
38.1
|
1.0
|
|
Iodine binding site 6 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 6 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I204
b:27.6
occ:0.50
|
N
|
B:SER102
|
3.6
|
25.9
|
1.0
|
O
|
B:HOH362
|
3.9
|
38.8
|
1.0
|
C16
|
B:HBF201
|
4.0
|
35.8
|
1.0
|
N
|
B:SER75
|
4.1
|
26.0
|
1.0
|
CA
|
B:SER101
|
4.1
|
24.4
|
1.0
|
CB
|
B:SER101
|
4.1
|
25.7
|
1.0
|
CB
|
B:SER102
|
4.1
|
29.7
|
1.0
|
CB
|
B:GLU74
|
4.2
|
32.2
|
1.0
|
CB
|
B:SER75
|
4.2
|
24.5
|
1.0
|
OG
|
B:SER73
|
4.3
|
27.9
|
1.0
|
C
|
B:GLU74
|
4.3
|
27.5
|
1.0
|
OG
|
B:SER101
|
4.3
|
26.1
|
1.0
|
C
|
B:SER101
|
4.4
|
24.9
|
1.0
|
C15
|
B:HBF201
|
4.4
|
37.9
|
1.0
|
CA
|
B:SER102
|
4.4
|
27.9
|
1.0
|
N
|
B:GLU74
|
4.4
|
29.5
|
1.0
|
O
|
B:SER102
|
4.4
|
30.5
|
1.0
|
CA
|
B:SER75
|
4.5
|
23.9
|
1.0
|
CA
|
B:GLU74
|
4.5
|
29.8
|
1.0
|
OE1
|
B:GLU74
|
4.8
|
42.8
|
1.0
|
O
|
B:GLU74
|
4.9
|
26.9
|
1.0
|
C
|
B:SER102
|
4.9
|
30.4
|
1.0
|
|
Iodine binding site 7 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 7 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I205
b:42.9
occ:0.50
|
O
|
B:HOH302
|
3.5
|
31.2
|
1.0
|
NH2
|
D:ARG114
|
3.6
|
36.4
|
1.0
|
O
|
B:LYS111
|
3.8
|
22.6
|
1.0
|
CG
|
B:LYS111
|
4.2
|
31.4
|
1.0
|
CB
|
B:SER101
|
4.2
|
25.7
|
1.0
|
CE
|
B:LYS111
|
4.3
|
37.1
|
1.0
|
CD
|
B:LYS111
|
4.4
|
35.1
|
1.0
|
C
|
B:LYS111
|
4.4
|
23.4
|
1.0
|
CA
|
B:ALA112
|
4.5
|
20.9
|
1.0
|
CG1
|
B:VAL103
|
4.5
|
30.1
|
1.0
|
OG
|
B:SER101
|
4.6
|
26.1
|
1.0
|
CZ
|
D:ARG114
|
4.6
|
35.0
|
1.0
|
NH1
|
B:ARG114
|
4.7
|
34.0
|
1.0
|
NE
|
D:ARG114
|
4.8
|
33.2
|
1.0
|
N
|
B:ALA112
|
4.8
|
22.0
|
1.0
|
CB
|
B:LYS111
|
4.9
|
29.3
|
1.0
|
NZ
|
B:LYS111
|
5.0
|
41.5
|
1.0
|
|
Iodine binding site 8 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 8 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I206
b:43.8
occ:1.00
|
O
|
B:HOH366
|
3.4
|
63.9
|
1.0
|
OG1
|
B:THR32
|
3.5
|
27.9
|
1.0
|
OG1
|
B:THR19
|
3.7
|
37.9
|
1.0
|
OG1
|
B:THR34
|
3.7
|
33.9
|
1.0
|
CA
|
B:MET18
|
3.9
|
30.1
|
1.0
|
N
|
B:THR19
|
3.9
|
32.0
|
1.0
|
O
|
B:ASN17
|
4.0
|
28.4
|
1.0
|
O
|
B:THR32
|
4.0
|
26.1
|
1.0
|
C
|
B:MET18
|
4.0
|
31.3
|
1.0
|
C
|
B:ASN17
|
4.1
|
29.4
|
1.0
|
CB
|
B:ASN17
|
4.2
|
32.0
|
1.0
|
N
|
B:MET18
|
4.2
|
27.7
|
1.0
|
OE2
|
B:GLU46
|
4.2
|
42.0
|
1.0
|
C
|
B:THR32
|
4.2
|
25.6
|
1.0
|
N
|
B:THR34
|
4.3
|
26.7
|
1.0
|
CB
|
B:THR34
|
4.3
|
31.6
|
1.0
|
CB
|
B:THR19
|
4.4
|
35.7
|
1.0
|
CB
|
B:THR32
|
4.5
|
27.6
|
1.0
|
CE
|
B:LYS9
|
4.5
|
43.4
|
1.0
|
N
|
B:TYR33
|
4.5
|
25.5
|
1.0
|
CA
|
B:TYR33
|
4.7
|
24.0
|
1.0
|
C
|
B:TYR33
|
4.7
|
26.1
|
1.0
|
CA
|
B:THR19
|
4.8
|
33.5
|
1.0
|
O
|
B:MET18
|
4.8
|
30.8
|
1.0
|
CD
|
B:GLU46
|
4.9
|
39.7
|
1.0
|
CA
|
B:ASN17
|
4.9
|
29.1
|
1.0
|
O
|
B:HOH346
|
4.9
|
39.3
|
1.0
|
CA
|
B:THR34
|
5.0
|
29.3
|
1.0
|
CG
|
B:GLU46
|
5.0
|
35.4
|
1.0
|
CA
|
B:THR32
|
5.0
|
26.5
|
1.0
|
|
Iodine binding site 9 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 9 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I207
b:49.2
occ:0.70
|
N
|
B:PRO48
|
3.8
|
29.6
|
1.0
|
C
|
B:SER47
|
3.9
|
28.9
|
1.0
|
CG2
|
B:THR32
|
3.9
|
29.0
|
1.0
|
CD
|
B:PRO48
|
4.0
|
32.3
|
1.0
|
O
|
B:GLU46
|
4.0
|
32.2
|
1.0
|
CE
|
B:LYS71
|
4.2
|
45.2
|
1.0
|
CA
|
B:SER47
|
4.2
|
29.1
|
1.0
|
CA
|
B:PRO48
|
4.2
|
29.1
|
1.0
|
CB
|
B:PRO48
|
4.2
|
31.3
|
1.0
|
O
|
B:SER47
|
4.3
|
27.7
|
1.0
|
C
|
B:GLU46
|
4.4
|
31.0
|
1.0
|
N
|
B:SER47
|
4.4
|
30.4
|
1.0
|
CG
|
B:GLU46
|
4.4
|
35.4
|
1.0
|
CG
|
B:PRO48
|
4.6
|
32.0
|
1.0
|
O
|
B:HOH354
|
4.6
|
37.4
|
1.0
|
CB
|
B:THR32
|
4.7
|
27.6
|
1.0
|
O
|
A:HOH468
|
4.7
|
38.6
|
1.0
|
CD
|
B:GLU46
|
4.7
|
39.7
|
1.0
|
O
|
B:HOH330
|
4.8
|
30.8
|
1.0
|
CB
|
B:GLU46
|
4.9
|
35.3
|
1.0
|
OE2
|
B:GLU46
|
5.0
|
42.0
|
1.0
|
|
Iodine binding site 10 out
of 21 in 5myq
Go back to
Iodine Binding Sites List in 5myq
Iodine binding site 10 out
of 21 in the Crystal Structure of Avidin in Complex with Ferrocene Homobiotin Derivative
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 Avidin in Complex with Ferrocene Homobiotin Derivative within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I208
b:58.9
occ:0.50
|
NH2
|
B:ARG2
|
3.4
|
37.1
|
1.0
|
N
|
B:ARG2
|
3.5
|
44.0
|
1.0
|
CG
|
B:ARG2
|
3.9
|
44.1
|
1.0
|
CD
|
B:ARG2
|
4.0
|
43.5
|
1.0
|
CG2
|
B:ILE85
|
4.1
|
32.8
|
1.0
|
CZ
|
B:ARG2
|
4.4
|
36.0
|
1.0
|
CB
|
B:ARG2
|
4.5
|
43.5
|
1.0
|
CG1
|
B:ILE85
|
4.5
|
30.6
|
1.0
|
CA
|
B:ARG2
|
4.6
|
43.6
|
1.0
|
NE
|
B:ARG2
|
4.7
|
42.3
|
1.0
|
CB
|
B:ILE85
|
4.9
|
30.2
|
1.0
|
O
|
B:ARG2
|
5.0
|
39.9
|
1.0
|
CD1
|
B:ILE85
|
5.0
|
31.3
|
1.0
|
|
Reference:
P.Strzelczyk,
D.Plazuk,
G.Bujacz.
Structural Investigation of the Interactions of Ferrocene Homobiotin Derivative with Avidin. To Be Published.
Page generated: Sun Aug 11 21:32:30 2024
|