Iodine in PDB 1oxx: Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
Protein crystallography data
The structure of Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus, PDB code: 1oxx
was solved by
G.Verdon,
S.-V.Albers,
N.Van Oosterwijk,
B.W.Dijkstra,
A.J.M.Driessen,
A.M.W.H.Thunnissen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.52 /
1.45
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.282,
48.427,
183.533,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.2 /
21.3
|
Iodine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
30;
Page 4, Binding sites: 31 -
34;
Binding sites:
The binding sites of Iodine atom in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
(pdb code 1oxx). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 34 binding sites of Iodine where determined in the
Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus, PDB code: 1oxx:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iodine binding site 1 out
of 34 in 1oxx
Go back to
Iodine Binding Sites List in 1oxx
Iodine binding site 1 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1901
b:14.7
occ:1.00
|
O
|
K:HOH2001
|
3.5
|
26.4
|
1.0
|
O
|
K:HOH2053
|
3.6
|
22.4
|
1.0
|
N
|
K:LEU295
|
3.7
|
4.4
|
1.0
|
O
|
K:HOH2029
|
3.9
|
28.4
|
1.0
|
CB
|
K:LEU295
|
4.1
|
6.5
|
1.0
|
CA
|
K:ILE294
|
4.3
|
7.2
|
1.0
|
CG
|
K:LEU295
|
4.3
|
12.2
|
1.0
|
CD1
|
K:LEU295
|
4.4
|
12.9
|
1.0
|
O
|
K:TRP293
|
4.4
|
9.9
|
1.0
|
C
|
K:ILE294
|
4.6
|
5.2
|
1.0
|
CA
|
K:LEU295
|
4.6
|
4.1
|
1.0
|
CE2
|
K:TYR341
|
4.7
|
4.9
|
1.0
|
CB
|
K:ILE294
|
4.9
|
7.6
|
1.0
|
|
Iodine binding site 2 out
of 34 in 1oxx
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Iodine Binding Sites List in 1oxx
Iodine binding site 2 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1902
b:17.0
occ:0.80
|
NZ
|
K:LYS17
|
3.4
|
6.0
|
1.0
|
CE
|
K:LYS17
|
4.0
|
4.3
|
1.0
|
I
|
K:IOD1903
|
5.0
|
29.3
|
0.7
|
|
Iodine binding site 3 out
of 34 in 1oxx
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Iodine Binding Sites List in 1oxx
Iodine binding site 3 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1903
b:29.3
occ:0.65
|
O
|
K:HOH2342
|
2.0
|
29.4
|
1.0
|
CE
|
K:LYS17
|
4.3
|
4.3
|
1.0
|
CE
|
K:LYS14
|
4.3
|
32.2
|
1.0
|
CD
|
K:LYS14
|
4.4
|
23.3
|
1.0
|
NZ
|
K:LYS14
|
4.6
|
25.5
|
1.0
|
CG2
|
K:VAL18
|
4.7
|
15.4
|
1.0
|
O
|
K:HOH2257
|
4.8
|
29.6
|
1.0
|
NZ
|
K:LYS17
|
4.8
|
6.0
|
1.0
|
CD
|
K:LYS17
|
4.9
|
4.5
|
1.0
|
I
|
K:IOD1902
|
5.0
|
17.0
|
0.8
|
|
Iodine binding site 4 out
of 34 in 1oxx
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Iodine Binding Sites List in 1oxx
Iodine binding site 4 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1904
b:24.8
occ:0.40
|
O
|
K:HOH2396
|
2.1
|
28.3
|
1.0
|
CB
|
K:SER40
|
3.3
|
14.8
|
1.0
|
O
|
K:HOH2007
|
3.4
|
24.8
|
1.0
|
I
|
K:IOD1933
|
3.5
|
25.1
|
0.3
|
N
|
K:GLY217
|
3.5
|
11.8
|
1.0
|
N
|
K:LYS216
|
3.7
|
15.9
|
1.0
|
O
|
K:LEU214
|
3.8
|
13.9
|
1.0
|
N
|
K:SER40
|
4.0
|
21.8
|
1.0
|
C
|
K:LEU214
|
4.1
|
10.2
|
1.0
|
C
|
K:VAL215
|
4.2
|
7.7
|
1.0
|
CB
|
K:LEU214
|
4.2
|
9.5
|
1.0
|
CA
|
K:SER40
|
4.2
|
13.9
|
1.0
|
CA
|
K:LYS216
|
4.3
|
12.6
|
1.0
|
CA
|
K:VAL215
|
4.3
|
9.6
|
1.0
|
CA
|
K:GLY217
|
4.3
|
11.1
|
1.0
|
N
|
K:VAL215
|
4.3
|
9.0
|
1.0
|
OG
|
K:SER40
|
4.3
|
20.2
|
1.0
|
C
|
K:LYS216
|
4.4
|
9.9
|
1.0
|
CD
|
K:PRO39
|
4.4
|
13.9
|
1.0
|
O
|
K:SER40
|
4.6
|
9.7
|
1.0
|
CA
|
K:LEU214
|
4.8
|
5.2
|
1.0
|
CA
|
K:GLY43
|
4.9
|
22.3
|
1.0
|
N
|
K:PRO39
|
4.9
|
13.8
|
1.0
|
C
|
K:SER40
|
5.0
|
16.5
|
1.0
|
CD1
|
K:LEU214
|
5.0
|
13.3
|
0.5
|
|
Iodine binding site 5 out
of 34 in 1oxx
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Iodine Binding Sites List in 1oxx
Iodine binding site 5 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1905
b:16.6
occ:0.30
|
O
|
K:HOH2556
|
1.8
|
46.1
|
1.0
|
O
|
K:HOH2087
|
3.4
|
22.7
|
1.0
|
CE
|
K:MET110
|
3.5
|
18.3
|
1.0
|
O
|
K:HOH2271
|
3.7
|
35.2
|
1.0
|
CB
|
K:LYS157
|
4.1
|
9.8
|
1.0
|
CA
|
K:LYS157
|
4.1
|
5.9
|
1.0
|
CG
|
K:LYS157
|
4.1
|
16.0
|
0.5
|
CG
|
K:LYS157
|
4.1
|
8.7
|
0.5
|
CB
|
K:MET110
|
4.2
|
10.6
|
1.0
|
CG
|
K:MET110
|
4.3
|
12.8
|
1.0
|
O
|
K:LYS157
|
4.3
|
13.4
|
1.0
|
SD
|
K:MET112
|
4.4
|
12.2
|
1.0
|
CD2
|
K:LEU107
|
4.4
|
7.3
|
1.0
|
C
|
K:LYS157
|
4.6
|
14.9
|
1.0
|
CD
|
K:LYS157
|
4.6
|
10.6
|
0.5
|
SD
|
K:MET110
|
4.7
|
18.3
|
1.0
|
CE
|
K:LYS157
|
4.8
|
18.4
|
0.5
|
|
Iodine binding site 6 out
of 34 in 1oxx
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Iodine Binding Sites List in 1oxx
Iodine binding site 6 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1906
b:27.6
occ:1.00
|
I
|
K:IOD1906
|
0.0
|
27.6
|
1.0
|
NH2
|
K:ARG189
|
3.2
|
29.1
|
1.0
|
I
|
K:IOD1906
|
3.2
|
52.4
|
0.3
|
NH1
|
K:ARG189
|
3.4
|
19.0
|
1.0
|
O
|
K:HOH2013
|
3.5
|
23.7
|
1.0
|
CZ
|
K:ARG189
|
3.8
|
22.1
|
1.0
|
CD1
|
K:LEU155
|
4.1
|
10.9
|
1.0
|
CD1
|
K:ILE127
|
4.2
|
19.5
|
1.0
|
CB
|
K:LEU155
|
4.3
|
6.7
|
1.0
|
CG1
|
K:VAL124
|
4.3
|
10.3
|
1.0
|
CG2
|
K:VAL124
|
4.4
|
12.7
|
1.0
|
CD1
|
K:LEU190
|
4.4
|
10.3
|
1.0
|
CD2
|
K:LEU190
|
4.4
|
9.8
|
1.0
|
CG2
|
K:ILE127
|
4.5
|
18.6
|
1.0
|
NH2
|
K:ARG120
|
4.6
|
12.7
|
1.0
|
CB
|
K:VAL124
|
4.8
|
8.7
|
1.0
|
CG
|
K:LEU155
|
4.8
|
6.8
|
1.0
|
CG
|
K:LEU190
|
4.9
|
7.1
|
1.0
|
CA
|
K:VAL124
|
4.9
|
6.7
|
1.0
|
CB
|
K:ILE127
|
4.9
|
10.2
|
1.0
|
O
|
K:HOH2320
|
5.0
|
36.7
|
1.0
|
O
|
K:LEU155
|
5.0
|
6.2
|
1.0
|
|
Iodine binding site 7 out
of 34 in 1oxx
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Iodine Binding Sites List in 1oxx
Iodine binding site 7 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1906
b:52.4
occ:0.30
|
I
|
K:IOD1906
|
0.0
|
52.4
|
0.3
|
NH1
|
K:ARG120
|
2.8
|
13.5
|
1.0
|
O
|
K:HOH2320
|
3.1
|
36.7
|
1.0
|
I
|
K:IOD1906
|
3.2
|
27.6
|
1.0
|
NH2
|
K:ARG120
|
3.7
|
12.7
|
1.0
|
CZ
|
K:ARG120
|
3.7
|
11.3
|
1.0
|
CD1
|
K:ILE127
|
3.8
|
19.5
|
1.0
|
O
|
K:HOH2013
|
4.1
|
23.7
|
1.0
|
NH1
|
K:ARG189
|
4.3
|
19.0
|
1.0
|
O
|
K:HOH2623
|
4.4
|
30.7
|
1.0
|
CD
|
K:GLU123
|
4.5
|
25.3
|
1.0
|
O
|
K:HOH2189
|
4.5
|
32.1
|
1.0
|
OE1
|
K:GLU123
|
4.5
|
19.8
|
1.0
|
CG2
|
K:VAL124
|
4.6
|
12.7
|
1.0
|
CG
|
K:GLU123
|
4.7
|
20.9
|
1.0
|
O
|
K:HOH2197
|
4.7
|
42.9
|
1.0
|
O
|
K:HOH2622
|
4.8
|
33.1
|
1.0
|
OE2
|
K:GLU123
|
4.9
|
43.1
|
1.0
|
CD2
|
K:LEU190
|
4.9
|
9.8
|
1.0
|
NE
|
K:ARG120
|
5.0
|
8.5
|
1.0
|
OD1
|
K:ASP158
|
5.0
|
23.0
|
1.0
|
|
Iodine binding site 8 out
of 34 in 1oxx
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Iodine Binding Sites List in 1oxx
Iodine binding site 8 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1908
b:19.0
occ:0.40
|
NE
|
K:ARG67
|
3.3
|
6.1
|
0.5
|
O
|
K:HOH1952
|
3.6
|
14.4
|
1.0
|
O
|
K:ASP81
|
3.8
|
17.7
|
1.0
|
CD
|
K:ARG67
|
4.0
|
16.8
|
0.5
|
CG1
|
K:VAL69
|
4.0
|
7.0
|
1.0
|
O
|
K:HOH2594
|
4.0
|
54.6
|
1.0
|
CB
|
K:PHE64
|
4.1
|
8.2
|
1.0
|
CZ
|
K:ARG67
|
4.1
|
23.5
|
0.5
|
CG1
|
K:VAL77
|
4.1
|
9.7
|
1.0
|
CA
|
K:ARG82
|
4.1
|
10.6
|
1.0
|
NH2
|
K:ARG67
|
4.2
|
12.0
|
0.5
|
CD2
|
K:PHE64
|
4.5
|
5.5
|
1.0
|
CG
|
K:ARG67
|
4.6
|
7.5
|
0.5
|
CG
|
K:ARG82
|
4.6
|
7.2
|
1.0
|
CG
|
K:PHE64
|
4.6
|
4.7
|
1.0
|
C
|
K:ASP81
|
4.7
|
13.7
|
1.0
|
CB
|
K:ARG67
|
4.7
|
3.4
|
0.5
|
CD
|
K:ARG67
|
4.8
|
13.7
|
0.5
|
CB
|
K:ARG82
|
4.8
|
9.0
|
1.0
|
C
|
K:ARG82
|
4.8
|
11.4
|
1.0
|
CG2
|
K:VAL77
|
4.8
|
8.6
|
1.0
|
O
|
K:ARG82
|
4.8
|
12.0
|
1.0
|
CB
|
K:VAL77
|
4.8
|
8.7
|
1.0
|
NH1
|
K:ARG67
|
4.9
|
9.2
|
0.5
|
CG
|
K:ARG67
|
4.9
|
13.3
|
0.5
|
N
|
K:ARG82
|
4.9
|
9.3
|
1.0
|
|
Iodine binding site 9 out
of 34 in 1oxx
Go back to
Iodine Binding Sites List in 1oxx
Iodine binding site 9 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1909
b:24.7
occ:0.70
|
N
|
K:ASN96
|
3.6
|
3.8
|
1.0
|
CB
|
K:TYR94
|
3.7
|
13.7
|
1.0
|
CD2
|
K:TYR94
|
3.7
|
35.5
|
1.0
|
CB
|
K:ASN96
|
3.8
|
6.1
|
1.0
|
CD
|
K:PRO95
|
4.0
|
6.3
|
1.0
|
CA
|
K:ASN96
|
4.0
|
5.9
|
1.0
|
N
|
K:PRO95
|
4.1
|
5.0
|
1.0
|
CG
|
K:TYR94
|
4.1
|
23.9
|
1.0
|
C
|
K:TYR94
|
4.2
|
6.8
|
1.0
|
CA
|
K:TYR94
|
4.2
|
9.5
|
1.0
|
CG
|
K:PRO95
|
4.3
|
12.2
|
1.0
|
C
|
K:ASN96
|
4.3
|
9.2
|
1.0
|
N
|
K:LEU97
|
4.5
|
6.1
|
1.0
|
C
|
K:PRO95
|
4.7
|
7.5
|
1.0
|
CG
|
K:LEU97
|
4.8
|
9.5
|
1.0
|
CE2
|
K:TYR94
|
4.8
|
26.5
|
1.0
|
O
|
K:TYR94
|
4.8
|
8.8
|
1.0
|
O
|
K:ASN96
|
4.8
|
9.4
|
1.0
|
CA
|
K:PRO95
|
4.9
|
7.0
|
1.0
|
|
Iodine binding site 10 out
of 34 in 1oxx
Go back to
Iodine Binding Sites List in 1oxx
Iodine binding site 10 out
of 34 in the Crystal Structure of Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus
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 Glcv, the Abc-Atpase of the Glucose Abc Transporter From Sulfolobus Solfataricus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:I1910
b:28.3
occ:0.50
|
O
|
K:HOH2205
|
3.0
|
22.2
|
1.0
|
OG
|
K:SER234
|
3.2
|
8.5
|
1.0
|
O
|
K:HOH2349
|
3.5
|
34.8
|
1.0
|
O
|
K:HOH2406
|
3.7
|
33.9
|
1.0
|
O
|
K:HOH2432
|
3.8
|
36.7
|
1.0
|
CB
|
K:SER234
|
3.8
|
6.7
|
1.0
|
CG1
|
K:VAL220
|
3.9
|
7.3
|
1.0
|
CG2
|
K:VAL220
|
4.0
|
7.3
|
1.0
|
CB
|
K:VAL220
|
4.1
|
4.9
|
1.0
|
CG2
|
K:VAL215
|
4.3
|
12.7
|
1.0
|
O
|
K:HOH2347
|
4.3
|
39.0
|
1.0
|
CG2
|
K:VAL237
|
4.5
|
8.3
|
1.0
|
CB
|
K:VAL215
|
4.5
|
9.7
|
1.0
|
CG1
|
K:VAL215
|
4.5
|
12.4
|
1.0
|
NE2
|
K:GLN236
|
4.5
|
20.5
|
1.0
|
CB
|
K:GLN236
|
4.6
|
10.9
|
1.0
|
O
|
K:HOH2024
|
4.7
|
26.1
|
1.0
|
CG1
|
K:VAL233
|
5.0
|
7.1
|
1.0
|
|
Reference:
G.Verdon,
S.-V.Albers,
N.Van Oosterwijk,
B.W.Dijkstra,
A.J.M.Driessen,
A.M.W.H.Thunnissen.
Formation of the Productive Atp-MG2+-Bound Dimer of Glcv, An Abc-Atpase From Sulfolobus Solfataricus J.Mol.Biol. V. 334 255 2003.
ISSN: ISSN 0022-2836
PubMed: 14607117
DOI: 10.1016/J.JMB.2003.08.065
Page generated: Sun Aug 11 12:34:49 2024
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