Iodine in PDB 7mzp: Crystal Structure of the Ucld Lectin-Binding Domain
Protein crystallography data
The structure of Crystal Structure of the Ucld Lectin-Binding Domain, PDB code: 7mzp
was solved by
T.Ve,
A.W.Lo,
M.A.Schembri,
B.Kobe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.85 /
2.20
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
39.04,
58.12,
175.42,
90,
90,
90
|
R / Rfree (%)
|
24.8 /
30.6
|
Iodine Binding Sites:
The binding sites of Iodine atom in the Crystal Structure of the Ucld Lectin-Binding Domain
(pdb code 7mzp). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the
Crystal Structure of the Ucld Lectin-Binding Domain, PDB code: 7mzp:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
Iodine binding site 1 out
of 6 in 7mzp
Go back to
Iodine Binding Sites List in 7mzp
Iodine binding site 1 out
of 6 in the Crystal Structure of the Ucld Lectin-Binding Domain
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 the Ucld Lectin-Binding Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I301
b:22.0
occ:1.00
|
HB3
|
A:TRP123
|
3.0
|
26.8
|
1.0
|
HD2
|
A:PRO124
|
3.3
|
29.1
|
1.0
|
HB3
|
A:ALA125
|
3.4
|
30.4
|
1.0
|
H
|
A:ALA125
|
3.5
|
26.1
|
1.0
|
HB2
|
A:ALA125
|
3.6
|
30.4
|
1.0
|
CB
|
A:ALA125
|
3.9
|
25.0
|
1.0
|
CB
|
A:TRP123
|
4.0
|
22.1
|
1.0
|
HG2
|
A:PRO124
|
4.0
|
29.1
|
1.0
|
CD
|
A:PRO124
|
4.2
|
23.9
|
1.0
|
HB2
|
A:TRP123
|
4.2
|
26.8
|
1.0
|
N
|
A:ALA125
|
4.3
|
21.5
|
1.0
|
HE3
|
A:TRP123
|
4.4
|
26.8
|
1.0
|
CG
|
A:TRP123
|
4.6
|
19.6
|
1.0
|
CG
|
A:PRO124
|
4.6
|
23.9
|
1.0
|
HB1
|
A:ALA125
|
4.7
|
30.4
|
1.0
|
N
|
A:PRO124
|
4.7
|
21.6
|
1.0
|
CA
|
A:ALA125
|
4.8
|
21.4
|
1.0
|
CE3
|
A:TRP123
|
4.8
|
22.0
|
1.0
|
CD2
|
A:TRP123
|
4.9
|
19.5
|
1.0
|
HD3
|
A:PRO124
|
4.9
|
29.1
|
1.0
|
C
|
A:TRP123
|
4.9
|
23.9
|
1.0
|
CA
|
A:TRP123
|
5.0
|
23.1
|
1.0
|
|
Iodine binding site 2 out
of 6 in 7mzp
Go back to
Iodine Binding Sites List in 7mzp
Iodine binding site 2 out
of 6 in the Crystal Structure of the Ucld Lectin-Binding Domain
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 the Ucld Lectin-Binding Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I302
b:25.2
occ:1.00
|
H
|
A:LEU73
|
2.8
|
23.4
|
1.0
|
HB3
|
A:LYS191
|
3.1
|
25.7
|
1.0
|
HH11
|
A:ARG192
|
3.1
|
27.1
|
1.0
|
HB3
|
A:ARG192
|
3.2
|
27.2
|
1.0
|
H
|
A:ARG192
|
3.3
|
19.4
|
1.0
|
HA
|
A:ALA72
|
3.3
|
22.0
|
1.0
|
HG2
|
A:ARG192
|
3.4
|
27.2
|
1.0
|
HG
|
A:LEU73
|
3.4
|
25.6
|
1.0
|
N
|
A:LEU73
|
3.7
|
19.2
|
1.0
|
NH1
|
A:ARG192
|
3.7
|
22.3
|
1.0
|
HH12
|
A:ARG192
|
3.8
|
27.1
|
1.0
|
HB1
|
A:ALA72
|
3.8
|
29.8
|
1.0
|
N
|
A:ARG192
|
3.9
|
17.0
|
1.0
|
HB2
|
A:LEU73
|
3.9
|
23.7
|
1.0
|
CB
|
A:ARG192
|
4.0
|
22.3
|
1.0
|
CB
|
A:LYS191
|
4.1
|
21.1
|
1.0
|
CG
|
A:ARG192
|
4.1
|
22.3
|
1.0
|
CA
|
A:ALA72
|
4.1
|
18.0
|
1.0
|
CG
|
A:LEU73
|
4.2
|
21.0
|
1.0
|
CB
|
A:ALA72
|
4.3
|
24.5
|
1.0
|
H
|
A:LYS191
|
4.3
|
24.3
|
1.0
|
C
|
A:ALA72
|
4.4
|
19.1
|
1.0
|
CB
|
A:LEU73
|
4.4
|
19.5
|
1.0
|
HD3
|
A:ARG192
|
4.4
|
26.1
|
1.0
|
HG3
|
A:LYS191
|
4.5
|
28.6
|
1.0
|
HB2
|
A:ALA72
|
4.5
|
29.8
|
1.0
|
CA
|
A:ARG192
|
4.5
|
22.1
|
1.0
|
HB2
|
A:LYS191
|
4.5
|
25.7
|
1.0
|
CA
|
A:LEU73
|
4.6
|
17.4
|
1.0
|
HG2
|
A:LYS191
|
4.6
|
28.6
|
1.0
|
CG
|
A:LYS191
|
4.7
|
23.5
|
1.0
|
HD12
|
A:LEU73
|
4.7
|
25.2
|
1.0
|
C
|
A:LYS191
|
4.7
|
21.8
|
1.0
|
CZ
|
A:ARG192
|
4.7
|
23.7
|
1.0
|
CD
|
A:ARG192
|
4.7
|
21.4
|
1.0
|
HB2
|
A:ARG192
|
4.7
|
27.2
|
1.0
|
CA
|
A:LYS191
|
4.8
|
20.2
|
1.0
|
N
|
A:LYS191
|
4.8
|
19.9
|
1.0
|
O
|
A:LEU73
|
4.8
|
19.4
|
1.0
|
HB1
|
A:ALA190
|
4.8
|
21.6
|
1.0
|
HA
|
A:ARG192
|
4.8
|
26.9
|
1.0
|
HG3
|
A:ARG192
|
4.8
|
27.2
|
1.0
|
|
Iodine binding site 3 out
of 6 in 7mzp
Go back to
Iodine Binding Sites List in 7mzp
Iodine binding site 3 out
of 6 in the Crystal Structure of the Ucld Lectin-Binding Domain
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 the Ucld Lectin-Binding Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I303
b:56.3
occ:1.00
|
O
|
A:HOH422
|
3.1
|
17.4
|
1.0
|
HG21
|
A:THR149
|
3.4
|
29.1
|
1.0
|
HA3
|
A:GLY142
|
3.6
|
32.5
|
1.0
|
HG23
|
A:THR149
|
4.1
|
29.1
|
1.0
|
CG2
|
A:THR149
|
4.2
|
24.0
|
1.0
|
H
|
A:GLY142
|
4.5
|
28.6
|
1.0
|
CA
|
A:GLY142
|
4.5
|
26.8
|
1.0
|
HG22
|
A:THR149
|
4.6
|
29.1
|
1.0
|
HB2
|
A:PRO140
|
4.6
|
28.1
|
1.0
|
HG1
|
A:THR149
|
4.7
|
33.0
|
1.0
|
HA2
|
A:GLY142
|
4.9
|
32.5
|
1.0
|
O
|
A:HOH456
|
4.9
|
23.3
|
1.0
|
N
|
A:GLY142
|
5.0
|
23.5
|
1.0
|
|
Iodine binding site 4 out
of 6 in 7mzp
Go back to
Iodine Binding Sites List in 7mzp
Iodine binding site 4 out
of 6 in the Crystal Structure of the Ucld Lectin-Binding Domain
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 the Ucld Lectin-Binding Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I304
b:48.8
occ:1.00
|
HA
|
A:PRO22
|
3.1
|
31.3
|
1.0
|
HB2
|
A:ALA70
|
3.3
|
29.7
|
1.0
|
O
|
A:HOH461
|
3.6
|
29.0
|
1.0
|
HG3
|
A:PRO22
|
3.6
|
32.3
|
1.0
|
N
|
A:PRO22
|
3.7
|
24.1
|
1.0
|
CA
|
A:PRO22
|
3.8
|
25.8
|
1.0
|
C
|
A:GLY21
|
3.8
|
25.4
|
1.0
|
O
|
A:GLY21
|
3.9
|
29.8
|
1.0
|
HB3
|
A:PRO22
|
4.1
|
33.0
|
1.0
|
CG
|
A:PRO22
|
4.2
|
26.6
|
1.0
|
HD3
|
A:PRO22
|
4.2
|
28.8
|
1.0
|
CB
|
A:ALA70
|
4.2
|
24.4
|
1.0
|
HA2
|
A:GLY21
|
4.3
|
29.2
|
1.0
|
CB
|
A:PRO22
|
4.3
|
27.2
|
1.0
|
CD
|
A:PRO22
|
4.3
|
23.6
|
1.0
|
CA
|
A:GLY21
|
4.5
|
24.0
|
1.0
|
HB3
|
A:ALA70
|
4.7
|
29.7
|
1.0
|
HB1
|
A:ALA70
|
4.7
|
29.7
|
1.0
|
H
|
A:ALA70
|
4.7
|
27.9
|
1.0
|
N
|
A:GLY21
|
4.8
|
21.7
|
1.0
|
HA
|
A:ALA70
|
4.8
|
26.6
|
1.0
|
N
|
A:ALA70
|
4.8
|
23.0
|
1.0
|
CA
|
A:ALA70
|
4.9
|
21.9
|
1.0
|
|
Iodine binding site 5 out
of 6 in 7mzp
Go back to
Iodine Binding Sites List in 7mzp
Iodine binding site 5 out
of 6 in the Crystal Structure of the Ucld Lectin-Binding Domain
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 the Ucld Lectin-Binding Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I305
b:72.9
occ:1.00
|
HA
|
A:ILE30
|
2.9
|
28.4
|
1.0
|
H
|
A:ALA31
|
3.0
|
28.6
|
1.0
|
HB2
|
A:ASN62
|
3.7
|
32.2
|
1.0
|
N
|
A:ALA31
|
3.7
|
23.6
|
1.0
|
HG13
|
A:ILE30
|
3.8
|
28.9
|
1.0
|
O
|
A:GLN29
|
3.8
|
25.5
|
1.0
|
CA
|
A:ILE30
|
3.9
|
23.3
|
1.0
|
HB3
|
A:ALA31
|
4.2
|
31.8
|
1.0
|
C
|
A:ILE30
|
4.3
|
24.4
|
1.0
|
HD22
|
A:ASN62
|
4.4
|
22.5
|
1.0
|
O
|
A:ALA31
|
4.4
|
21.6
|
1.0
|
HB
|
A:THR60
|
4.4
|
28.3
|
1.0
|
HG3
|
A:GLN29
|
4.5
|
26.8
|
1.0
|
C
|
A:GLN29
|
4.6
|
26.4
|
1.0
|
CB
|
A:ASN62
|
4.6
|
26.6
|
1.0
|
CG1
|
A:ILE30
|
4.7
|
23.8
|
1.0
|
N
|
A:ILE30
|
4.7
|
19.6
|
1.0
|
CA
|
A:ALA31
|
4.7
|
26.6
|
1.0
|
CB
|
A:ILE30
|
4.8
|
23.2
|
1.0
|
CB
|
A:ALA31
|
4.8
|
26.2
|
1.0
|
ND2
|
A:ASN62
|
4.8
|
18.5
|
1.0
|
HB
|
A:ILE30
|
4.8
|
28.2
|
1.0
|
HB2
|
A:ALA31
|
4.8
|
31.8
|
1.0
|
O
|
A:SER61
|
4.9
|
22.3
|
1.0
|
HG21
|
A:THR60
|
4.9
|
33.0
|
1.0
|
O
|
A:HOH460
|
5.0
|
31.8
|
1.0
|
HB3
|
A:ASN62
|
5.0
|
32.2
|
1.0
|
|
Iodine binding site 6 out
of 6 in 7mzp
Go back to
Iodine Binding Sites List in 7mzp
Iodine binding site 6 out
of 6 in the Crystal Structure of the Ucld Lectin-Binding Domain
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 the Ucld Lectin-Binding Domain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:I301
b:45.4
occ:1.00
|
HZ2
|
A:LYS84
|
2.8
|
49.1
|
1.0
|
H
|
B:ALA31
|
2.9
|
29.8
|
1.0
|
HA
|
B:ILE30
|
2.9
|
30.5
|
1.0
|
HG13
|
B:ILE30
|
3.4
|
27.4
|
1.0
|
HB2
|
B:ASN62
|
3.5
|
26.1
|
1.0
|
NZ
|
A:LYS84
|
3.6
|
40.6
|
1.0
|
N
|
B:ALA31
|
3.6
|
24.5
|
1.0
|
HZ3
|
A:LYS84
|
3.8
|
49.1
|
1.0
|
CA
|
B:ILE30
|
3.9
|
25.1
|
1.0
|
HD3
|
A:LYS84
|
3.9
|
39.5
|
1.0
|
HB
|
B:THR60
|
4.0
|
28.9
|
1.0
|
O
|
B:GLN29
|
4.0
|
30.5
|
1.0
|
O
|
B:ALA31
|
4.2
|
21.8
|
1.0
|
HE2
|
A:LYS84
|
4.2
|
40.8
|
1.0
|
HZ1
|
A:LYS84
|
4.2
|
49.1
|
1.0
|
HB3
|
B:ALA31
|
4.3
|
26.9
|
1.0
|
C
|
B:ILE30
|
4.3
|
25.4
|
1.0
|
CG1
|
B:ILE30
|
4.3
|
22.6
|
1.0
|
HD22
|
B:ASN62
|
4.3
|
28.4
|
1.0
|
CE
|
A:LYS84
|
4.4
|
33.7
|
1.0
|
CB
|
B:ASN62
|
4.4
|
21.4
|
1.0
|
HG12
|
B:ILE30
|
4.6
|
27.4
|
1.0
|
CB
|
B:ILE30
|
4.6
|
22.4
|
1.0
|
HG21
|
B:THR60
|
4.6
|
31.0
|
1.0
|
CD
|
A:LYS84
|
4.6
|
32.6
|
1.0
|
HG1
|
B:THR60
|
4.6
|
32.4
|
1.0
|
CA
|
B:ALA31
|
4.7
|
26.2
|
1.0
|
ND2
|
B:ASN62
|
4.7
|
23.3
|
1.0
|
C
|
B:GLN29
|
4.7
|
25.0
|
1.0
|
HB
|
B:ILE30
|
4.8
|
27.2
|
1.0
|
N
|
B:ILE30
|
4.8
|
25.8
|
1.0
|
HG3
|
B:GLN29
|
4.8
|
31.4
|
1.0
|
O
|
B:SER61
|
4.8
|
25.7
|
1.0
|
CB
|
B:THR60
|
4.8
|
23.8
|
1.0
|
CG
|
B:ASN62
|
4.8
|
23.6
|
1.0
|
C
|
B:ALA31
|
4.9
|
24.6
|
1.0
|
CB
|
B:ALA31
|
4.9
|
22.1
|
1.0
|
HB3
|
B:ASN62
|
4.9
|
26.1
|
1.0
|
|
Reference:
S.Hancock,
A.W.Lo,
T.Ve,
C.J.Day,
L.Tan,
A.Mendez,
M.Phan,
N.Nhu,
K.M.Peters,
A.Richards,
B.A.Fleming,
B.M.Forde,
T.Haselhorst,
K.G.K.Goh,
X.Jia,
M.Mobli,
S.A.Beatson,
M.P.Jennings,
M.A.Mulvey,
B.Kobe,
M.A.Schembri.
Regulatory and Binding Specificity Features of Escherichia Coli Ucl Fimbriae To Be Published.
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