Iodine in PDB 1q8c: A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
Protein crystallography data
The structure of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins, PDB code: 1q8c
was solved by
J.Liu,
H.Yokota,
R.Kim,
S.-H.Kim,
Berkeley Structural Genomics Center(Bsgc),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.00
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
41.401,
41.401,
99.008,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
25.4 /
27.2
|
Other elements in 1q8c:
The structure of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins also contains other interesting chemical elements:
Iodine Binding Sites:
The binding sites of Iodine atom in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
(pdb code 1q8c). This binding sites where shown within
5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the
A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins, PDB code: 1q8c:
Jump to Iodine binding site number:
1;
2;
3;
4;
5;
6;
7;
Iodine binding site 1 out
of 7 in 1q8c
Go back to
Iodine Binding Sites List in 1q8c
Iodine binding site 1 out
of 7 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I152
b:57.2
occ:0.60
|
O
|
A:GLU55
|
4.0
|
43.5
|
1.0
|
C
|
A:GLU55
|
4.1
|
43.5
|
1.0
|
CE1
|
A:HIS116
|
4.1
|
42.4
|
1.0
|
N
|
A:TRP56
|
4.2
|
43.3
|
1.0
|
CA
|
A:TRP56
|
4.2
|
43.5
|
1.0
|
CG
|
A:LEU59
|
4.2
|
45.1
|
1.0
|
CB
|
A:GLU55
|
4.4
|
43.9
|
1.0
|
O
|
A:HOH214
|
4.4
|
57.4
|
1.0
|
CD1
|
A:LEU59
|
4.6
|
44.8
|
1.0
|
CB
|
A:LEU59
|
4.6
|
43.9
|
1.0
|
CA
|
A:GLU55
|
4.9
|
43.7
|
1.0
|
ND1
|
A:HIS116
|
4.9
|
43.3
|
1.0
|
CB
|
A:TRP56
|
5.0
|
43.9
|
1.0
|
|
Iodine binding site 2 out
of 7 in 1q8c
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Iodine Binding Sites List in 1q8c
Iodine binding site 2 out
of 7 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I153
b:58.8
occ:0.70
|
I
|
A:IOD158
|
2.6
|
63.2
|
0.3
|
ND2
|
A:ASN54
|
3.6
|
44.5
|
1.0
|
NH2
|
A:ARG14
|
3.7
|
43.0
|
1.0
|
CB
|
A:TRP56
|
3.8
|
43.9
|
1.0
|
NE
|
A:ARG14
|
4.0
|
43.8
|
1.0
|
CG
|
A:TRP56
|
4.1
|
43.5
|
1.0
|
CZ
|
A:ARG14
|
4.3
|
43.5
|
1.0
|
NA
|
A:NA162
|
4.4
|
66.3
|
1.0
|
CD1
|
A:TRP56
|
4.4
|
42.2
|
1.0
|
O
|
A:HOH208
|
4.6
|
55.1
|
1.0
|
CG
|
A:ASN54
|
4.7
|
44.6
|
1.0
|
CD2
|
A:TRP56
|
4.8
|
43.4
|
1.0
|
|
Iodine binding site 3 out
of 7 in 1q8c
Go back to
Iodine Binding Sites List in 1q8c
Iodine binding site 3 out
of 7 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I154
b:58.6
occ:0.40
|
CB
|
A:PRO33
|
3.6
|
45.3
|
1.0
|
CG2
|
A:ILE68
|
4.2
|
44.9
|
1.0
|
CD1
|
A:PHE69
|
4.2
|
43.5
|
1.0
|
CG1
|
A:ILE68
|
4.3
|
45.9
|
1.0
|
CA
|
A:PRO33
|
4.3
|
45.1
|
1.0
|
CD1
|
A:LEU32
|
4.3
|
46.4
|
1.0
|
N
|
A:PHE69
|
4.5
|
44.2
|
1.0
|
CA
|
A:PHE69
|
4.6
|
43.9
|
1.0
|
CB
|
A:PHE69
|
4.7
|
43.9
|
1.0
|
CG
|
A:PRO33
|
4.8
|
45.4
|
1.0
|
CB
|
A:ILE68
|
4.9
|
45.2
|
1.0
|
CB
|
A:LEU32
|
4.9
|
46.1
|
1.0
|
CG
|
A:PHE69
|
4.9
|
43.8
|
1.0
|
C
|
A:ILE68
|
4.9
|
44.5
|
1.0
|
CD1
|
A:ILE68
|
5.0
|
46.4
|
1.0
|
N
|
A:PRO33
|
5.0
|
45.5
|
1.0
|
|
Iodine binding site 4 out
of 7 in 1q8c
Go back to
Iodine Binding Sites List in 1q8c
Iodine binding site 4 out
of 7 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I155
b:59.3
occ:0.40
|
CE
|
A:LYS120
|
3.6
|
44.4
|
1.0
|
CA
|
A:PRO121
|
4.1
|
43.5
|
1.0
|
CD1
|
A:ILE124
|
4.2
|
44.4
|
1.0
|
CG
|
A:PRO121
|
4.2
|
43.6
|
1.0
|
N
|
A:PRO121
|
4.3
|
43.7
|
1.0
|
O
|
A:HOH175
|
4.3
|
62.3
|
1.0
|
CG
|
A:LYS120
|
4.3
|
44.4
|
1.0
|
O
|
A:HOH200
|
4.3
|
56.7
|
1.0
|
CB
|
A:PRO121
|
4.4
|
43.6
|
1.0
|
NZ
|
A:LYS120
|
4.5
|
45.3
|
1.0
|
CD
|
A:LYS120
|
4.6
|
44.6
|
1.0
|
CD2
|
A:LEU150
|
4.6
|
44.9
|
1.0
|
CD
|
A:PRO121
|
4.6
|
43.8
|
1.0
|
C
|
A:LYS120
|
4.7
|
43.9
|
1.0
|
CB
|
A:LYS120
|
4.7
|
44.1
|
1.0
|
O
|
A:LYS120
|
4.9
|
44.1
|
1.0
|
|
Iodine binding site 5 out
of 7 in 1q8c
Go back to
Iodine Binding Sites List in 1q8c
Iodine binding site 5 out
of 7 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I156
b:59.9
occ:0.40
|
CB
|
A:ALA63
|
3.9
|
43.4
|
1.0
|
NA
|
A:NA163
|
3.9
|
62.2
|
1.0
|
CA
|
A:ALA63
|
4.2
|
43.0
|
1.0
|
CA
|
A:ALA115
|
4.2
|
43.8
|
1.0
|
N
|
A:ALA63
|
4.4
|
43.5
|
1.0
|
O
|
A:LEU59
|
4.4
|
43.9
|
1.0
|
CB
|
A:ALA115
|
4.4
|
43.9
|
1.0
|
CD2
|
A:LEU59
|
4.8
|
44.8
|
1.0
|
CG
|
A:LYS62
|
4.8
|
44.6
|
1.0
|
O
|
A:LYS114
|
4.8
|
44.5
|
1.0
|
CD1
|
A:LEU59
|
4.8
|
44.8
|
1.0
|
CG
|
A:LYS114
|
4.9
|
45.2
|
1.0
|
N
|
A:ALA115
|
4.9
|
44.2
|
1.0
|
|
Iodine binding site 6 out
of 7 in 1q8c
Go back to
Iodine Binding Sites List in 1q8c
Iodine binding site 6 out
of 7 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I157
b:62.6
occ:0.30
|
ND2
|
A:ASN82
|
3.1
|
44.8
|
1.0
|
CA
|
A:GLN79
|
3.9
|
44.7
|
1.0
|
CG
|
A:GLN79
|
3.9
|
45.4
|
1.0
|
CE1
|
A:HIS144
|
4.1
|
44.4
|
1.0
|
CB
|
A:GLN79
|
4.1
|
44.6
|
1.0
|
CG
|
A:ASN82
|
4.1
|
45.0
|
1.0
|
CG
|
A:LYS141
|
4.2
|
44.7
|
1.0
|
CB
|
A:ASN82
|
4.3
|
44.8
|
1.0
|
O
|
A:GLN79
|
4.4
|
45.0
|
1.0
|
OE1
|
A:GLN79
|
4.4
|
46.5
|
1.0
|
C
|
A:GLN79
|
4.6
|
44.5
|
1.0
|
CD
|
A:GLN79
|
4.7
|
46.3
|
1.0
|
N
|
A:GLN79
|
4.9
|
44.5
|
1.0
|
ND1
|
A:HIS144
|
4.9
|
45.0
|
1.0
|
NZ
|
A:LYS141
|
4.9
|
45.1
|
1.0
|
NE2
|
A:HIS144
|
5.0
|
43.8
|
1.0
|
|
Iodine binding site 7 out
of 7 in 1q8c
Go back to
Iodine Binding Sites List in 1q8c
Iodine binding site 7 out
of 7 in the A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins
Mono view
Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I158
b:63.2
occ:0.30
|
I
|
A:IOD153
|
2.6
|
58.8
|
0.7
|
NA
|
A:NA162
|
2.7
|
66.3
|
1.0
|
NE
|
A:ARG14
|
3.2
|
43.8
|
1.0
|
CD
|
A:ARG17
|
3.4
|
46.0
|
1.0
|
ND2
|
A:ASN54
|
3.5
|
44.5
|
1.0
|
O
|
A:HOH187
|
3.7
|
55.7
|
1.0
|
CD
|
A:ARG14
|
3.8
|
44.3
|
1.0
|
CG
|
A:ARG14
|
4.0
|
43.6
|
1.0
|
NH1
|
A:ARG17
|
4.0
|
46.2
|
1.0
|
CZ
|
A:ARG14
|
4.3
|
43.5
|
1.0
|
NE
|
A:ARG17
|
4.3
|
47.3
|
1.0
|
NH2
|
A:ARG14
|
4.4
|
43.0
|
1.0
|
CE3
|
A:TRP56
|
4.4
|
43.2
|
1.0
|
CG
|
A:ARG17
|
4.4
|
45.4
|
1.0
|
CB
|
A:TRP56
|
4.5
|
43.9
|
1.0
|
CD2
|
A:TRP56
|
4.5
|
43.4
|
1.0
|
CG
|
A:TRP56
|
4.5
|
43.5
|
1.0
|
CG
|
A:ASN54
|
4.6
|
44.6
|
1.0
|
CZ
|
A:ARG17
|
4.6
|
45.6
|
1.0
|
OD1
|
A:ASN54
|
4.8
|
44.1
|
1.0
|
CA
|
A:ARG14
|
4.9
|
43.5
|
1.0
|
|
Reference:
J.Liu,
H.Yokota,
R.Kim,
S.-H.Kim.
A Conserved Hypothetical Protein From Mycoplasma Genitalium Shows Structural Homology to Nusb Proteins Proteins V. 55 1082 2004.
ISSN: ISSN 0887-3585
PubMed: 15146506
DOI: 10.1002/PROT.20119
Page generated: Sun Aug 11 12:45:00 2024
|