Iridium in PDB 4r0d: Crystal Structure of A Eukaryotic Group II Intron Lariat
Protein crystallography data
The structure of Crystal Structure of A Eukaryotic Group II Intron Lariat, PDB code: 4r0d
was solved by
A.R.Robart,
R.T.Chan,
J.K.Peters,
K.R.Rajashankar,
N.Toor,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
81.82 /
3.68
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
163.639,
255.361,
136.786,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.9 /
27.4
|
Other elements in 4r0d:
The structure of Crystal Structure of A Eukaryotic Group II Intron Lariat also contains other interesting chemical elements:
Iridium Binding Sites:
Iridium binding site 1 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 1 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 1 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir703
b:0.1
occ:1.00
|
IR
|
A:IRI703
|
0.0
|
0.1
|
1.0
|
N1
|
A:IRI703
|
2.0
|
0.0
|
1.0
|
N4
|
A:IRI703
|
2.0
|
0.0
|
1.0
|
N2
|
A:IRI703
|
2.0
|
0.6
|
1.0
|
N3
|
A:IRI703
|
2.0
|
1.0
|
1.0
|
N6
|
A:IRI703
|
2.0
|
0.1
|
1.0
|
N5
|
A:IRI703
|
2.0
|
0.8
|
1.0
|
O6
|
A:G18
|
3.9
|
0.8
|
1.0
|
N7
|
A:G18
|
4.4
|
0.4
|
1.0
|
C6
|
A:G18
|
4.7
|
0.8
|
1.0
|
C5
|
A:G18
|
4.9
|
0.9
|
1.0
|
|
Iridium binding site 2 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 2 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 2 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir704
b:0.4
occ:1.00
|
IR
|
A:IRI704
|
0.0
|
0.4
|
1.0
|
N3
|
A:IRI704
|
2.2
|
0.2
|
1.0
|
N6
|
A:IRI704
|
2.2
|
0.1
|
1.0
|
N4
|
A:IRI704
|
2.2
|
0.1
|
1.0
|
N5
|
A:IRI704
|
2.2
|
0.3
|
0.0
|
N2
|
A:IRI704
|
2.2
|
0.5
|
0.0
|
N1
|
A:IRI704
|
2.3
|
0.9
|
0.0
|
O2'
|
A:A171
|
3.7
|
0.1
|
1.0
|
OP1
|
A:C554
|
4.1
|
99.7
|
1.0
|
OP1
|
A:C570
|
4.2
|
0.4
|
1.0
|
OP2
|
A:C570
|
4.3
|
0.7
|
1.0
|
O3'
|
A:A171
|
4.4
|
80.8
|
1.0
|
O3'
|
A:C553
|
4.4
|
73.3
|
1.0
|
OP1
|
A:U569
|
4.5
|
93.2
|
1.0
|
OP1
|
A:G172
|
4.5
|
90.5
|
1.0
|
P
|
A:C570
|
4.6
|
92.9
|
1.0
|
OP1
|
A:U170
|
4.7
|
0.9
|
1.0
|
O3'
|
A:U569
|
4.7
|
89.1
|
1.0
|
|
Iridium binding site 3 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 3 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 3 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir705
b:0.9
occ:1.00
|
IR
|
A:IRI705
|
0.0
|
0.9
|
1.0
|
N2
|
A:IRI705
|
2.2
|
0.3
|
0.0
|
N1
|
A:IRI705
|
2.2
|
0.6
|
0.0
|
N5
|
A:IRI705
|
2.2
|
0.2
|
0.0
|
N6
|
A:IRI705
|
2.3
|
0.8
|
0.0
|
N3
|
A:IRI705
|
2.3
|
0.2
|
0.0
|
N4
|
A:IRI705
|
2.3
|
0.1
|
1.0
|
N7
|
A:G114
|
3.8
|
0.3
|
1.0
|
OP2
|
A:A113
|
4.0
|
0.7
|
1.0
|
O6
|
A:G114
|
4.0
|
0.3
|
1.0
|
N3
|
A:IRI713
|
4.1
|
0.8
|
1.0
|
C5
|
A:G114
|
4.5
|
0.1
|
1.0
|
C6
|
A:G114
|
4.5
|
0.6
|
1.0
|
C8
|
A:G114
|
4.8
|
0.6
|
1.0
|
OP2
|
A:G114
|
4.8
|
0.8
|
1.0
|
OP1
|
A:A113
|
4.9
|
0.8
|
1.0
|
P
|
A:A113
|
5.0
|
0.6
|
1.0
|
|
Iridium binding site 4 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 4 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 4 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir706
b:1.0
occ:1.00
|
IR
|
A:IRI706
|
0.0
|
1.0
|
1.0
|
N3
|
A:IRI706
|
2.2
|
0.2
|
0.0
|
N6
|
A:IRI706
|
2.2
|
0.3
|
0.0
|
N2
|
A:IRI706
|
2.2
|
0.4
|
0.0
|
N5
|
A:IRI706
|
2.3
|
0.1
|
0.0
|
N4
|
A:IRI706
|
2.3
|
0.2
|
1.0
|
N1
|
A:IRI706
|
2.3
|
0.1
|
0.0
|
OP2
|
A:A194
|
3.8
|
0.9
|
1.0
|
O3'
|
A:U192
|
3.8
|
0.8
|
1.0
|
P
|
A:A194
|
4.3
|
0.1
|
1.0
|
N7
|
A:G195
|
4.4
|
0.8
|
1.0
|
O6
|
A:G293
|
4.7
|
0.6
|
1.0
|
N4
|
A:C197
|
4.7
|
0.5
|
1.0
|
O4
|
A:U294
|
4.8
|
0.2
|
1.0
|
N7
|
A:G196
|
4.9
|
0.6
|
1.0
|
O6
|
A:G196
|
4.9
|
0.1
|
1.0
|
C3'
|
A:U192
|
5.0
|
0.9
|
1.0
|
|
Iridium binding site 5 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 5 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 5 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir707
b:0.3
occ:1.00
|
IR
|
A:IRI707
|
0.0
|
0.3
|
1.0
|
N5
|
A:IRI707
|
2.2
|
0.8
|
0.0
|
N2
|
A:IRI707
|
2.2
|
0.7
|
0.0
|
N3
|
A:IRI707
|
2.2
|
0.7
|
0.0
|
N1
|
A:IRI707
|
2.3
|
0.6
|
0.0
|
N4
|
A:IRI707
|
2.3
|
0.1
|
0.0
|
N6
|
A:IRI707
|
2.3
|
0.8
|
0.0
|
OP2
|
A:U520
|
3.2
|
0.8
|
1.0
|
OP2
|
A:G521
|
3.5
|
0.3
|
1.0
|
O2'
|
A:A519
|
3.7
|
0.2
|
1.0
|
N7
|
A:G521
|
4.2
|
0.8
|
1.0
|
O3'
|
A:U520
|
4.3
|
0.3
|
1.0
|
O6
|
A:G521
|
4.5
|
0.4
|
1.0
|
P
|
A:G521
|
4.5
|
0.1
|
1.0
|
P
|
A:U520
|
4.7
|
0.1
|
1.0
|
C5'
|
A:U520
|
4.8
|
0.3
|
1.0
|
C5
|
A:G521
|
4.8
|
0.8
|
1.0
|
C6
|
A:G521
|
5.0
|
0.2
|
1.0
|
|
Iridium binding site 6 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 6 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 6 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir708
b:0.7
occ:1.00
|
IR
|
A:IRI708
|
0.0
|
0.7
|
1.0
|
N1
|
A:IRI708
|
2.2
|
0.1
|
0.0
|
N5
|
A:IRI708
|
2.2
|
0.3
|
0.0
|
N4
|
A:IRI708
|
2.3
|
0.5
|
1.0
|
N2
|
A:IRI708
|
2.3
|
0.7
|
0.0
|
N3
|
A:IRI708
|
2.3
|
0.1
|
1.0
|
N6
|
A:IRI708
|
2.3
|
0.2
|
1.0
|
O6
|
A:G493
|
3.3
|
0.4
|
1.0
|
O6
|
A:G431
|
3.8
|
0.1
|
1.0
|
OP2
|
A:A492
|
4.4
|
0.6
|
1.0
|
C6
|
A:G493
|
4.4
|
0.3
|
1.0
|
OP1
|
A:C491
|
4.6
|
0.7
|
1.0
|
OP2
|
A:C491
|
4.9
|
0.4
|
1.0
|
C6
|
A:G431
|
4.9
|
0.4
|
1.0
|
|
Iridium binding site 7 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 7 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 7 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir709
b:0.4
occ:1.00
|
IR
|
A:IRI709
|
0.0
|
0.4
|
1.0
|
N6
|
A:IRI709
|
2.2
|
0.2
|
1.0
|
N2
|
A:IRI709
|
2.2
|
0.7
|
0.0
|
N3
|
A:IRI709
|
2.2
|
64.9
|
1.0
|
N1
|
A:IRI709
|
2.2
|
0.1
|
0.0
|
N4
|
A:IRI709
|
2.2
|
80.9
|
1.0
|
N5
|
A:IRI709
|
2.3
|
1.0
|
0.0
|
O6
|
A:G338
|
3.9
|
0.0
|
1.0
|
O4
|
A:U14
|
4.1
|
81.3
|
1.0
|
N7
|
A:G338
|
4.4
|
0.3
|
1.0
|
O2'
|
A:G10
|
4.5
|
0.7
|
1.0
|
O6
|
A:G339
|
4.6
|
0.5
|
1.0
|
C6
|
A:G338
|
4.7
|
0.1
|
1.0
|
C5
|
A:G338
|
4.9
|
0.3
|
1.0
|
|
Iridium binding site 8 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 8 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 8 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir710
b:0.0
occ:1.00
|
IR
|
A:IRI710
|
0.0
|
0.0
|
1.0
|
N1
|
A:IRI710
|
2.2
|
0.1
|
0.0
|
N5
|
A:IRI710
|
2.2
|
0.2
|
0.0
|
N2
|
A:IRI710
|
2.3
|
0.6
|
0.0
|
N3
|
A:IRI710
|
2.3
|
0.5
|
0.0
|
N4
|
A:IRI710
|
2.3
|
0.5
|
1.0
|
N6
|
A:IRI710
|
2.3
|
0.6
|
1.0
|
OP1
|
A:A577
|
4.1
|
0.4
|
1.0
|
OP1
|
A:C578
|
4.2
|
0.4
|
1.0
|
OP2
|
A:C578
|
4.3
|
0.6
|
1.0
|
OP2
|
A:G421
|
4.4
|
0.1
|
1.0
|
O2'
|
A:A6
|
4.6
|
0.6
|
1.0
|
P
|
A:C578
|
4.7
|
0.4
|
1.0
|
O3'
|
A:A6
|
5.0
|
0.7
|
1.0
|
|
Iridium binding site 9 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 9 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 9 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir711
b:0.4
occ:1.00
|
IR
|
A:IRI711
|
0.0
|
0.4
|
1.0
|
N1
|
A:IRI711
|
2.2
|
1.0
|
0.0
|
N2
|
A:IRI711
|
2.2
|
0.1
|
0.0
|
N6
|
A:IRI711
|
2.2
|
0.7
|
1.0
|
N4
|
A:IRI711
|
2.3
|
97.4
|
1.0
|
N5
|
A:IRI711
|
2.3
|
0.1
|
0.0
|
N3
|
A:IRI711
|
2.3
|
0.8
|
1.0
|
O2'
|
A:A165
|
3.7
|
0.3
|
1.0
|
OP2
|
A:G167
|
4.0
|
0.6
|
1.0
|
O
|
A:HOH982
|
4.0
|
0.3
|
1.0
|
O6
|
A:G168
|
4.3
|
0.2
|
1.0
|
N7
|
A:G168
|
4.4
|
0.7
|
1.0
|
O3'
|
A:A165
|
4.7
|
0.1
|
1.0
|
N7
|
A:G167
|
4.9
|
0.4
|
1.0
|
C2'
|
A:A165
|
4.9
|
0.2
|
1.0
|
OP2
|
A:U166
|
4.9
|
0.2
|
1.0
|
|
Iridium binding site 10 out
of 38 in 4r0d
Go back to
Iridium Binding Sites List in 4r0d
Iridium binding site 10 out
of 38 in the Crystal Structure of A Eukaryotic Group II Intron Lariat
 Mono view
 Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 10 of Crystal Structure of A Eukaryotic Group II Intron Lariat within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir712
b:0.1
occ:1.00
|
IR
|
A:IRI712
|
0.0
|
0.1
|
1.0
|
N3
|
A:IRI712
|
2.2
|
67.3
|
1.0
|
N6
|
A:IRI712
|
2.2
|
68.8
|
1.0
|
N2
|
A:IRI712
|
2.2
|
76.1
|
0.0
|
N1
|
A:IRI712
|
2.2
|
73.5
|
0.0
|
N5
|
A:IRI712
|
2.2
|
75.6
|
0.0
|
N4
|
A:IRI712
|
2.2
|
60.0
|
1.0
|
O4
|
A:U183
|
4.5
|
91.9
|
1.0
|
O4
|
A:U301
|
4.9
|
0.5
|
1.0
|
|
Reference:
A.R.Robart,
R.T.Chan,
J.K.Peters,
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ISSN: ISSN 0028-0836
PubMed: 25252982
DOI: 10.1038/NATURE13790
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