Iridium in PDB 5od5: Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Protein crystallography data
The structure of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst, PDB code: 5od5
was solved by
A.K.Duhme-Klair,
D.J.Raines,
J.E.Clarke,
E.V.Blagova,
E.J.Dodson,
K.S.Wilson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
66.42 /
1.90
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.692,
62.759,
68.195,
87.38,
76.90,
79.27
|
R / Rfree (%)
|
17.7 /
22.3
|
Other elements in 5od5:
The structure of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst also contains other interesting chemical elements:
Iridium Binding Sites:
The binding sites of Iridium atom in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
(pdb code 5od5). This binding sites where shown within
5.0 Angstroms radius around Iridium atom.
In total 8 binding sites of Iridium where determined in the
Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst, PDB code: 5od5:
Jump to Iridium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iridium binding site 1 out
of 8 in 5od5
Go back to
Iridium Binding Sites List in 5od5
Iridium binding site 1 out
of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 1 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir402
b:46.0
occ:0.31
|
C6
|
A:9RT404
|
1.2
|
62.7
|
0.4
|
N2
|
A:9RT404
|
1.4
|
52.3
|
0.4
|
C5
|
A:9RT404
|
1.7
|
58.6
|
0.4
|
S1
|
A:9RT404
|
1.8
|
55.7
|
0.4
|
C4
|
A:9RT404
|
1.9
|
54.7
|
0.4
|
NE2
|
A:HIS227
|
2.5
|
32.8
|
0.5
|
CE1
|
A:HIS227
|
2.6
|
38.4
|
0.5
|
CE1
|
A:HIS227
|
2.7
|
67.5
|
0.0
|
O1
|
A:9RT404
|
2.7
|
51.8
|
0.4
|
C7
|
A:9RT404
|
2.7
|
57.9
|
0.4
|
O2
|
A:9RT404
|
2.8
|
54.5
|
0.4
|
C12
|
A:9RT404
|
2.8
|
51.4
|
0.4
|
IR1
|
A:RIR405
|
3.1
|
59.0
|
0.4
|
C3
|
A:9RT404
|
3.1
|
56.5
|
0.4
|
N3
|
A:9RT404
|
3.5
|
58.9
|
0.4
|
NE2
|
A:HIS227
|
3.6
|
67.8
|
0.0
|
ND1
|
A:HIS227
|
3.7
|
67.5
|
0.0
|
C8
|
A:9RT404
|
3.7
|
60.2
|
0.4
|
C13
|
A:9RT404
|
3.7
|
55.7
|
0.4
|
CD2
|
A:HIS227
|
3.8
|
40.8
|
0.5
|
C2
|
A:9RT404
|
3.9
|
57.5
|
0.4
|
ND1
|
A:HIS227
|
4.0
|
36.6
|
0.5
|
C20
|
A:RIR405
|
4.3
|
57.9
|
0.4
|
C25
|
A:RIR405
|
4.4
|
55.6
|
0.4
|
C19
|
A:RIR405
|
4.4
|
57.7
|
0.4
|
CG
|
A:HIS227
|
4.5
|
40.1
|
0.5
|
C24
|
A:RIR405
|
4.7
|
54.9
|
0.4
|
C21
|
A:RIR405
|
4.7
|
58.8
|
0.4
|
CAQ
|
A:95B403
|
4.7
|
53.0
|
1.0
|
C11
|
A:9RT404
|
4.8
|
63.5
|
0.4
|
CD2
|
A:HIS227
|
4.8
|
67.5
|
0.0
|
CG
|
A:HIS227
|
4.8
|
67.5
|
0.0
|
C18
|
A:RIR405
|
4.9
|
57.4
|
0.4
|
C9
|
A:9RT404
|
5.0
|
61.1
|
0.4
|
|
Iridium binding site 2 out
of 8 in 5od5
Go back to
Iridium Binding Sites List in 5od5
Iridium binding site 2 out
of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 2 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir405
b:59.0
occ:0.43
|
IR1
|
A:RIR405
|
0.0
|
59.0
|
0.4
|
NE2
|
A:HIS227
|
1.5
|
67.8
|
0.0
|
N3
|
A:9RT404
|
1.9
|
58.9
|
0.4
|
N2
|
A:9RT404
|
1.9
|
52.3
|
0.4
|
C19
|
A:RIR405
|
2.0
|
57.7
|
0.4
|
C20
|
A:RIR405
|
2.0
|
57.9
|
0.4
|
C21
|
A:RIR405
|
2.0
|
58.8
|
0.4
|
C18
|
A:RIR405
|
2.0
|
57.4
|
0.4
|
C17
|
A:RIR405
|
2.0
|
57.1
|
0.4
|
CE1
|
A:HIS227
|
2.1
|
67.5
|
0.0
|
NE2
|
A:HIS227
|
2.2
|
32.8
|
0.5
|
C7
|
A:9RT404
|
2.4
|
57.9
|
0.4
|
CD2
|
A:HIS227
|
2.5
|
40.8
|
0.5
|
C6
|
A:9RT404
|
2.5
|
62.7
|
0.4
|
CD2
|
A:HIS227
|
2.8
|
67.5
|
0.0
|
C11
|
A:9RT404
|
2.9
|
63.5
|
0.4
|
IR
|
A:IR402
|
3.1
|
46.0
|
0.3
|
C24
|
A:RIR405
|
3.1
|
54.9
|
0.4
|
C25
|
A:RIR405
|
3.1
|
55.6
|
0.4
|
C26
|
A:RIR405
|
3.1
|
56.5
|
0.4
|
C23
|
A:RIR405
|
3.1
|
57.7
|
0.4
|
C22
|
A:RIR405
|
3.1
|
54.3
|
0.4
|
ND1
|
A:HIS227
|
3.3
|
67.5
|
0.0
|
S1
|
A:9RT404
|
3.4
|
55.7
|
0.4
|
CE1
|
A:HIS227
|
3.5
|
38.4
|
0.5
|
C8
|
A:9RT404
|
3.6
|
60.2
|
0.4
|
CG
|
A:HIS227
|
3.7
|
67.5
|
0.0
|
O1
|
A:9RT404
|
3.7
|
51.8
|
0.4
|
CG
|
A:HIS227
|
3.8
|
40.1
|
0.5
|
C10
|
A:9RT404
|
4.0
|
64.0
|
0.4
|
O2
|
A:9RT404
|
4.0
|
54.5
|
0.4
|
C9
|
A:9RT404
|
4.2
|
61.1
|
0.4
|
ND1
|
A:HIS227
|
4.3
|
36.6
|
0.5
|
OG1
|
A:THR226
|
4.6
|
71.7
|
1.0
|
C5
|
A:9RT404
|
4.6
|
58.6
|
0.4
|
C4
|
A:9RT404
|
4.8
|
54.7
|
0.4
|
|
Iridium binding site 3 out
of 8 in 5od5
Go back to
Iridium Binding Sites List in 5od5
Iridium binding site 3 out
of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 3 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir403
b:81.8
occ:0.16
|
OG1
|
B:THR226
|
2.0
|
99.0
|
1.0
|
CB
|
B:THR226
|
3.4
|
0.7
|
1.0
|
O
|
B:GLY225
|
4.0
|
0.9
|
1.0
|
N
|
B:THR226
|
4.1
|
0.1
|
1.0
|
CG2
|
B:THR226
|
4.1
|
0.2
|
1.0
|
C
|
B:GLY225
|
4.1
|
0.2
|
1.0
|
CA
|
B:THR226
|
4.3
|
0.5
|
1.0
|
CA
|
B:GLY225
|
5.0
|
0.1
|
1.0
|
|
Iridium binding site 4 out
of 8 in 5od5
Go back to
Iridium Binding Sites List in 5od5
Iridium binding site 4 out
of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 4 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir404
b:90.4
occ:0.16
|
IR
|
B:IR405
|
2.0
|
94.5
|
0.2
|
O
|
B:THR226
|
2.9
|
0.7
|
1.0
|
CB
|
B:THR226
|
3.1
|
0.7
|
1.0
|
OG1
|
B:THR226
|
3.7
|
99.0
|
1.0
|
C
|
B:THR226
|
3.8
|
0.8
|
1.0
|
CG2
|
B:THR226
|
3.8
|
0.2
|
1.0
|
CA
|
B:THR226
|
4.0
|
0.5
|
1.0
|
ND1
|
B:HIS227
|
4.5
|
0.5
|
1.0
|
|
Iridium binding site 5 out
of 8 in 5od5
Go back to
Iridium Binding Sites List in 5od5
Iridium binding site 5 out
of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 5 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir405
b:94.5
occ:0.21
|
IR
|
B:IR404
|
2.0
|
90.4
|
0.2
|
O
|
B:THR226
|
2.8
|
0.7
|
1.0
|
ND1
|
B:HIS227
|
3.1
|
0.5
|
1.0
|
CE1
|
B:HIS227
|
3.4
|
0.5
|
1.0
|
C
|
B:THR226
|
4.0
|
0.8
|
1.0
|
CG
|
B:HIS227
|
4.2
|
0.7
|
1.0
|
CB
|
B:THR226
|
4.5
|
0.7
|
1.0
|
NE2
|
B:HIS227
|
4.5
|
0.5
|
1.0
|
CA
|
B:THR226
|
4.8
|
0.5
|
1.0
|
CB
|
B:HIS227
|
4.9
|
0.1
|
1.0
|
N
|
B:HIS227
|
5.0
|
0.8
|
1.0
|
|
Iridium binding site 6 out
of 8 in 5od5
Go back to
Iridium Binding Sites List in 5od5
Iridium binding site 6 out
of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 6 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ir402
b:52.8
occ:0.17
|
C4
|
C:9RT405
|
1.4
|
42.7
|
0.6
|
C5
|
C:9RT405
|
1.5
|
41.6
|
0.6
|
S1
|
C:9RT405
|
1.9
|
43.8
|
0.6
|
N2
|
C:9RT405
|
2.0
|
38.2
|
0.6
|
C6
|
C:9RT405
|
2.5
|
36.7
|
0.6
|
O1
|
C:9RT405
|
2.6
|
41.7
|
0.6
|
C3
|
C:9RT405
|
2.6
|
39.7
|
0.6
|
C12
|
C:9RT405
|
2.7
|
38.0
|
0.6
|
O2
|
C:9RT405
|
3.2
|
43.8
|
0.6
|
CE1
|
C:HIS227
|
3.3
|
70.0
|
1.0
|
C7
|
C:9RT405
|
3.5
|
33.6
|
0.6
|
C2
|
C:9RT405
|
3.5
|
36.8
|
0.6
|
NE2
|
C:HIS227
|
3.5
|
68.8
|
1.0
|
C13
|
C:9RT405
|
3.5
|
34.6
|
0.6
|
IR1
|
C:RIR406
|
3.8
|
43.6
|
0.6
|
ND1
|
C:HIS227
|
4.1
|
74.1
|
1.0
|
N3
|
C:9RT405
|
4.1
|
28.2
|
0.6
|
C8
|
C:9RT405
|
4.3
|
33.1
|
0.6
|
CD2
|
C:HIS227
|
4.5
|
70.8
|
1.0
|
CG
|
C:HIS227
|
4.8
|
73.5
|
1.0
|
C1
|
C:9RT405
|
4.9
|
38.9
|
0.6
|
C20
|
C:RIR406
|
5.0
|
49.3
|
0.6
|
C19
|
C:RIR406
|
5.0
|
45.6
|
0.6
|
|
Iridium binding site 7 out
of 8 in 5od5
Go back to
Iridium Binding Sites List in 5od5
Iridium binding site 7 out
of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 7 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ir403
b:66.0
occ:0.44
|
ND1
|
C:HIS227
|
2.3
|
74.1
|
1.0
|
CE1
|
C:HIS227
|
3.0
|
70.0
|
1.0
|
CG
|
C:HIS227
|
3.4
|
73.5
|
1.0
|
CB
|
C:HIS227
|
3.8
|
67.0
|
1.0
|
NE2
|
C:HIS227
|
4.2
|
68.8
|
1.0
|
CD2
|
C:HIS227
|
4.3
|
70.8
|
1.0
|
|
Iridium binding site 8 out
of 8 in 5od5
Go back to
Iridium Binding Sites List in 5od5
Iridium binding site 8 out
of 8 in the Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 8 of Periplasmic Binding Protein Ceue Complexed with A Synthetic Catalyst within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ir406
b:43.6
occ:0.63
|
IR1
|
C:RIR406
|
0.0
|
43.6
|
0.6
|
C18
|
C:RIR406
|
2.0
|
49.1
|
0.6
|
C17
|
C:RIR406
|
2.0
|
49.7
|
0.6
|
N2
|
C:9RT405
|
2.0
|
38.2
|
0.6
|
C21
|
C:RIR406
|
2.0
|
53.3
|
0.6
|
C19
|
C:RIR406
|
2.0
|
45.6
|
0.6
|
C20
|
C:RIR406
|
2.0
|
49.3
|
0.6
|
N3
|
C:9RT405
|
2.1
|
28.2
|
0.6
|
NE2
|
C:HIS227
|
2.2
|
68.8
|
1.0
|
C6
|
C:9RT405
|
2.8
|
36.7
|
0.6
|
C7
|
C:9RT405
|
2.8
|
33.6
|
0.6
|
C11
|
C:9RT405
|
3.1
|
35.4
|
0.6
|
C22
|
C:RIR406
|
3.1
|
54.4
|
0.6
|
C26
|
C:RIR406
|
3.1
|
51.1
|
0.6
|
C25
|
C:RIR406
|
3.2
|
44.8
|
0.6
|
CD2
|
C:HIS227
|
3.2
|
70.8
|
1.0
|
C23
|
C:RIR406
|
3.2
|
53.2
|
0.6
|
C24
|
C:RIR406
|
3.2
|
52.9
|
0.6
|
CE1
|
C:HIS227
|
3.2
|
70.0
|
1.0
|
S1
|
C:9RT405
|
3.4
|
43.8
|
0.6
|
O1
|
C:9RT405
|
3.5
|
41.7
|
0.6
|
IR
|
C:IR402
|
3.8
|
52.8
|
0.2
|
O2
|
C:9RT405
|
4.0
|
43.8
|
0.6
|
C8
|
C:9RT405
|
4.2
|
33.1
|
0.6
|
ND1
|
C:HIS227
|
4.3
|
74.1
|
1.0
|
CG
|
C:HIS227
|
4.3
|
73.5
|
1.0
|
C10
|
C:9RT405
|
4.4
|
35.3
|
0.6
|
C5
|
C:9RT405
|
4.7
|
41.6
|
0.6
|
C9
|
C:9RT405
|
4.8
|
33.1
|
0.6
|
|
Reference:
A.D.J.Raines,
J.E.Clarke,
E.Blagova,
E.J.Dodson,
K.S.Wilson,
A.K.Duhme-Klair.
Redox-Switchable Siderophore Anchor Enables Reversible Artificial Metalloenzyme Assembly Nat Catal 2018.
DOI: 10.1038/S41929-018-0124-3
Page generated: Mon Aug 12 03:37:26 2024
|