Iridium in PDB 6s4q: Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Protein crystallography data
The structure of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes, PDB code: 6s4q
was solved by
J.G.Rebelein,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.82 /
1.85
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
184.219,
57.201,
57.201,
90.00,
108.09,
90.00
|
R / Rfree (%)
|
19.5 /
23.1
|
Other elements in 6s4q:
The structure of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes also contains other interesting chemical elements:
Iridium Binding Sites:
The binding sites of Iridium atom in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
(pdb code 6s4q). This binding sites where shown within
5.0 Angstroms radius around Iridium atom.
In total 8 binding sites of Iridium where determined in the
Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes, PDB code: 6s4q:
Jump to Iridium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Iridium binding site 1 out
of 8 in 6s4q
Go back to
Iridium Binding Sites List in 6s4q
Iridium binding site 1 out
of 8 in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 1 of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir401
b:45.6
occ:0.50
|
IR1
|
A:4IR401
|
0.0
|
45.6
|
0.5
|
N5
|
A:4IR401
|
2.0
|
47.6
|
0.5
|
N4
|
A:4IR401
|
2.1
|
44.7
|
0.5
|
C18
|
A:4IR401
|
2.1
|
47.8
|
0.5
|
C17
|
A:4IR401
|
2.1
|
48.1
|
0.5
|
C19
|
A:4IR401
|
2.1
|
49.0
|
0.5
|
C21
|
A:4IR401
|
2.1
|
49.2
|
0.5
|
C20
|
A:4IR401
|
2.1
|
47.3
|
0.5
|
CL1
|
A:4IR401
|
2.4
|
57.3
|
0.5
|
C28
|
A:4IR401
|
2.8
|
37.5
|
0.5
|
C27
|
A:4IR401
|
3.0
|
40.0
|
0.5
|
O4
|
A:4IR401
|
3.0
|
39.1
|
0.5
|
S2
|
A:4IR401
|
3.1
|
40.0
|
0.5
|
CL1
|
B:4IR402
|
3.2
|
51.2
|
0.5
|
C23
|
A:4IR401
|
3.2
|
49.0
|
0.5
|
C22
|
A:4IR401
|
3.2
|
50.0
|
0.5
|
C24
|
A:4IR401
|
3.2
|
51.5
|
0.5
|
C26
|
A:4IR401
|
3.2
|
44.5
|
0.5
|
C25
|
A:4IR401
|
3.2
|
48.0
|
0.5
|
O3
|
A:4IR401
|
4.1
|
39.4
|
0.5
|
C16
|
A:4IR401
|
4.4
|
35.7
|
0.5
|
O4
|
B:4IR402
|
4.6
|
35.4
|
0.5
|
O
|
A:ALA121
|
4.7
|
27.3
|
1.0
|
O3
|
A:4IR401
|
4.8
|
46.3
|
0.5
|
C13
|
A:4IR401
|
4.8
|
31.6
|
0.5
|
|
Iridium binding site 2 out
of 8 in 6s4q
Go back to
Iridium Binding Sites List in 6s4q
Iridium binding site 2 out
of 8 in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 2 of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir401
b:41.7
occ:0.50
|
IR1
|
A:4IR401
|
0.0
|
41.7
|
0.5
|
N4
|
A:4IR401
|
2.0
|
43.8
|
0.5
|
N5
|
A:4IR401
|
2.1
|
45.3
|
0.5
|
C19
|
A:4IR401
|
2.1
|
48.1
|
0.5
|
C18
|
A:4IR401
|
2.1
|
47.0
|
0.5
|
C20
|
A:4IR401
|
2.1
|
48.2
|
0.5
|
C17
|
A:4IR401
|
2.1
|
48.1
|
0.5
|
C21
|
A:4IR401
|
2.1
|
45.8
|
0.5
|
CL1
|
A:4IR401
|
2.4
|
52.0
|
0.5
|
O4
|
A:4IR401
|
2.8
|
45.7
|
0.5
|
C28
|
A:4IR401
|
2.9
|
38.7
|
0.5
|
C27
|
A:4IR401
|
2.9
|
39.3
|
0.5
|
S2
|
A:4IR401
|
3.0
|
44.7
|
0.5
|
C24
|
A:4IR401
|
3.1
|
48.0
|
0.5
|
C23
|
A:4IR401
|
3.2
|
46.5
|
0.5
|
C25
|
A:4IR401
|
3.2
|
43.6
|
0.5
|
C22
|
A:4IR401
|
3.2
|
48.0
|
0.5
|
C26
|
A:4IR401
|
3.2
|
46.5
|
0.5
|
O3
|
A:4IR401
|
3.8
|
46.3
|
0.5
|
C16
|
A:4IR401
|
4.3
|
41.4
|
0.5
|
C23
|
A:4IR401
|
4.8
|
49.0
|
0.5
|
CD2
|
A:HIS87
|
4.9
|
46.0
|
1.0
|
|
Iridium binding site 3 out
of 8 in 6s4q
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Iridium Binding Sites List in 6s4q
Iridium binding site 3 out
of 8 in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 3 of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir402
b:44.9
occ:0.50
|
IR1
|
A:4IR402
|
0.0
|
44.9
|
0.5
|
N5
|
A:4IR402
|
2.0
|
45.3
|
0.5
|
N4
|
A:4IR402
|
2.1
|
42.0
|
0.5
|
C19
|
A:4IR402
|
2.1
|
43.3
|
0.5
|
C20
|
A:4IR402
|
2.1
|
44.9
|
0.5
|
C21
|
A:4IR402
|
2.1
|
44.3
|
0.5
|
C18
|
A:4IR402
|
2.1
|
46.1
|
0.5
|
C17
|
A:4IR402
|
2.1
|
47.2
|
0.5
|
CL1
|
A:4IR402
|
2.4
|
56.8
|
0.5
|
C28
|
A:4IR402
|
2.8
|
36.5
|
0.5
|
O4
|
A:4IR402
|
3.0
|
35.3
|
0.5
|
C27
|
A:4IR402
|
3.0
|
38.8
|
0.5
|
S2
|
A:4IR402
|
3.0
|
39.9
|
0.5
|
C24
|
A:4IR402
|
3.1
|
46.3
|
0.5
|
C25
|
A:4IR402
|
3.2
|
45.8
|
0.5
|
C26
|
A:4IR402
|
3.2
|
45.0
|
0.5
|
C23
|
A:4IR402
|
3.2
|
43.1
|
0.5
|
C22
|
A:4IR402
|
3.2
|
45.6
|
0.5
|
CL1
|
B:4IR401
|
3.3
|
54.1
|
0.5
|
O3
|
A:4IR402
|
3.7
|
35.4
|
0.5
|
O4
|
A:4IR402
|
4.2
|
50.4
|
0.5
|
C16
|
A:4IR402
|
4.5
|
32.4
|
0.5
|
O3
|
B:4IR401
|
4.6
|
35.5
|
0.5
|
O
|
A:LYS305
|
4.7
|
25.2
|
1.0
|
C15
|
A:4IR402
|
4.8
|
57.7
|
0.5
|
C13
|
A:4IR402
|
4.9
|
30.4
|
0.5
|
|
Iridium binding site 4 out
of 8 in 6s4q
Go back to
Iridium Binding Sites List in 6s4q
Iridium binding site 4 out
of 8 in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 4 of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ir402
b:42.1
occ:0.50
|
IR1
|
A:4IR402
|
0.0
|
42.1
|
0.5
|
N4
|
A:4IR402
|
2.0
|
45.4
|
0.5
|
N5
|
A:4IR402
|
2.0
|
44.3
|
0.5
|
C18
|
A:4IR402
|
2.1
|
47.8
|
0.5
|
C19
|
A:4IR402
|
2.1
|
48.2
|
0.5
|
C17
|
A:4IR402
|
2.1
|
48.0
|
0.5
|
C20
|
A:4IR402
|
2.1
|
48.4
|
0.5
|
C21
|
A:4IR402
|
2.1
|
46.5
|
0.5
|
CL1
|
A:4IR402
|
2.4
|
47.6
|
0.5
|
C27
|
A:4IR402
|
2.9
|
40.2
|
0.5
|
C28
|
A:4IR402
|
2.9
|
39.6
|
0.5
|
S2
|
A:4IR402
|
3.1
|
49.6
|
0.5
|
C23
|
A:4IR402
|
3.1
|
47.2
|
0.5
|
C24
|
A:4IR402
|
3.1
|
50.0
|
0.5
|
O3
|
A:4IR402
|
3.2
|
44.7
|
0.5
|
C22
|
A:4IR402
|
3.2
|
48.4
|
0.5
|
C25
|
A:4IR402
|
3.2
|
42.2
|
0.5
|
C26
|
A:4IR402
|
3.2
|
49.2
|
0.5
|
O4
|
A:4IR402
|
3.6
|
50.4
|
0.5
|
C16
|
A:4IR402
|
4.4
|
52.5
|
0.5
|
C25
|
A:4IR402
|
4.4
|
45.8
|
0.5
|
C13
|
A:4IR402
|
5.0
|
54.5
|
0.5
|
|
Iridium binding site 5 out
of 8 in 6s4q
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Iridium Binding Sites List in 6s4q
Iridium binding site 5 out
of 8 in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 5 of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir401
b:46.4
occ:0.50
|
IR1
|
B:4IR401
|
0.0
|
46.4
|
0.5
|
N5
|
B:4IR401
|
2.1
|
44.6
|
0.5
|
N4
|
B:4IR401
|
2.1
|
41.6
|
0.5
|
C19
|
B:4IR401
|
2.1
|
46.5
|
0.5
|
C18
|
B:4IR401
|
2.1
|
47.1
|
0.5
|
C20
|
B:4IR401
|
2.1
|
47.5
|
0.5
|
C17
|
B:4IR401
|
2.1
|
48.5
|
0.5
|
C21
|
B:4IR401
|
2.1
|
46.1
|
0.5
|
CL1
|
B:4IR401
|
2.4
|
54.1
|
0.5
|
C28
|
B:4IR401
|
2.9
|
36.5
|
0.5
|
C27
|
B:4IR401
|
3.0
|
37.8
|
0.5
|
O4
|
B:4IR401
|
3.1
|
35.4
|
0.5
|
S2
|
B:4IR401
|
3.1
|
40.3
|
0.5
|
C24
|
B:4IR401
|
3.2
|
47.3
|
0.5
|
C23
|
B:4IR401
|
3.2
|
51.0
|
0.5
|
C25
|
B:4IR401
|
3.2
|
49.8
|
0.5
|
C22
|
B:4IR401
|
3.2
|
44.1
|
0.5
|
C26
|
B:4IR401
|
3.2
|
47.7
|
0.5
|
O3
|
B:4IR401
|
3.8
|
35.5
|
0.5
|
CL1
|
A:4IR402
|
4.0
|
56.8
|
0.5
|
C16
|
B:4IR401
|
4.5
|
33.1
|
0.5
|
O3
|
B:4IR401
|
4.6
|
54.4
|
0.5
|
O3
|
A:4IR402
|
4.6
|
35.4
|
0.5
|
O
|
B:ALA121
|
4.7
|
28.1
|
1.0
|
C13
|
B:4IR401
|
4.9
|
30.8
|
0.5
|
N5
|
A:4IR402
|
5.0
|
45.3
|
0.5
|
|
Iridium binding site 6 out
of 8 in 6s4q
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Iridium Binding Sites List in 6s4q
Iridium binding site 6 out
of 8 in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 6 of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir401
b:41.6
occ:0.50
|
IR1
|
B:4IR401
|
0.0
|
41.6
|
0.5
|
N5
|
B:4IR401
|
2.0
|
45.9
|
0.5
|
N4
|
B:4IR401
|
2.0
|
47.6
|
0.5
|
C19
|
B:4IR401
|
2.1
|
48.5
|
0.5
|
C18
|
B:4IR401
|
2.1
|
48.0
|
0.5
|
C17
|
B:4IR401
|
2.1
|
49.1
|
0.5
|
C20
|
B:4IR401
|
2.1
|
49.3
|
0.5
|
C21
|
B:4IR401
|
2.1
|
46.8
|
0.5
|
CL1
|
B:4IR401
|
2.4
|
51.6
|
0.5
|
O4
|
B:4IR401
|
2.8
|
53.9
|
0.5
|
C28
|
B:4IR401
|
2.9
|
40.2
|
0.5
|
C27
|
B:4IR401
|
2.9
|
42.5
|
0.5
|
S2
|
B:4IR401
|
3.0
|
50.8
|
0.5
|
C23
|
B:4IR401
|
3.2
|
46.6
|
0.5
|
C24
|
B:4IR401
|
3.2
|
48.5
|
0.5
|
C25
|
B:4IR401
|
3.2
|
45.1
|
0.5
|
C22
|
B:4IR401
|
3.2
|
49.5
|
0.5
|
C26
|
B:4IR401
|
3.2
|
48.5
|
0.5
|
O3
|
B:4IR401
|
3.8
|
54.4
|
0.5
|
C16
|
B:4IR401
|
4.3
|
47.3
|
0.5
|
CD2
|
B:HIS87
|
4.8
|
49.0
|
1.0
|
C15
|
B:4IR401
|
4.9
|
44.4
|
0.5
|
C25
|
B:4IR401
|
4.9
|
49.8
|
0.5
|
|
Iridium binding site 7 out
of 8 in 6s4q
Go back to
Iridium Binding Sites List in 6s4q
Iridium binding site 7 out
of 8 in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 7 of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir402
b:43.5
occ:0.50
|
IR1
|
B:4IR402
|
0.0
|
43.5
|
0.5
|
N5
|
B:4IR402
|
2.1
|
42.3
|
0.5
|
N4
|
B:4IR402
|
2.1
|
41.3
|
0.5
|
C19
|
B:4IR402
|
2.1
|
44.8
|
0.5
|
C18
|
B:4IR402
|
2.1
|
44.1
|
0.5
|
C17
|
B:4IR402
|
2.1
|
46.6
|
0.5
|
C20
|
B:4IR402
|
2.1
|
44.5
|
0.5
|
C21
|
B:4IR402
|
2.1
|
43.5
|
0.5
|
CL1
|
B:4IR402
|
2.4
|
51.2
|
0.5
|
C28
|
B:4IR402
|
2.9
|
33.9
|
0.5
|
C27
|
B:4IR402
|
3.0
|
37.5
|
0.5
|
O3
|
B:4IR402
|
3.0
|
36.8
|
0.5
|
S2
|
B:4IR402
|
3.1
|
39.2
|
0.5
|
C24
|
B:4IR402
|
3.2
|
48.6
|
0.5
|
C23
|
B:4IR402
|
3.2
|
47.3
|
0.5
|
C22
|
B:4IR402
|
3.2
|
41.8
|
0.5
|
C25
|
B:4IR402
|
3.2
|
49.3
|
0.5
|
C26
|
B:4IR402
|
3.2
|
45.5
|
0.5
|
O4
|
B:4IR402
|
3.7
|
35.4
|
0.5
|
C25
|
A:4IR401
|
4.5
|
48.0
|
0.5
|
C16
|
B:4IR402
|
4.5
|
33.7
|
0.5
|
O3
|
A:4IR401
|
4.5
|
39.4
|
0.5
|
O
|
B:LYS305
|
4.7
|
29.1
|
1.0
|
N4
|
A:4IR401
|
4.9
|
44.7
|
0.5
|
C15
|
B:4IR402
|
4.9
|
30.1
|
0.5
|
|
Iridium binding site 8 out
of 8 in 6s4q
Go back to
Iridium Binding Sites List in 6s4q
Iridium binding site 8 out
of 8 in the Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes
Mono view
Stereo pair view
|
A full contact list of Iridium with other atoms in the Ir binding
site number 8 of Scdsav(Sask) - Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ir402
b:41.5
occ:0.50
|
IR1
|
B:4IR402
|
0.0
|
41.5
|
0.5
|
N4
|
B:4IR402
|
2.0
|
43.7
|
0.5
|
N5
|
B:4IR402
|
2.1
|
43.2
|
0.5
|
C19
|
B:4IR402
|
2.1
|
47.1
|
0.5
|
C18
|
B:4IR402
|
2.1
|
46.5
|
0.5
|
C17
|
B:4IR402
|
2.1
|
48.4
|
0.5
|
C20
|
B:4IR402
|
2.1
|
48.0
|
0.5
|
C21
|
B:4IR402
|
2.1
|
45.6
|
0.5
|
CL1
|
B:4IR402
|
2.4
|
48.4
|
0.5
|
O4
|
B:4IR402
|
2.6
|
45.6
|
0.5
|
C28
|
B:4IR402
|
2.9
|
36.8
|
0.5
|
S2
|
B:4IR402
|
2.9
|
45.9
|
0.5
|
C27
|
B:4IR402
|
2.9
|
39.3
|
0.5
|
C23
|
B:4IR402
|
3.2
|
45.4
|
0.5
|
C24
|
B:4IR402
|
3.2
|
50.2
|
0.5
|
C22
|
B:4IR402
|
3.2
|
47.6
|
0.5
|
C25
|
B:4IR402
|
3.2
|
45.6
|
0.5
|
C26
|
B:4IR402
|
3.2
|
47.4
|
0.5
|
O3
|
B:4IR402
|
3.6
|
46.1
|
0.5
|
C16
|
B:4IR402
|
4.2
|
43.4
|
0.5
|
CD2
|
B:HIS271
|
4.9
|
46.5
|
1.0
|
C13
|
B:4IR402
|
4.9
|
40.9
|
0.5
|
|
Reference:
S.Wu,
Y.Zhou,
J.G.Rebelein,
M.Kuhn,
H.Mallin,
J.Zhao,
N.V.Igareta,
T.R.Ward.
Breaking Symmetry: Engineering Single-Chain Dimeric Streptavidin As Host For Artificial Metalloenzymes. J.Am.Chem.Soc. V. 141 15869 2019.
ISSN: ESSN 1520-5126
PubMed: 31509711
DOI: 10.1021/JACS.9B06923
Page generated: Mon Aug 12 03:42:30 2024
|