Iron in PDB 6q8w: Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Enzymatic activity of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
All present enzymatic activity of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.:
1.6.5.11;
Protein crystallography data
The structure of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin., PDB code: 6q8w
was solved by
J.Gutierrez-Fernandez,
G.S.Minhas,
L.A.Sazanov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.71 /
3.40
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.980,
340.500,
264.270,
90.00,
100.44,
90.00
|
R / Rfree (%)
|
21.3 /
23.4
|
Iron Binding Sites:
Iron binding site 1 out
of 64 in 6q8w
Go back to
Iron Binding Sites List in 6q8w
Iron binding site 1 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Fe501
b:47.2
occ:1.00
|
FE1
|
1:SF4501
|
0.0
|
47.2
|
1.0
|
S2
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
S3
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
S4
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
SG
|
1:CYS356
|
2.3
|
44.7
|
1.0
|
FE2
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
FE4
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
FE3
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
CB
|
1:CYS356
|
3.1
|
41.4
|
1.0
|
N
|
1:CYS356
|
3.7
|
44.0
|
1.0
|
S1
|
1:SF4501
|
3.9
|
47.2
|
1.0
|
CA
|
1:CYS356
|
4.0
|
41.8
|
1.0
|
CB
|
1:PHE399
|
4.3
|
59.6
|
1.0
|
CB
|
1:CYS359
|
4.3
|
70.6
|
1.0
|
SG
|
1:CYS400
|
4.4
|
58.2
|
1.0
|
N
|
1:CYS400
|
4.5
|
61.8
|
1.0
|
N
|
1:PHE399
|
4.5
|
67.5
|
1.0
|
SG
|
1:CYS359
|
4.6
|
73.3
|
1.0
|
SG
|
1:CYS353
|
4.8
|
26.3
|
1.0
|
CB
|
1:LYS355
|
4.8
|
39.1
|
1.0
|
C
|
1:LYS355
|
4.9
|
43.4
|
1.0
|
CA
|
1:PHE399
|
4.9
|
62.6
|
1.0
|
O
|
1:CYS356
|
5.0
|
43.9
|
1.0
|
C
|
1:CYS356
|
5.0
|
42.3
|
1.0
|
|
Iron binding site 2 out
of 64 in 6q8w
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Iron Binding Sites List in 6q8w
Iron binding site 2 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Fe501
b:47.2
occ:1.00
|
FE2
|
1:SF4501
|
0.0
|
47.2
|
1.0
|
S1
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
S3
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
S4
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
SG
|
1:CYS359
|
2.3
|
73.3
|
1.0
|
FE3
|
1:SF4501
|
2.6
|
47.2
|
1.0
|
FE1
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
FE4
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
CB
|
1:CYS359
|
3.0
|
70.6
|
1.0
|
S2
|
1:SF4501
|
3.8
|
47.2
|
1.0
|
OG
|
1:SER352
|
4.4
|
29.5
|
1.0
|
SG
|
1:CYS400
|
4.4
|
58.2
|
1.0
|
CA
|
1:CYS359
|
4.5
|
66.3
|
1.0
|
N
|
1:CYS353
|
4.8
|
44.2
|
1.0
|
SG
|
1:CYS356
|
4.8
|
44.7
|
1.0
|
CB
|
1:CYS356
|
4.8
|
41.4
|
1.0
|
N
|
1:ARG360
|
4.8
|
45.2
|
1.0
|
CB
|
1:LEU402
|
4.9
|
33.5
|
1.0
|
SG
|
1:CYS353
|
4.9
|
26.3
|
1.0
|
C
|
1:CYS359
|
5.0
|
59.7
|
1.0
|
|
Iron binding site 3 out
of 64 in 6q8w
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Iron Binding Sites List in 6q8w
Iron binding site 3 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Fe501
b:47.2
occ:1.00
|
FE3
|
1:SF4501
|
0.0
|
47.2
|
1.0
|
SG
|
1:CYS400
|
1.9
|
58.2
|
1.0
|
S4
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
S1
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
S2
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
FE2
|
1:SF4501
|
2.6
|
47.2
|
1.0
|
FE1
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
FE4
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
CB
|
1:CYS400
|
3.3
|
58.8
|
1.0
|
O
|
1:CYS400
|
3.7
|
62.2
|
1.0
|
N
|
1:CYS400
|
3.9
|
61.8
|
1.0
|
S3
|
1:SF4501
|
3.9
|
47.2
|
1.0
|
CA
|
1:CYS400
|
4.0
|
60.3
|
1.0
|
C
|
1:CYS400
|
4.1
|
61.4
|
1.0
|
CB
|
1:LEU402
|
4.1
|
33.5
|
1.0
|
CD1
|
1:ILE181
|
4.5
|
20.9
|
1.0
|
N
|
1:LEU402
|
4.7
|
32.2
|
1.0
|
SG
|
1:CYS359
|
4.7
|
73.3
|
1.0
|
SG
|
1:CYS353
|
4.8
|
26.3
|
1.0
|
CG
|
1:PRO199
|
4.8
|
25.9
|
1.0
|
SG
|
1:CYS356
|
4.9
|
44.7
|
1.0
|
CA
|
1:LEU402
|
5.0
|
33.2
|
1.0
|
|
Iron binding site 4 out
of 64 in 6q8w
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Iron Binding Sites List in 6q8w
Iron binding site 4 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Fe501
b:47.2
occ:1.00
|
FE4
|
1:SF4501
|
0.0
|
47.2
|
1.0
|
S2
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
S1
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
S3
|
1:SF4501
|
2.3
|
47.2
|
1.0
|
SG
|
1:CYS353
|
2.3
|
26.3
|
1.0
|
FE1
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
FE2
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
FE3
|
1:SF4501
|
2.7
|
47.2
|
1.0
|
CB
|
1:CYS353
|
3.3
|
28.9
|
1.0
|
N
|
1:CYS353
|
3.9
|
44.2
|
1.0
|
S4
|
1:SF4501
|
4.0
|
47.2
|
1.0
|
CA
|
1:CYS353
|
4.1
|
39.2
|
1.0
|
N
|
1:GLY354
|
4.1
|
46.1
|
1.0
|
N
|
1:LYS355
|
4.2
|
41.9
|
1.0
|
SG
|
1:CYS400
|
4.3
|
58.2
|
1.0
|
CB
|
1:LYS355
|
4.4
|
39.1
|
1.0
|
C
|
1:CYS353
|
4.4
|
43.5
|
1.0
|
N
|
1:CYS356
|
4.5
|
44.0
|
1.0
|
CD
|
1:PRO199
|
4.7
|
26.2
|
1.0
|
SG
|
1:CYS356
|
4.7
|
44.7
|
1.0
|
CA
|
1:LYS355
|
4.8
|
42.2
|
1.0
|
CG
|
1:PRO199
|
4.8
|
25.9
|
1.0
|
SG
|
1:CYS359
|
4.9
|
73.3
|
1.0
|
OG
|
1:SER352
|
5.0
|
29.5
|
1.0
|
CD1
|
1:ILE181
|
5.0
|
20.9
|
1.0
|
|
Iron binding site 5 out
of 64 in 6q8w
Go back to
Iron Binding Sites List in 6q8w
Iron binding site 5 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Fe201
b:47.8
occ:1.00
|
FE1
|
2:FES201
|
0.0
|
47.8
|
1.0
|
S2
|
2:FES201
|
2.2
|
47.8
|
1.0
|
S1
|
2:FES201
|
2.2
|
47.8
|
1.0
|
SG
|
2:CYS83
|
2.3
|
70.2
|
1.0
|
SG
|
2:CYS88
|
2.3
|
22.5
|
1.0
|
FE2
|
2:FES201
|
3.1
|
47.8
|
1.0
|
CB
|
2:CYS88
|
3.1
|
23.6
|
1.0
|
CB
|
2:CYS83
|
3.6
|
62.7
|
1.0
|
N
|
2:CYS88
|
4.0
|
28.8
|
1.0
|
CA
|
2:CYS88
|
4.2
|
27.3
|
1.0
|
CG2
|
2:VAL133
|
4.3
|
57.9
|
1.0
|
N
|
2:LEU125
|
4.4
|
80.9
|
1.0
|
CA
|
2:CYS124
|
4.5
|
73.8
|
1.0
|
O
|
2:SER127
|
4.5
|
77.1
|
1.0
|
OG1
|
2:THR85
|
4.5
|
47.7
|
1.0
|
CB
|
2:THR85
|
4.6
|
48.0
|
1.0
|
SG
|
2:CYS124
|
4.8
|
73.6
|
1.0
|
CA
|
2:CYS128
|
4.8
|
78.3
|
1.0
|
CB
|
2:VAL133
|
4.9
|
60.6
|
1.0
|
N
|
2:THR85
|
4.9
|
41.8
|
1.0
|
SG
|
2:CYS128
|
4.9
|
77.5
|
1.0
|
CA
|
2:CYS83
|
4.9
|
55.0
|
1.0
|
|
Iron binding site 6 out
of 64 in 6q8w
Go back to
Iron Binding Sites List in 6q8w
Iron binding site 6 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Fe201
b:47.8
occ:1.00
|
FE2
|
2:FES201
|
0.0
|
47.8
|
1.0
|
S1
|
2:FES201
|
2.2
|
47.8
|
1.0
|
S2
|
2:FES201
|
2.2
|
47.8
|
1.0
|
SG
|
2:CYS124
|
2.3
|
73.6
|
1.0
|
SG
|
2:CYS128
|
2.3
|
77.5
|
1.0
|
FE1
|
2:FES201
|
3.1
|
47.8
|
1.0
|
CB
|
2:CYS124
|
3.5
|
73.1
|
1.0
|
CB
|
2:CYS128
|
3.6
|
79.2
|
1.0
|
CA
|
2:CYS124
|
3.9
|
73.8
|
1.0
|
N
|
2:GLY126
|
3.9
|
84.6
|
1.0
|
CA
|
2:CYS128
|
3.9
|
78.3
|
1.0
|
N
|
2:CYS128
|
4.1
|
78.3
|
1.0
|
N
|
2:SER127
|
4.1
|
84.0
|
1.0
|
N
|
2:LEU125
|
4.1
|
80.9
|
1.0
|
C
|
2:SER127
|
4.3
|
77.1
|
1.0
|
C
|
2:CYS124
|
4.3
|
78.5
|
1.0
|
CA
|
2:GLY126
|
4.4
|
87.0
|
1.0
|
CA
|
1:PRO98
|
4.5
|
31.9
|
1.0
|
O
|
2:SER127
|
4.5
|
77.1
|
1.0
|
N
|
1:GLY99
|
4.6
|
27.1
|
1.0
|
C
|
2:GLY126
|
4.6
|
88.8
|
1.0
|
SG
|
2:CYS83
|
4.7
|
70.2
|
1.0
|
CB
|
2:SER87
|
4.8
|
42.7
|
1.0
|
C
|
2:LEU125
|
4.8
|
84.0
|
1.0
|
CB
|
1:PRO98
|
4.8
|
32.2
|
1.0
|
CA
|
2:SER127
|
4.9
|
79.2
|
1.0
|
SG
|
2:CYS88
|
4.9
|
22.5
|
1.0
|
|
Iron binding site 7 out
of 64 in 6q8w
Go back to
Iron Binding Sites List in 6q8w
Iron binding site 7 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Fe801
b:24.6
occ:1.00
|
FE1
|
3:SF4801
|
0.0
|
24.6
|
1.0
|
S2
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
S3
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
S4
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
SG
|
3:CYS128
|
2.3
|
35.4
|
1.0
|
FE3
|
3:SF4801
|
2.7
|
24.6
|
1.0
|
FE4
|
3:SF4801
|
2.7
|
24.6
|
1.0
|
FE2
|
3:SF4801
|
2.8
|
24.6
|
1.0
|
CB
|
3:CYS128
|
3.4
|
34.6
|
1.0
|
S1
|
3:SF4801
|
3.9
|
24.6
|
1.0
|
NE2
|
3:HIS115
|
4.5
|
28.1
|
1.0
|
SG
|
3:CYS122
|
4.8
|
40.4
|
1.0
|
CA
|
3:CYS128
|
4.8
|
39.9
|
1.0
|
CG
|
3:GLN131
|
4.8
|
28.5
|
1.0
|
CG1
|
3:VAL232
|
4.8
|
12.7
|
1.0
|
CB
|
3:LEU130
|
4.8
|
39.5
|
1.0
|
CA
|
3:VAL232
|
4.9
|
22.6
|
1.0
|
N
|
3:GLN131
|
4.9
|
33.6
|
1.0
|
SG
|
3:CYS119
|
4.9
|
44.0
|
1.0
|
O
|
3:PRO231
|
5.0
|
43.2
|
1.0
|
CB
|
3:LYS124
|
5.0
|
35.4
|
1.0
|
|
Iron binding site 8 out
of 64 in 6q8w
Go back to
Iron Binding Sites List in 6q8w
Iron binding site 8 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Fe801
b:24.6
occ:1.00
|
FE2
|
3:SF4801
|
0.0
|
24.6
|
1.0
|
S4
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
S1
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
SG
|
3:CYS119
|
2.3
|
44.0
|
1.0
|
S3
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
FE3
|
3:SF4801
|
2.7
|
24.6
|
1.0
|
FE4
|
3:SF4801
|
2.8
|
24.6
|
1.0
|
FE1
|
3:SF4801
|
2.8
|
24.6
|
1.0
|
CB
|
3:CYS119
|
3.3
|
44.2
|
1.0
|
CA
|
3:CYS119
|
3.4
|
47.2
|
1.0
|
N
|
3:CYS119
|
3.8
|
44.0
|
1.0
|
S2
|
3:SF4801
|
3.9
|
24.6
|
1.0
|
CD2
|
3:HIS115
|
4.5
|
36.7
|
1.0
|
NE2
|
3:HIS115
|
4.5
|
28.1
|
1.0
|
NE2
|
3:GLN131
|
4.7
|
28.8
|
1.0
|
C
|
3:ASP118
|
4.7
|
41.4
|
1.0
|
CG
|
3:GLN131
|
4.8
|
28.5
|
1.0
|
SG
|
3:CYS122
|
4.8
|
40.4
|
1.0
|
CB
|
3:CYS122
|
4.8
|
40.3
|
1.0
|
C
|
3:CYS119
|
4.8
|
49.3
|
1.0
|
SG
|
3:CYS128
|
4.9
|
35.4
|
1.0
|
|
Iron binding site 9 out
of 64 in 6q8w
Go back to
Iron Binding Sites List in 6q8w
Iron binding site 9 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Fe801
b:24.6
occ:1.00
|
FE3
|
3:SF4801
|
0.0
|
24.6
|
1.0
|
NE2
|
3:HIS115
|
2.1
|
28.1
|
1.0
|
S4
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
S1
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
S2
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
FE1
|
3:SF4801
|
2.7
|
24.6
|
1.0
|
CD2
|
3:HIS115
|
2.7
|
36.7
|
1.0
|
FE2
|
3:SF4801
|
2.7
|
24.6
|
1.0
|
FE4
|
3:SF4801
|
2.7
|
24.6
|
1.0
|
CE1
|
3:HIS115
|
3.3
|
27.9
|
1.0
|
S3
|
3:SF4801
|
3.8
|
24.6
|
1.0
|
CG
|
3:HIS115
|
3.9
|
39.3
|
1.0
|
ND1
|
3:HIS115
|
4.2
|
28.2
|
1.0
|
CG
|
3:ARG180
|
4.6
|
14.9
|
1.0
|
CG1
|
3:VAL232
|
4.7
|
12.7
|
1.0
|
SG
|
3:CYS119
|
4.7
|
44.0
|
1.0
|
SG
|
3:CYS128
|
4.8
|
35.4
|
1.0
|
CD
|
3:ARG180
|
4.8
|
15.3
|
1.0
|
SG
|
3:CYS122
|
4.9
|
40.4
|
1.0
|
CD2
|
3:LEU130
|
4.9
|
38.6
|
1.0
|
CB
|
3:VAL232
|
5.0
|
21.8
|
1.0
|
|
Iron binding site 10 out
of 64 in 6q8w
Go back to
Iron Binding Sites List in 6q8w
Iron binding site 10 out
of 64 in the Respiratory Complex I From Thermus Thermophilus with Bound Aureothin.
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Respiratory Complex I From Thermus Thermophilus with Bound Aureothin. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Fe801
b:24.6
occ:1.00
|
FE4
|
3:SF4801
|
0.0
|
24.6
|
1.0
|
S2
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
S3
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
SG
|
3:CYS122
|
2.3
|
40.4
|
1.0
|
S1
|
3:SF4801
|
2.3
|
24.6
|
1.0
|
FE1
|
3:SF4801
|
2.7
|
24.6
|
1.0
|
FE3
|
3:SF4801
|
2.7
|
24.6
|
1.0
|
FE2
|
3:SF4801
|
2.8
|
24.6
|
1.0
|
CB
|
3:CYS122
|
3.2
|
40.3
|
1.0
|
S4
|
3:SF4801
|
3.9
|
24.6
|
1.0
|
CD
|
3:ARG180
|
4.2
|
15.3
|
1.0
|
CA
|
3:CYS119
|
4.4
|
47.2
|
1.0
|
N
|
3:GLY233
|
4.5
|
24.6
|
1.0
|
CB
|
3:LYS124
|
4.5
|
35.4
|
1.0
|
NE2
|
3:HIS115
|
4.6
|
28.1
|
1.0
|
N
|
3:CYS119
|
4.6
|
44.0
|
1.0
|
NE
|
3:ARG180
|
4.6
|
17.7
|
1.0
|
CA
|
3:CYS122
|
4.7
|
39.0
|
1.0
|
SG
|
3:CYS128
|
4.8
|
35.4
|
1.0
|
C
|
3:ASP118
|
4.8
|
41.4
|
1.0
|
SG
|
3:CYS119
|
4.8
|
44.0
|
1.0
|
CG
|
3:ARG180
|
4.9
|
14.9
|
1.0
|
O
|
3:ASP118
|
4.9
|
36.0
|
1.0
|
CA
|
3:GLY233
|
4.9
|
12.2
|
1.0
|
|
Reference:
J.Gutierrez-Fernandez,
K.Kaszuba,
G.S.Minhas,
R.Baradaran,
M.Tambalo,
D.T.Gallagher,
L.A.Sazanov.
Key Role of Quinone in the Mechanism of Respiratory Complex I. Nat Commun V. 11 4135 2020.
ISSN: ESSN 2041-1723
PubMed: 32811817
DOI: 10.1038/S41467-020-17957-0
Page generated: Wed Aug 7 06:56:24 2024
|