Iron in PDB 6zkr: Native Complex I, OPEN3
Enzymatic activity of Native Complex I, OPEN3
All present enzymatic activity of Native Complex I, OPEN3:
1.6.99.3;
7.1.1.2;
Other elements in 6zkr:
The structure of Native Complex I, OPEN3 also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
28;
Binding sites:
The binding sites of Iron atom in the Native Complex I, OPEN3
(pdb code 6zkr). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 28 binding sites of Iron where determined in the
Native Complex I, OPEN3, PDB code: 6zkr:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 1 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Fe500
b:29.3
occ:1.00
|
FE1
|
1:SF4500
|
0.0
|
29.3
|
1.0
|
S3
|
1:SF4500
|
2.3
|
39.6
|
1.0
|
S2
|
1:SF4500
|
2.3
|
27.1
|
1.0
|
S4
|
1:SF4500
|
2.3
|
89.5
|
1.0
|
SG
|
1:CYS365
|
2.3
|
43.6
|
1.0
|
FE2
|
1:SF4500
|
2.7
|
44.9
|
1.0
|
FE3
|
1:SF4500
|
2.7
|
34.6
|
1.0
|
FE4
|
1:SF4500
|
2.8
|
39.4
|
1.0
|
CB
|
1:CYS365
|
2.9
|
27.5
|
1.0
|
OG
|
1:SER358
|
3.4
|
25.8
|
1.0
|
S1
|
1:SF4500
|
4.2
|
99.7
|
1.0
|
CA
|
1:CYS365
|
4.3
|
28.4
|
1.0
|
CD2
|
1:LEU407
|
4.4
|
46.8
|
1.0
|
N
|
1:CYS359
|
4.6
|
30.2
|
1.0
|
CB
|
1:SER358
|
4.6
|
32.0
|
1.0
|
CB
|
1:LEU407
|
4.7
|
29.2
|
1.0
|
C
|
1:CYS365
|
4.7
|
31.0
|
1.0
|
CA
|
1:SER358
|
4.8
|
35.3
|
1.0
|
N
|
1:GLY360
|
4.8
|
31.8
|
1.0
|
N
|
1:ARG366
|
4.8
|
29.8
|
1.0
|
SG
|
1:CYS362
|
4.9
|
64.3
|
1.0
|
|
Iron binding site 2 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 2 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Fe500
b:44.9
occ:1.00
|
FE2
|
1:SF4500
|
0.0
|
44.9
|
1.0
|
S3
|
1:SF4500
|
2.3
|
39.6
|
1.0
|
S1
|
1:SF4500
|
2.3
|
99.7
|
1.0
|
S4
|
1:SF4500
|
2.4
|
89.5
|
1.0
|
FE3
|
1:SF4500
|
2.5
|
34.6
|
1.0
|
FE4
|
1:SF4500
|
2.5
|
39.4
|
1.0
|
FE1
|
1:SF4500
|
2.7
|
29.3
|
1.0
|
SG
|
1:CYS362
|
3.0
|
64.3
|
1.0
|
N
|
1:CYS362
|
3.3
|
29.3
|
1.0
|
CB
|
1:CYS362
|
3.7
|
49.6
|
1.0
|
S2
|
1:SF4500
|
3.8
|
27.1
|
1.0
|
CA
|
1:CYS362
|
4.0
|
28.3
|
1.0
|
N
|
1:GLN361
|
4.2
|
31.2
|
1.0
|
CB
|
1:GLN361
|
4.2
|
29.9
|
1.0
|
CB
|
1:CYS365
|
4.2
|
27.5
|
1.0
|
O
|
1:CYS362
|
4.3
|
35.8
|
1.0
|
C
|
1:GLN361
|
4.3
|
28.5
|
1.0
|
CA
|
1:GLN361
|
4.4
|
48.3
|
1.0
|
CB
|
1:ILE404
|
4.6
|
34.4
|
1.0
|
CD1
|
1:ILE404
|
4.6
|
25.6
|
1.0
|
C
|
1:CYS362
|
4.6
|
24.1
|
1.0
|
SG
|
1:CYS365
|
4.6
|
43.6
|
1.0
|
CG1
|
1:ILE404
|
4.7
|
22.4
|
1.0
|
N
|
1:ILE404
|
4.7
|
34.1
|
1.0
|
SG
|
1:CYS359
|
4.8
|
42.9
|
1.0
|
|
Iron binding site 3 out
of 28 in 6zkr
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Iron Binding Sites List in 6zkr
Iron binding site 3 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Fe500
b:34.6
occ:1.00
|
FE3
|
1:SF4500
|
0.0
|
34.6
|
1.0
|
S4
|
1:SF4500
|
2.3
|
89.5
|
1.0
|
S1
|
1:SF4500
|
2.3
|
99.7
|
1.0
|
S2
|
1:SF4500
|
2.4
|
27.1
|
1.0
|
FE4
|
1:SF4500
|
2.4
|
39.4
|
1.0
|
FE2
|
1:SF4500
|
2.5
|
44.9
|
1.0
|
FE1
|
1:SF4500
|
2.7
|
29.3
|
1.0
|
SG
|
1:CYS359
|
2.9
|
42.9
|
1.0
|
S3
|
1:SF4500
|
3.7
|
39.6
|
1.0
|
CD
|
1:PRO203
|
3.9
|
27.2
|
1.0
|
CB
|
1:CYS359
|
3.9
|
35.3
|
1.0
|
N
|
1:CYS359
|
4.0
|
30.2
|
1.0
|
N
|
1:GLN361
|
4.2
|
31.2
|
1.0
|
CG
|
1:PRO203
|
4.2
|
32.0
|
1.0
|
N
|
1:GLY360
|
4.3
|
31.8
|
1.0
|
CB
|
1:GLN361
|
4.3
|
29.9
|
1.0
|
CA
|
1:CYS359
|
4.4
|
33.3
|
1.0
|
CG1
|
1:ILE185
|
4.6
|
30.5
|
1.0
|
C
|
1:CYS359
|
4.6
|
29.6
|
1.0
|
CD1
|
1:ILE185
|
4.7
|
32.5
|
1.0
|
SG
|
1:CYS405
|
4.7
|
37.4
|
1.0
|
CA
|
1:GLN361
|
4.8
|
48.3
|
1.0
|
N
|
1:CYS362
|
4.9
|
29.3
|
1.0
|
SG
|
1:CYS365
|
5.0
|
43.6
|
1.0
|
OG
|
1:SER358
|
5.0
|
25.8
|
1.0
|
|
Iron binding site 4 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 4 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Fe500
b:39.4
occ:1.00
|
FE4
|
1:SF4500
|
0.0
|
39.4
|
1.0
|
S2
|
1:SF4500
|
2.3
|
27.1
|
1.0
|
S1
|
1:SF4500
|
2.3
|
99.7
|
1.0
|
S3
|
1:SF4500
|
2.3
|
39.6
|
1.0
|
FE3
|
1:SF4500
|
2.4
|
34.6
|
1.0
|
FE2
|
1:SF4500
|
2.5
|
44.9
|
1.0
|
FE1
|
1:SF4500
|
2.8
|
29.3
|
1.0
|
SG
|
1:CYS405
|
3.0
|
37.4
|
1.0
|
N
|
1:CYS405
|
3.7
|
43.6
|
1.0
|
S4
|
1:SF4500
|
3.8
|
89.5
|
1.0
|
CB
|
1:CYS405
|
4.0
|
28.4
|
1.0
|
CG
|
1:PRO203
|
4.1
|
32.0
|
1.0
|
O
|
1:CYS405
|
4.2
|
35.4
|
1.0
|
CA
|
1:CYS405
|
4.2
|
30.4
|
1.0
|
C
|
1:CYS405
|
4.4
|
28.4
|
1.0
|
CB
|
1:ILE404
|
4.5
|
34.4
|
1.0
|
CD
|
1:PRO203
|
4.6
|
27.2
|
1.0
|
N
|
1:ILE404
|
4.7
|
34.1
|
1.0
|
C
|
1:ILE404
|
4.8
|
32.2
|
1.0
|
CB
|
1:LEU407
|
4.8
|
29.2
|
1.0
|
CB
|
1:PRO203
|
4.8
|
30.5
|
1.0
|
CD1
|
1:ILE185
|
4.8
|
32.5
|
1.0
|
SG
|
1:CYS362
|
4.9
|
64.3
|
1.0
|
CA
|
1:ILE404
|
4.9
|
32.4
|
1.0
|
SG
|
1:CYS365
|
4.9
|
43.6
|
1.0
|
|
Iron binding site 5 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 5 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Fe300
b:0.6
occ:1.00
|
FE1
|
2:FES300
|
0.0
|
0.6
|
1.0
|
S2
|
2:FES300
|
2.2
|
55.4
|
1.0
|
S1
|
2:FES300
|
2.2
|
82.8
|
1.0
|
SG
|
2:CYS103
|
2.3
|
98.4
|
1.0
|
SG
|
2:CYS108
|
2.3
|
50.1
|
1.0
|
FE2
|
2:FES300
|
3.0
|
53.4
|
1.0
|
CB
|
2:CYS103
|
3.4
|
72.5
|
1.0
|
CB
|
2:CYS108
|
3.5
|
40.0
|
1.0
|
OG1
|
2:THR105
|
3.6
|
57.4
|
1.0
|
N
|
2:CYS108
|
4.3
|
45.4
|
1.0
|
CA
|
2:CYS144
|
4.4
|
41.5
|
1.0
|
O
|
2:CYS103
|
4.4
|
45.5
|
1.0
|
N
|
2:LEU145
|
4.4
|
36.6
|
1.0
|
CA
|
2:CYS108
|
4.5
|
46.8
|
1.0
|
C
|
2:CYS103
|
4.5
|
40.2
|
1.0
|
CA
|
2:CYS103
|
4.6
|
45.1
|
1.0
|
SG
|
2:CYS144
|
4.7
|
65.5
|
1.0
|
N
|
2:THR105
|
4.7
|
41.5
|
1.0
|
SD
|
2:MET153
|
4.8
|
66.9
|
1.0
|
CG
|
2:MET153
|
4.8
|
62.5
|
1.0
|
CB
|
2:CYS144
|
4.9
|
45.9
|
1.0
|
CB
|
2:THR105
|
4.9
|
42.0
|
1.0
|
C
|
2:CYS144
|
4.9
|
38.8
|
1.0
|
|
Iron binding site 6 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 6 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Fe300
b:53.4
occ:1.00
|
FE2
|
2:FES300
|
0.0
|
53.4
|
1.0
|
S2
|
2:FES300
|
2.2
|
55.4
|
1.0
|
S1
|
2:FES300
|
2.2
|
82.8
|
1.0
|
SG
|
2:CYS148
|
2.3
|
89.5
|
1.0
|
SG
|
2:CYS144
|
2.3
|
65.5
|
1.0
|
FE1
|
2:FES300
|
3.0
|
0.6
|
1.0
|
CB
|
2:CYS144
|
3.4
|
45.9
|
1.0
|
CB
|
2:CYS148
|
3.6
|
66.0
|
1.0
|
CA
|
2:CYS148
|
3.8
|
49.8
|
1.0
|
CA
|
2:CYS144
|
3.8
|
41.5
|
1.0
|
N
|
2:GLY146
|
4.0
|
46.5
|
1.0
|
N
|
2:CYS148
|
4.0
|
52.2
|
1.0
|
N
|
2:LEU145
|
4.1
|
36.6
|
1.0
|
C
|
2:CYS144
|
4.2
|
38.8
|
1.0
|
N
|
2:ALA147
|
4.2
|
47.9
|
1.0
|
OG1
|
2:THR105
|
4.2
|
57.4
|
1.0
|
N
|
1:GLY103
|
4.4
|
39.1
|
1.0
|
CA
|
2:GLY146
|
4.5
|
53.4
|
1.0
|
CA
|
1:PRO102
|
4.5
|
43.0
|
1.0
|
SG
|
2:CYS103
|
4.5
|
98.4
|
1.0
|
C
|
2:ALA147
|
4.6
|
53.2
|
1.0
|
C
|
2:GLY146
|
4.7
|
45.6
|
1.0
|
C
|
2:LEU145
|
4.9
|
42.5
|
1.0
|
SG
|
2:CYS108
|
4.9
|
50.1
|
1.0
|
|
Iron binding site 7 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 7 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Fe801
b:82.8
occ:1.00
|
FE1
|
3:SF4801
|
0.0
|
82.8
|
1.0
|
S3
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
S2
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
S4
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
SG
|
3:CYS114
|
2.3
|
70.6
|
1.0
|
FE4
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
FE2
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
FE3
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
CB
|
3:CYS114
|
3.3
|
27.6
|
1.0
|
S1
|
3:SF4801
|
3.9
|
82.8
|
1.0
|
CG
|
3:GLN117
|
4.0
|
34.8
|
1.0
|
NE2
|
3:HIS101
|
4.1
|
54.0
|
1.0
|
NE2
|
3:GLN117
|
4.5
|
29.9
|
1.0
|
CB
|
3:LEU116
|
4.5
|
22.0
|
1.0
|
CD
|
3:GLN117
|
4.5
|
25.8
|
1.0
|
N
|
3:GLY206
|
4.6
|
20.0
|
1.0
|
N
|
3:GLN117
|
4.6
|
63.4
|
1.0
|
CA
|
3:CYS114
|
4.7
|
29.9
|
1.0
|
SG
|
3:CYS108
|
4.7
|
72.9
|
1.0
|
CA
|
3:VAL205
|
4.8
|
21.7
|
1.0
|
CD2
|
3:LEU116
|
4.8
|
40.6
|
1.0
|
SG
|
3:CYS105
|
4.8
|
60.6
|
1.0
|
CE1
|
3:HIS101
|
4.8
|
66.7
|
1.0
|
CB
|
3:VAL205
|
4.9
|
32.5
|
1.0
|
CB
|
3:GLN110
|
4.9
|
22.0
|
1.0
|
CB
|
3:GLN117
|
5.0
|
36.0
|
1.0
|
CG
|
3:GLN110
|
5.0
|
26.0
|
1.0
|
CG
|
3:LEU116
|
5.0
|
26.1
|
1.0
|
|
Iron binding site 8 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 8 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Fe801
b:82.8
occ:1.00
|
FE2
|
3:SF4801
|
0.0
|
82.8
|
1.0
|
S3
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
S1
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
S4
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
SG
|
3:CYS105
|
2.3
|
60.6
|
1.0
|
FE3
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
FE4
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
FE1
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
NE2
|
3:GLN117
|
3.4
|
29.9
|
1.0
|
CB
|
3:CYS105
|
3.4
|
16.6
|
1.0
|
CA
|
3:CYS105
|
3.6
|
12.1
|
1.0
|
N
|
3:CYS105
|
3.8
|
20.9
|
1.0
|
S2
|
3:SF4801
|
3.9
|
82.8
|
1.0
|
CE
|
4:MET342
|
4.0
|
42.6
|
1.0
|
CG
|
3:GLN117
|
4.1
|
34.8
|
1.0
|
CD
|
3:GLN117
|
4.2
|
25.8
|
1.0
|
NE2
|
3:HIS101
|
4.3
|
54.0
|
1.0
|
C
|
3:ASP104
|
4.7
|
23.2
|
1.0
|
CD2
|
3:HIS101
|
4.8
|
52.7
|
1.0
|
SG
|
3:CYS108
|
4.8
|
72.9
|
1.0
|
SG
|
3:CYS114
|
4.8
|
70.6
|
1.0
|
CB
|
3:CYS108
|
4.9
|
60.2
|
1.0
|
C
|
3:CYS105
|
5.0
|
22.7
|
1.0
|
CG1
|
4:ILE346
|
5.0
|
25.5
|
1.0
|
|
Iron binding site 9 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 9 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Fe801
b:82.8
occ:1.00
|
FE3
|
3:SF4801
|
0.0
|
82.8
|
1.0
|
NE2
|
3:HIS101
|
1.9
|
54.0
|
1.0
|
S1
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
S2
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
S4
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
FE2
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
FE1
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
FE4
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
CE1
|
3:HIS101
|
2.9
|
66.7
|
1.0
|
CD2
|
3:HIS101
|
3.0
|
52.7
|
1.0
|
S3
|
3:SF4801
|
3.9
|
82.8
|
1.0
|
ND1
|
3:HIS101
|
4.0
|
44.5
|
1.0
|
CG
|
3:HIS101
|
4.0
|
59.7
|
1.0
|
O
|
3:PRO102
|
4.4
|
23.7
|
1.0
|
CE
|
4:MET342
|
4.4
|
42.6
|
1.0
|
CD2
|
3:LEU116
|
4.6
|
40.6
|
1.0
|
CB
|
3:ARG152
|
4.7
|
43.5
|
1.0
|
CG
|
3:ARG152
|
4.7
|
53.6
|
1.0
|
SG
|
3:CYS105
|
4.7
|
60.6
|
1.0
|
SG
|
3:CYS114
|
4.8
|
70.6
|
1.0
|
SG
|
3:CYS108
|
4.8
|
72.9
|
1.0
|
CD
|
3:ARG152
|
4.9
|
68.8
|
1.0
|
N
|
3:GLY206
|
5.0
|
20.0
|
1.0
|
|
Iron binding site 10 out
of 28 in 6zkr
Go back to
Iron Binding Sites List in 6zkr
Iron binding site 10 out
of 28 in the Native Complex I, OPEN3
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Native Complex I, OPEN3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Fe801
b:82.8
occ:1.00
|
FE4
|
3:SF4801
|
0.0
|
82.8
|
1.0
|
S2
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
S3
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
S1
|
3:SF4801
|
2.3
|
82.8
|
1.0
|
SG
|
3:CYS108
|
2.3
|
72.9
|
1.0
|
FE2
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
FE1
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
FE3
|
3:SF4801
|
2.7
|
82.8
|
1.0
|
CB
|
3:CYS108
|
3.1
|
60.2
|
1.0
|
S4
|
3:SF4801
|
3.9
|
82.8
|
1.0
|
N
|
3:GLY206
|
4.2
|
20.0
|
1.0
|
CA
|
3:GLY206
|
4.4
|
20.1
|
1.0
|
CD
|
3:ARG152
|
4.4
|
68.8
|
1.0
|
CA
|
3:CYS105
|
4.5
|
12.1
|
1.0
|
CB
|
3:GLN110
|
4.5
|
22.0
|
1.0
|
CA
|
3:CYS108
|
4.6
|
27.1
|
1.0
|
NE2
|
3:HIS101
|
4.6
|
54.0
|
1.0
|
N
|
3:CYS105
|
4.7
|
20.9
|
1.0
|
SG
|
3:CYS114
|
4.7
|
70.6
|
1.0
|
N
|
3:GLY111
|
4.7
|
18.5
|
1.0
|
SG
|
3:CYS105
|
4.8
|
60.6
|
1.0
|
C
|
3:ASP104
|
4.9
|
23.2
|
1.0
|
NH1
|
3:ARG152
|
4.9
|
43.4
|
1.0
|
NE
|
3:ARG152
|
4.9
|
58.6
|
1.0
|
C
|
3:GLN110
|
5.0
|
22.4
|
1.0
|
|
Reference:
D.Kampjut,
L.A.Sazanov.
The Coupling Mechanism of Mammalian Respiratory Complex I. Science V. 370 2020.
ISSN: ESSN 1095-9203
PubMed: 32972993
DOI: 10.1126/SCIENCE.ABC4209
Page generated: Wed Aug 7 20:22:22 2024
|