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Iodine in PDB 5u84: Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved

Enzymatic activity of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved

All present enzymatic activity of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved:
3.5.1.23;

Protein crystallography data

The structure of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved, PDB code: 5u84 was solved by A.Gebai, A.Gorelik, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.66 / 2.34
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.815, 109.267, 79.541, 90.00, 102.97, 90.00
R / Rfree (%) 20 / 23.1

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 67;

Binding sites:

The binding sites of Iodine atom in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved (pdb code 5u84). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 67 binding sites of Iodine where determined in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved, PDB code: 5u84:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 67 in 5u84

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Iodine binding site 1 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:56.3
occ:0.55
I3 A:I3C406 0.0 56.3 0.6
C6 A:I3C406 2.1 52.7 0.6
C5 A:I3C406 3.0 49.6 0.6
C1 A:I3C406 3.1 37.6 0.6
N13 A:I3C406 3.2 42.3 0.6
HN13 A:I3C406 3.2 50.7 0.6
C7 A:I3C406 3.3 29.5 0.6
H3 B:NAG403 3.4 71.2 1.0
O9 A:I3C406 3.4 31.1 0.6
HN1A A:I3C406 3.6 50.7 0.6
HO3 B:NAG403 3.8 84.6 1.0
O3 B:NAG403 4.0 70.5 1.0
O8 A:I3C406 4.0 29.4 0.6
C3 B:NAG403 4.1 59.3 1.0
C4 A:I3C406 4.3 56.7 0.6
C2 A:I3C406 4.4 43.8 0.6
HN2 B:NAG403 4.5 65.4 1.0
O4 B:NAG403 4.5 71.5 1.0
C3 A:I3C406 4.9 47.7 0.6
C4 B:NAG403 5.0 64.7 1.0

Iodine binding site 2 out of 67 in 5u84

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Iodine binding site 2 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:58.0
occ:0.55
I2 A:I3C406 0.0 58.0 0.6
C4 A:I3C406 2.1 56.7 0.6
C5 A:I3C406 3.0 49.6 0.6
C3 A:I3C406 3.0 47.7 0.6
N13 A:I3C406 3.2 42.3 0.6
C10 A:I3C406 3.2 37.1 0.6
HN1A A:I3C406 3.3 50.7 0.6
HN13 A:I3C406 3.6 50.7 0.6
O12 A:I3C406 3.7 37.6 0.6
O11 A:I3C406 3.7 40.1 0.6
C6 A:I3C406 4.3 52.7 0.6
C2 A:I3C406 4.4 43.8 0.6
H5 B:NAG403 4.7 59.7 1.0
O4 B:NAG403 4.8 71.5 1.0
O6 B:NAG403 4.9 64.4 1.0
C1 A:I3C406 4.9 37.6 0.6
H62 B:NAG403 4.9 66.8 1.0

Iodine binding site 3 out of 67 in 5u84

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Iodine binding site 3 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:40.1
occ:0.55
I1 A:I3C406 0.0 40.1 0.6
C2 A:I3C406 2.1 43.8 0.6
HO3 B:NAG401 3.0 55.7 1.0
C1 A:I3C406 3.0 37.6 0.6
C3 A:I3C406 3.1 47.7 0.6
H3 B:FUC402 3.1 55.8 1.0
O B:HOH529 3.2 26.4 1.0
C7 A:I3C406 3.2 29.5 0.6
C10 A:I3C406 3.3 37.1 0.6
O8 A:I3C406 3.3 29.4 0.6
H1 B:NAG403 3.6 59.4 1.0
H4 B:NAG401 3.7 44.5 1.0
O11 A:I3C406 3.7 40.1 0.6
O12 A:I3C406 3.7 37.6 0.6
O3 B:NAG401 3.8 46.4 1.0
HO3 B:FUC402 3.8 49.5 1.0
O9 A:I3C406 4.0 31.1 0.6
H2 B:NAG401 4.1 48.6 1.0
C3 B:FUC402 4.1 46.5 1.0
H5 B:NAG403 4.2 59.7 1.0
H4 B:FUC402 4.2 44.7 1.0
O3 B:FUC402 4.3 41.2 1.0
C6 A:I3C406 4.4 52.7 0.6
C4 A:I3C406 4.4 56.7 0.6
O7 B:NAG401 4.4 33.2 1.0
HO2 B:FUC402 4.5 57.5 1.0
C4 B:NAG401 4.5 37.1 1.0
C1 B:NAG403 4.5 49.5 1.0
H5 B:FUC402 4.6 49.1 1.0
C3 B:NAG401 4.6 44.2 1.0
C4 B:FUC402 4.7 37.3 1.0
C2 B:NAG401 4.8 40.5 1.0
C5 A:I3C406 4.9 49.6 0.6
H3 B:NAG403 4.9 71.2 1.0
O5 B:NAG403 4.9 54.9 1.0
C5 B:NAG403 5.0 49.8 1.0
O6 B:NAG401 5.0 38.9 1.0

Iodine binding site 4 out of 67 in 5u84

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Iodine binding site 4 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:56.9
occ:0.28
I3 A:I3C407 0.0 56.9 0.3
I1 A:I3C407 1.0 27.6 0.3
C2 A:I3C407 1.6 44.0 0.3
C6 A:I3C407 2.1 48.9 0.3
C3 A:I3C407 2.2 43.1 0.3
C10 A:I3C407 2.3 43.7 0.3
O12 A:I3C407 2.5 51.5 0.3
HN13 A:I3C407 2.8 61.4 0.3
C1 A:I3C407 2.9 39.3 0.3
C5 A:I3C407 3.0 49.1 0.3
O11 A:I3C407 3.1 42.0 0.3
HE3 A:LYS378 3.1 0.7 1.0
C1 A:I3C407 3.1 46.9 0.3
HG2 A:GLN380 3.2 77.7 1.0
N13 A:I3C407 3.2 51.1 0.3
C7 A:I3C407 3.3 38.7 0.3
C7 A:I3C407 3.5 36.9 0.3
C4 A:I3C407 3.5 44.7 0.3
CD2 A:PHE351 3.6 28.7 1.0
CE2 A:PHE351 3.7 30.0 1.0
O9 A:I3C407 3.7 32.9 0.3
HZ1 A:LYS378 3.8 0.6 1.0
CG A:PHE351 3.8 26.5 1.0
O8 A:I3C407 3.9 40.4 0.3
CZ A:PHE351 3.9 23.6 1.0
O9 A:I3C407 3.9 32.2 0.3
CE A:LYS378 3.9 93.9 1.0
HN1A A:I3C407 3.9 61.4 0.3
HD2 A:PHE351 3.9 34.5 1.0
HE2 A:PHE351 4.0 36.0 1.0
C6 A:I3C407 4.0 40.2 0.3
CD1 A:PHE351 4.0 27.1 1.0
HE21 A:GLN380 4.0 68.1 1.0
CE1 A:PHE351 4.0 27.9 1.0
CG A:GLN380 4.1 64.7 1.0
HB2 A:PHE351 4.1 36.8 1.0
HB2 A:GLN380 4.1 51.3 1.0
HB3 A:GLN380 4.1 51.3 1.0
NZ A:LYS378 4.2 92.1 1.0
HZ2 A:LYS378 4.2 0.6 1.0
O8 A:I3C407 4.2 41.4 0.3
HE2 A:LYS378 4.2 0.7 1.0
HB2 A:ASP375 4.2 50.2 1.0
C5 A:I3C407 4.3 43.9 0.3
HZ A:PHE351 4.3 28.3 1.0
C4 A:I3C407 4.3 52.4 0.3
CB A:GLN380 4.4 42.7 1.0
C2 A:I3C407 4.4 49.5 0.3
HD1 A:PHE351 4.5 32.5 1.0
HG3 A:GLN380 4.6 77.7 1.0
HE1 A:PHE351 4.6 33.5 1.0
CB A:PHE351 4.6 30.7 1.0
HB3 A:ASP375 4.6 50.2 1.0
OD2 A:ASP375 4.7 57.1 1.0
NE2 A:GLN380 4.8 56.8 1.0
CB A:ASP375 4.8 41.9 1.0
HD2 A:LYS378 4.9 79.5 1.0
C3 A:I3C407 4.9 53.6 0.3

Iodine binding site 5 out of 67 in 5u84

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Iodine binding site 5 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:46.3
occ:0.31
I3 A:I3C407 0.0 46.3 0.3
C6 A:I3C407 2.1 40.2 0.3
O8 A:I3C407 2.2 40.4 0.3
HN13 A:I3C407 2.8 55.1 0.3
C1 A:I3C407 3.0 39.3 0.3
C5 A:I3C407 3.0 43.9 0.3
N13 A:I3C407 3.2 45.9 0.3
H A:ALA352 3.3 39.1 1.0
C7 A:I3C407 3.3 38.7 0.3
C7 A:I3C407 3.3 36.9 0.3
HB2 A:SER350 3.3 38.0 1.0
HB2 A:ALA352 3.5 32.2 1.0
HB2 A:PHE351 3.5 36.8 1.0
O8 A:I3C407 3.6 41.4 0.3
HG A:SER350 3.6 36.8 1.0
H A:PHE351 3.8 35.2 1.0
I1 A:I3C407 3.8 37.6 0.3
O9 A:I3C407 3.9 32.2 0.3
HB3 A:ALA352 3.9 32.2 1.0
OG A:SER350 3.9 30.7 1.0
O9 A:I3C407 4.0 32.9 0.3
N A:ALA352 4.0 32.6 1.0
CB A:SER350 4.1 31.7 1.0
HN1A A:I3C407 4.1 55.1 0.3
CB A:ALA352 4.1 26.9 1.0
C1 A:I3C407 4.2 46.9 0.3
N A:PHE351 4.3 29.3 1.0
C2 A:I3C407 4.3 44.0 0.3
C4 A:I3C407 4.3 44.7 0.3
CB A:PHE351 4.4 30.7 1.0
C2 A:I3C407 4.5 49.5 0.3
HB3 A:PHE351 4.5 36.8 1.0
I A:IOD415 4.5 0.9 0.6
HE2 A:TYR36 4.5 41.0 1.0
HB3 A:SER350 4.6 38.0 1.0
HD2 A:TYR36 4.7 42.2 1.0
CA A:ALA352 4.7 31.1 1.0
CA A:PHE351 4.8 26.9 1.0
C A:PHE351 4.9 29.0 1.0
C3 A:I3C407 4.9 43.1 0.3
CE2 A:TYR36 5.0 34.2 1.0
HB1 A:ALA352 5.0 32.2 1.0

Iodine binding site 6 out of 67 in 5u84

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Iodine binding site 6 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:85.6
occ:0.41
I3 A:I3C407 0.0 85.6 0.4
C6 A:I3C407 2.1 63.4 0.4
HG21 A:THR377 2.8 54.3 1.0
HN13 A:I3C407 2.9 67.3 0.4
C5 A:I3C407 3.0 55.3 0.4
C1 A:I3C407 3.0 68.2 0.4
HB A:THR377 3.1 49.5 1.0
HG3 A:LYS378 3.1 66.2 1.0
ND1 A:HIS154 3.1 77.2 1.0
N13 A:I3C407 3.2 56.1 0.4
O8 A:I3C407 3.2 54.8 0.4
HG22 A:THR377 3.2 54.3 1.0
C7 A:I3C407 3.3 67.3 0.4
CG2 A:THR377 3.4 45.2 1.0
CE1 A:HIS154 3.4 64.5 1.0
CG A:HIS154 3.6 66.4 1.0
HG2 A:LYS378 3.6 66.2 1.0
HE1 A:HIS154 3.6 77.4 1.0
CB A:THR377 3.7 41.2 1.0
CG A:LYS378 3.8 55.1 1.0
HB3 A:HIS154 3.8 74.3 1.0
HN1A A:I3C407 3.9 67.3 0.4
NE2 A:HIS154 3.9 70.2 1.0
HD3 A:LYS378 4.0 79.5 1.0
HZ3 A:LYS378 4.0 0.6 1.0
CD2 A:HIS154 4.1 61.0 1.0
HG1 A:THR377 4.1 50.2 1.0
O9 A:I3C407 4.1 72.4 0.4
CB A:HIS154 4.2 61.9 1.0
HG23 A:THR377 4.3 54.3 1.0
C4 A:I3C407 4.3 65.0 0.4
C2 A:I3C407 4.4 65.5 0.4
CD A:LYS378 4.4 66.2 1.0
HB2 A:HIS154 4.4 74.3 1.0
OG1 A:THR377 4.4 41.9 1.0
HE2 A:HIS154 4.5 84.2 1.0
H A:LYS378 4.6 50.6 1.0
HD2 A:HIS154 4.7 73.1 1.0
N A:LYS378 4.7 42.1 1.0
OE2 A:GLU152 4.7 95.9 1.0
NZ A:LYS378 4.7 92.1 1.0
OD1 A:ASP375 4.8 50.1 1.0
HE2 A:LYS378 4.9 0.7 1.0
C3 A:I3C407 4.9 61.1 0.4
C A:THR377 4.9 38.0 1.0
CA A:THR377 4.9 43.2 1.0
CE A:LYS378 4.9 93.9 1.0

Iodine binding site 7 out of 67 in 5u84

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Iodine binding site 7 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:47.6
occ:0.28
I2 A:I3C407 0.0 47.6 0.3
O12 A:I3C407 0.8 55.1 0.4
C10 A:I3C407 2.0 56.1 0.4
C4 A:I3C407 2.1 52.4 0.3
HN1A A:I3C407 2.8 61.4 0.3
C3 A:I3C407 2.8 61.1 0.4
O11 A:I3C407 3.0 55.4 0.4
C5 A:I3C407 3.0 49.1 0.3
C3 A:I3C407 3.1 53.6 0.3
N13 A:I3C407 3.2 51.1 0.3
O12 A:I3C407 3.2 47.5 0.3
C10 A:I3C407 3.2 48.5 0.3
I2 A:I3C407 3.3 72.4 0.4
C4 A:I3C407 3.3 65.0 0.4
HD2 A:LYS378 3.6 79.5 1.0
HD3 A:LYS378 3.7 79.5 1.0
C2 A:I3C407 3.9 65.5 0.4
HN13 A:I3C407 3.9 61.4 0.3
CD A:LYS378 4.1 66.2 1.0
O11 A:I3C407 4.1 45.8 0.3
C6 A:I3C407 4.3 48.9 0.3
C2 A:I3C407 4.4 49.5 0.3
HZ2 A:LYS378 4.4 0.6 1.0
C5 A:I3C407 4.5 55.3 0.4
HE3 A:LYS378 4.6 0.7 1.0
I1 A:I3C407 4.6 83.1 0.4
CE A:LYS378 4.8 93.9 1.0
C1 A:I3C407 4.9 46.9 0.3
C1 A:I3C407 5.0 68.2 0.4

Iodine binding site 8 out of 67 in 5u84

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Iodine binding site 8 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:64.5
occ:0.31
I2 A:I3C407 0.0 64.5 0.3
C4 A:I3C407 2.1 44.7 0.3
HN1A A:I3C407 2.8 55.1 0.3
C3 A:I3C407 3.0 43.1 0.3
C5 A:I3C407 3.1 43.9 0.3
C10 A:I3C407 3.1 43.7 0.3
O11 A:I3C407 3.2 42.0 0.3
N13 A:I3C407 3.3 45.9 0.3
I1 A:I3C408 3.5 42.4 0.4
OH A:TYR36 3.8 42.3 1.0
HE2 A:TYR36 3.8 41.0 1.0
OE2 A:GLU382 3.8 49.8 1.0
O12 A:I3C407 3.9 51.5 0.3
HN13 A:I3C407 4.1 55.1 0.3
HE21 A:GLN380 4.1 68.1 1.0
C2 A:I3C407 4.3 44.0 0.3
HH A:TYR36 4.4 50.7 1.0
C6 A:I3C407 4.4 40.2 0.3
CE2 A:TYR36 4.6 34.2 1.0
HD2 A:PHE351 4.7 34.5 1.0
CZ A:TYR36 4.7 41.5 1.0
NE2 A:GLN380 4.7 56.8 1.0
HE22 A:GLN380 4.7 68.1 1.0
C1 A:I3C407 4.9 39.3 0.3
CD A:GLU382 4.9 53.7 1.0
O12 A:I3C408 5.0 35.0 0.4

Iodine binding site 9 out of 67 in 5u84

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Iodine binding site 9 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:72.4
occ:0.41
I2 A:I3C407 0.0 72.4 0.4
C4 A:I3C407 2.1 65.0 0.4
HN1A A:I3C407 2.9 67.3 0.4
C5 A:I3C407 3.0 55.3 0.4
C3 A:I3C407 3.0 61.1 0.4
N13 A:I3C407 3.2 56.1 0.4
C10 A:I3C407 3.2 56.1 0.4
I2 A:I3C407 3.3 47.6 0.3
O12 A:I3C407 3.4 55.1 0.4
HN13 A:I3C407 3.9 67.3 0.4
O11 A:I3C407 4.0 55.4 0.4
HD3 A:LYS378 4.0 79.5 1.0
HD2 A:LYS378 4.3 79.5 1.0
HG2 A:LYS378 4.3 66.2 1.0
C6 A:I3C407 4.3 63.4 0.4
C2 A:I3C407 4.4 65.5 0.4
CD A:LYS378 4.6 66.2 1.0
HN1A A:I3C407 4.8 61.4 0.3
C1 A:I3C407 4.9 68.2 0.4
CG A:LYS378 5.0 55.1 1.0

Iodine binding site 10 out of 67 in 5u84

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Iodine binding site 10 out of 67 in the Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Acid Ceramidase (ASAH1, Acdase) From Common Minke Whale, CYS143ALA, Uncleaved within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I407

b:37.6
occ:0.28
I1 A:I3C407 0.0 37.6 0.3
C2 A:I3C407 2.1 49.5 0.3
O8 A:I3C407 2.2 41.4 0.3
C1 A:I3C407 3.0 46.9 0.3
C3 A:I3C407 3.1 53.6 0.3
C7 A:I3C407 3.1 38.7 0.3
C7 A:I3C407 3.3 36.9 0.3
O11 A:I3C407 3.3 45.8 0.3
C10 A:I3C407 3.4 48.5 0.3
O8 A:I3C407 3.5 40.4 0.3
O9 A:I3C407 3.6 32.9 0.3
I1 A:I3C407 3.8 83.1 0.4
HB2 A:SER350 3.8 38.0 1.0
I3 A:I3C407 3.8 46.3 0.3
C1 A:I3C407 4.0 39.3 0.3
O12 A:I3C407 4.2 47.5 0.3
C6 A:I3C407 4.2 40.2 0.3
O9 A:I3C407 4.3 32.2 0.3
C6 A:I3C407 4.3 48.9 0.3
C4 A:I3C407 4.4 52.4 0.3
HB3 A:SER350 4.4 38.0 1.0
CB A:SER350 4.6 31.7 1.0
C5 A:I3C407 4.9 49.1 0.3

Reference:

A.Gebai, A.Gorelik, Z.Li, K.Illes, B.Nagar. Structural Basis For the Activation of Acid Ceramidase. Nat Commun V. 9 1621 2018.
ISSN: ESSN 2041-1723
PubMed: 29692406
DOI: 10.1038/S41467-018-03844-2
Page generated: Sun Dec 13 19:41:20 2020

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