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Iodine in PDB 5udy: Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)

Enzymatic activity of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)

All present enzymatic activity of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7):
3.1.4.12;

Protein crystallography data

The structure of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7), PDB code: 5udy was solved by A.Gorelik, F.Liu, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.20 / 2.60
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.246, 103.246, 113.554, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 20.7

Other elements in 5udy:

The structure of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Sodium (Na) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Iodine atom in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) (pdb code 5udy). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 25 binding sites of Iodine where determined in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7), PDB code: 5udy:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 25 in 5udy

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Iodine binding site 1 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I512

b:38.4
occ:0.71
HG1 A:THR68 2.9 39.4 1.0
HB A:THR68 3.4 33.0 1.0
OG1 A:THR68 3.5 32.8 1.0
HA A:PHE382 3.5 30.5 1.0
HB2 A:PRO381 3.5 35.3 1.0
HG3 A:GLU383 3.6 37.4 1.0
O A:HOH720 3.7 41.1 1.0
CB A:THR68 3.9 27.5 1.0
C A:PHE382 3.9 28.6 1.0
CA A:PHE382 4.0 25.4 1.0
N A:PHE382 4.1 26.1 1.0
N A:GLU383 4.1 29.6 1.0
H A:GLU383 4.2 35.6 1.0
HG2 A:GLU383 4.2 37.4 1.0
C A:PRO381 4.2 29.5 1.0
HG21 A:THR68 4.2 31.1 1.0
HE1 A:TYR66 4.3 35.1 1.0
O A:PRO381 4.3 31.9 1.0
CG A:GLU383 4.3 31.2 1.0
CB A:PRO381 4.3 29.4 1.0
O A:PHE382 4.3 29.7 1.0
H A:PHE382 4.4 31.3 1.0
HB3 A:PRO381 4.4 35.3 1.0
O A:HOH710 4.6 15.7 1.0
H A:THR68 4.6 34.5 1.0
HA A:GLU383 4.6 33.8 1.0
CG2 A:THR68 4.7 25.9 1.0
O A:HOH759 4.7 24.1 1.0
HZ2 A:LYS363 4.8 34.3 1.0
CA A:GLU383 4.9 28.2 1.0
CA A:PRO381 4.9 29.3 1.0

Iodine binding site 2 out of 25 in 5udy

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Iodine binding site 2 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I513

b:45.7
occ:0.74
HD21 A:ASN165 2.9 50.4 1.0
HA A:ASN168 3.2 68.0 1.0
HG3 A:LYS167 3.3 60.6 1.0
HE3 A:LYS167 3.6 73.8 1.0
H81 A:NAG509 3.6 77.2 1.0
ND2 A:ASN165 3.7 42.0 1.0
HB2 A:ASN168 3.8 75.4 1.0
CA A:ASN168 4.0 56.6 1.0
H83 A:NAG509 4.0 77.2 1.0
O A:LYS167 4.0 54.9 1.0
HD22 A:ASN165 4.1 50.4 1.0
O A:HOH703 4.1 34.5 1.0
O A:HOH650 4.1 45.7 1.0
C8 A:NAG509 4.2 64.3 1.0
CG A:LYS167 4.2 50.5 1.0
CB A:ASN168 4.2 62.8 1.0
C A:LYS167 4.3 52.5 1.0
N A:ASN168 4.3 55.5 1.0
CE A:LYS167 4.5 61.5 1.0
C7 A:NAG509 4.5 62.7 1.0
HG2 A:LYS167 4.5 60.6 1.0
CG A:ASN168 4.6 68.0 1.0
O7 A:NAG509 4.6 63.0 1.0
CG A:ASN165 4.6 42.3 1.0
OD1 A:ASN165 4.6 43.2 1.0
HE2 A:LYS167 4.7 73.8 1.0
CD A:LYS167 4.8 54.7 1.0
HD2 A:LYS167 4.8 65.6 1.0
H A:GLU169 4.8 56.8 1.0
H A:ASN168 4.8 66.6 1.0
ND2 A:ASN168 4.9 72.2 1.0
HD21 A:ASN168 4.9 86.6 1.0
OD1 A:ASN168 5.0 69.1 1.0

Iodine binding site 3 out of 25 in 5udy

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Iodine binding site 3 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I514

b:53.9
occ:0.69
H A:GLU276 3.1 58.5 1.0
HA A:PHE275 3.2 61.4 1.0
HE2 A:LYS106 3.4 51.8 1.0
HG2 A:GLU276 3.5 64.0 1.0
HB3 A:LYS104 3.5 78.0 1.0
HD2 A:PHE275 3.6 55.0 1.0
HG3 A:GLU276 3.7 64.0 1.0
HD2 A:LYS104 3.8 86.4 1.0
N A:GLU276 3.8 48.8 1.0
CD2 A:PHE275 4.0 45.9 1.0
CG A:GLU276 4.0 53.3 1.0
CA A:PHE275 4.1 51.1 1.0
O A:GLU276 4.2 47.2 1.0
CE A:LYS106 4.3 43.1 1.0
HE2 A:LYS104 4.3 90.1 1.0
HA A:LYS104 4.4 76.7 1.0
HE3 A:LYS106 4.4 51.8 1.0
CB A:LYS104 4.4 65.0 1.0
O A:GLU274 4.4 57.7 1.0
CE2 A:PHE275 4.5 43.6 1.0
C A:PHE275 4.5 48.6 1.0
CG A:PHE275 4.5 47.4 1.0
O A:LYS104 4.5 58.4 1.0
HE2 A:PHE275 4.5 52.3 1.0
CD A:LYS104 4.6 72.0 1.0
HZ1 A:LYS106 4.7 52.7 1.0
CB A:PHE275 4.7 49.9 1.0
HB2 A:PHE275 4.7 59.9 1.0
CA A:GLU276 4.8 49.9 1.0
HG3 A:LYS104 4.8 82.4 1.0
CE A:LYS104 4.8 75.1 1.0
HG3 A:LYS106 4.8 50.5 1.0
CA A:LYS104 4.9 63.9 1.0
CG A:LYS104 4.9 68.7 1.0
C A:GLU276 4.9 48.1 1.0
HE3 A:LYS104 4.9 90.1 1.0
NZ A:LYS106 5.0 43.9 1.0
CB A:GLU276 5.0 51.7 1.0

Iodine binding site 4 out of 25 in 5udy

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Iodine binding site 4 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I515

b:76.0
occ:0.53
HZ3 A:LYS167 3.0 74.3 1.0
O A:HOH669 3.1 38.4 1.0
HD3 A:ARG204 3.2 51.6 1.0
HD3 A:LYS167 3.4 65.6 1.0
HE2 A:TYR205 3.5 42.9 1.0
HH11 A:ARG204 3.7 61.5 1.0
HD2 A:ARG204 3.8 51.6 1.0
NZ A:LYS167 3.8 61.9 1.0
HA A:THR201 3.9 38.1 1.0
CD A:ARG204 3.9 43.0 1.0
HE2 A:LYS167 3.9 73.8 1.0
HG A:SER200 4.0 42.6 1.0
O A:HOH724 4.0 39.5 1.0
HZ1 A:LYS167 4.2 74.3 1.0
CE A:LYS167 4.2 61.5 1.0
CD A:LYS167 4.2 54.7 1.0
HH A:TYR205 4.2 47.6 1.0
CE2 A:TYR205 4.3 35.7 1.0
HB3 A:ARG204 4.3 44.4 1.0
HZ2 A:LYS167 4.3 74.3 1.0
OG1 A:THR201 4.3 34.6 1.0
HG1 A:THR201 4.4 41.5 1.0
NH1 A:ARG204 4.4 51.2 1.0
HB2 A:ARG204 4.4 44.4 1.0
OG A:SER200 4.7 35.5 1.0
CA A:THR201 4.7 31.8 1.0
HB3 A:SER200 4.7 41.7 1.0
OE2 A:GLU197 4.7 29.8 1.0
CB A:ARG204 4.7 37.0 1.0
HD2 A:LYS167 4.8 65.6 1.0
NE A:ARG204 4.8 48.3 1.0
HH12 A:ARG204 4.8 61.5 1.0
O A:SER200 4.9 30.3 1.0
N A:THR201 4.9 31.8 1.0
OH A:TYR205 4.9 39.7 1.0
CG A:ARG204 4.9 39.5 1.0
HG23 A:THR201 4.9 41.2 1.0
HD2 A:TYR205 5.0 39.9 1.0
HG2 A:LYS167 5.0 60.6 1.0
C A:SER200 5.0 31.0 1.0
CZ A:ARG204 5.0 51.3 1.0

Iodine binding site 5 out of 25 in 5udy

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Iodine binding site 5 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I516

b:78.7
occ:0.69
HG A:SER103 2.5 82.9 1.0
HH A:TYR98 3.0 65.0 1.0
HG21 A:VAL105 3.0 66.1 1.0
OG A:SER103 3.3 69.1 1.0
HH21 A:ARG117 3.5 66.1 1.0
HE2 A:TYR98 3.7 62.1 1.0
HD21 A:ASN100 3.7 0.9 1.0
OH A:TYR98 3.8 54.1 1.0
CG2 A:VAL105 3.8 55.1 1.0
HG23 A:VAL105 3.8 66.1 1.0
HB A:VAL105 3.8 65.0 1.0
HB3 A:SER103 4.0 83.2 1.0
CB A:SER103 4.0 69.4 1.0
HB2 A:SER103 4.1 83.2 1.0
HB3 A:ASN100 4.1 95.6 1.0
ND2 A:ASN100 4.1 94.9 1.0
HG11 A:VAL105 4.2 64.8 1.0
NH2 A:ARG117 4.2 55.1 1.0
O A:HOH751 4.3 38.4 1.0
O5 A:NAG503 4.3 75.1 1.0
CB A:VAL105 4.3 54.1 1.0
CE2 A:TYR98 4.4 51.8 1.0
HH22 A:ARG117 4.4 66.1 1.0
HB2 A:ASN100 4.4 95.6 1.0
HG22 A:VAL105 4.5 66.1 1.0
CZ A:TYR98 4.5 52.6 1.0
CB A:ASN100 4.6 79.7 1.0
CG A:ASN100 4.6 90.0 1.0
O A:HOH726 4.7 50.8 1.0
CG1 A:VAL105 4.8 54.0 1.0
C1 A:NAG503 4.8 76.5 1.0
HE A:ARG117 4.9 71.1 1.0

Iodine binding site 6 out of 25 in 5udy

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Iodine binding site 6 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I517

b:81.3
occ:0.53
H A:ASN267 2.8 87.8 1.0
HD2 A:PRO266 2.8 90.7 1.0
HB3 A:PHE265 3.0 80.8 1.0
O A:ALA299 3.3 83.5 1.0
HB2 A:ASN267 3.4 86.3 1.0
N A:ASN267 3.6 73.2 1.0
CD A:PRO266 3.6 75.6 1.0
HB2 A:ALA303 3.7 68.8 1.0
N A:PRO266 3.7 76.3 1.0
HA A:PHE265 3.8 83.9 1.0
HA A:ALA303 3.8 72.8 1.0
CB A:PHE265 3.8 67.4 1.0
C A:PHE265 3.9 74.6 1.0
HB1 A:ALA299 4.0 93.6 1.0
HB1 A:ALA303 4.0 68.8 1.0
CA A:PHE265 4.1 69.9 1.0
HD3 A:PRO266 4.1 90.7 1.0
CB A:ALA303 4.2 57.4 1.0
CB A:ASN267 4.2 71.9 1.0
CA A:ASN267 4.3 71.8 1.0
C A:ALA299 4.3 80.6 1.0
H A:PHE268 4.3 84.6 1.0
HA A:ALA299 4.4 95.1 1.0
HB2 A:PHE268 4.4 82.5 1.0
HB2 A:PRO266 4.4 92.5 1.0
CA A:ALA303 4.5 60.7 1.0
N A:PHE268 4.5 70.5 1.0
C A:ASN267 4.5 71.1 1.0
C A:PRO266 4.5 76.2 1.0
CG A:PHE265 4.5 64.5 1.0
HB3 A:PHE268 4.5 82.5 1.0
HB2 A:PHE265 4.5 80.8 1.0
CA A:PRO266 4.6 76.8 1.0
O A:PHE265 4.6 74.7 1.0
CA A:ALA299 4.7 79.3 1.0
HD1 A:PHE265 4.7 76.9 1.0
CG A:PRO266 4.7 75.7 1.0
CB A:ALA299 4.8 78.0 1.0
HD23 A:LEU300 4.8 81.1 1.0
CB A:PRO266 4.8 77.1 1.0
HB3 A:ASN267 4.9 86.3 1.0
HG2 A:PRO266 4.9 90.9 1.0
HA A:LEU300 4.9 88.0 1.0
ND2 A:ASN267 4.9 74.2 1.0
CB A:PHE268 4.9 68.8 1.0
CD1 A:PHE265 4.9 64.1 1.0

Iodine binding site 7 out of 25 in 5udy

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Iodine binding site 7 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I518

b:58.7
occ:0.49
HZ1 A:LYS312 3.2 68.2 1.0
OD1 A:ASN323 3.3 70.9 1.0
HA A:PRO325 3.5 49.7 1.0
HE2 A:LYS312 3.5 65.9 1.0
C A:ASN324 3.5 42.4 1.0
N A:PRO325 3.6 41.9 1.0
HD3 A:PRO325 3.6 49.2 1.0
HG3 A:PRO325 3.7 49.1 1.0
HA A:ASN324 3.7 50.9 1.0
N A:ASN324 3.8 44.8 1.0
O A:ASN324 3.8 43.7 1.0
NZ A:LYS312 3.8 56.8 1.0
HA A:ASN323 3.9 61.9 1.0
HZ3 A:LYS312 3.9 68.2 1.0
CA A:ASN324 3.9 42.4 1.0
H A:ASN324 4.0 53.8 1.0
C A:ASN323 4.0 48.8 1.0
CA A:PRO325 4.0 41.4 1.0
CD A:PRO325 4.0 41.0 1.0
CE A:LYS312 4.1 55.0 1.0
CG A:ASN323 4.1 66.2 1.0
CG A:PRO325 4.3 40.9 1.0
HE3 A:LYS312 4.3 65.9 1.0
CA A:ASN323 4.4 51.6 1.0
O A:ASN323 4.4 50.1 1.0
HZ2 A:LYS312 4.6 68.2 1.0
CB A:PRO325 4.7 41.3 1.0
HD21 A:ASN323 4.7 83.0 1.0
ND2 A:ASN323 4.8 69.2 1.0
HB3 A:PRO325 4.8 49.6 1.0
CB A:ASN323 4.9 58.7 1.0
HD2 A:PRO325 5.0 49.2 1.0

Iodine binding site 8 out of 25 in 5udy

Go back to Iodine Binding Sites List in 5udy
Iodine binding site 8 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I519

b:56.1
occ:0.43
H A:THR148 2.8 44.7 1.0
HA A:VAL147 3.1 43.8 1.0
HE21 A:GLN116 3.1 0.9 1.0
HB2 A:GLN116 3.2 85.6 1.0
HB A:VAL147 3.5 43.7 1.0
O A:HOH633 3.6 46.9 1.0
OG1 A:THR148 3.6 45.2 1.0
N A:THR148 3.6 37.3 1.0
HG23 A:THR148 3.6 46.3 1.0
HG12 A:VAL147 3.7 43.5 1.0
NE2 A:GLN116 3.7 87.5 1.0
HG1 A:THR148 3.8 54.3 1.0
CA A:VAL147 3.8 36.5 1.0
HG3 A:GLN116 3.8 95.0 1.0
H83 A:NAG506 3.9 52.2 1.0
CB A:VAL147 4.0 36.4 1.0
CB A:GLN116 4.1 71.3 1.0
HE22 A:GLN116 4.1 0.9 1.0
C A:VAL147 4.2 35.4 1.0
CG A:GLN116 4.3 79.2 1.0
CG2 A:THR148 4.3 38.5 1.0
CG1 A:VAL147 4.3 36.3 1.0
CD A:GLN116 4.4 84.8 1.0
CB A:THR148 4.4 40.9 1.0
C8 A:NAG506 4.5 43.5 1.0
H81 A:NAG506 4.5 52.2 1.0
H82 A:NAG506 4.6 52.2 1.0
HB3 A:GLN116 4.6 85.6 1.0
HG21 A:THR148 4.6 46.3 1.0
CA A:THR148 4.6 39.4 1.0
O A:ASN146 4.7 41.9 1.0
HG11 A:VAL147 4.8 43.5 1.0
HA A:GLN116 5.0 74.3 1.0

Iodine binding site 9 out of 25 in 5udy

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Iodine binding site 9 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I520

b:70.5
occ:0.53
HZ3 A:LYS104 2.6 92.3 1.0
HG3 A:LYS104 3.3 82.4 1.0
NZ A:LYS104 3.4 77.0 1.0
HG2 A:LYS104 3.5 82.4 1.0
HZ1 A:LYS104 3.7 92.3 1.0
HZ2 A:LYS104 3.8 92.3 1.0
CG A:LYS104 3.8 68.7 1.0
I A:IOD525 4.1 77.4 0.5
CE A:LYS104 4.4 75.1 1.0
HE2 A:LYS104 4.4 90.1 1.0
CD A:LYS104 4.7 72.0 1.0
O A:THR102 4.7 68.6 1.0
HB2 A:LYS104 4.9 78.0 1.0
HD3 A:LYS104 4.9 86.4 1.0

Iodine binding site 10 out of 25 in 5udy

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Iodine binding site 10 out of 25 in the Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Human Alkaline Sphingomyelinase (Alk-Smase, ENPP7, NPP7) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I521

b:51.8
occ:0.33
HD13 A:LEU413 3.2 39.7 1.0
HB3 A:SER372 3.2 51.5 1.0
HD23 A:LEU394 3.4 34.3 1.0
O A:HOH735 3.6 32.5 1.0
HG3 A:ARG393 3.6 40.1 1.0
HA A:LEU394 3.7 40.6 1.0
CB A:SER372 4.0 42.9 1.0
HG A:SER372 4.1 53.9 1.0
OG A:SER372 4.1 44.9 1.0
CD1 A:LEU413 4.1 33.0 1.0
O A:ARG393 4.1 34.4 1.0
HD2 A:ARG393 4.2 39.6 1.0
HB3 A:LEU413 4.3 44.9 1.0
CD2 A:LEU394 4.3 28.6 1.0
HB2 A:SER372 4.4 51.5 1.0
CG A:ARG393 4.4 33.4 1.0
HD22 A:LEU413 4.5 41.6 1.0
HD12 A:LEU413 4.5 39.7 1.0
HD3 A:ARG393 4.5 39.6 1.0
HD11 A:LEU413 4.5 39.7 1.0
HD21 A:LEU394 4.6 34.3 1.0
CD A:ARG393 4.6 33.0 1.0
CA A:LEU394 4.6 33.8 1.0
HD22 A:LEU394 4.8 34.3 1.0
C A:ARG393 4.8 35.0 1.0
HG2 A:ARG393 4.8 40.1 1.0

Reference:

A.Gorelik, F.Liu, K.Illes, B.Nagar. Crystal Structure of the Human Alkaline Sphingomyelinase Provides Insights Into Substrate Recognition. J. Biol. Chem. V. 292 7087 2017.
ISSN: ESSN 1083-351X
PubMed: 28292932
DOI: 10.1074/JBC.M116.769273
Page generated: Sun Dec 13 19:41:20 2020

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