Iodine in PDB 5tcd: Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
Enzymatic activity of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
All present enzymatic activity of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine:
3.1.4.12;
Protein crystallography data
The structure of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine, PDB code: 5tcd
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)
|
38.44 /
2.40
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.223,
104.223,
113.893,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.3 /
20.8
|
Other elements in 5tcd:
The structure of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine also contains other interesting chemical elements:
Iodine Binding Sites:
Iodine binding site 1 out
of 37 in 5tcd
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Iodine Binding Sites List in 5tcd
Iodine binding site 1 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_01.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 1 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I515
b:30.1
occ:0.62
|
HG1
|
A:THR68
|
2.9
|
33.4
|
1.0
|
HB2
|
A:PRO381
|
3.4
|
33.7
|
1.0
|
HA
|
A:PHE382
|
3.4
|
34.4
|
1.0
|
OG1
|
A:THR68
|
3.4
|
27.9
|
1.0
|
HB
|
A:THR68
|
3.5
|
28.2
|
1.0
|
O
|
A:HOH746
|
3.7
|
37.1
|
1.0
|
HG3
|
A:GLU383
|
3.7
|
41.0
|
1.0
|
CA
|
A:PHE382
|
3.9
|
28.6
|
1.0
|
N
|
A:PHE382
|
4.0
|
27.6
|
1.0
|
C
|
A:PHE382
|
4.0
|
27.1
|
1.0
|
CB
|
A:THR68
|
4.0
|
23.5
|
1.0
|
HG2
|
A:GLU383
|
4.0
|
41.0
|
1.0
|
C
|
A:PRO381
|
4.1
|
27.6
|
1.0
|
O
|
A:PRO381
|
4.2
|
27.9
|
1.0
|
CB
|
A:PRO381
|
4.2
|
28.1
|
1.0
|
N
|
A:GLU383
|
4.2
|
30.7
|
1.0
|
H
|
A:PHE382
|
4.3
|
33.1
|
1.0
|
CG
|
A:GLU383
|
4.3
|
34.2
|
1.0
|
HE1
|
A:TYR66
|
4.3
|
31.1
|
1.0
|
H
|
A:GLU383
|
4.3
|
36.9
|
1.0
|
HG21
|
A:THR68
|
4.3
|
28.4
|
1.0
|
HB3
|
A:PRO381
|
4.3
|
33.7
|
1.0
|
O
|
A:PHE382
|
4.4
|
25.6
|
1.0
|
H
|
A:THR68
|
4.6
|
26.1
|
1.0
|
HZ2
|
A:LYS363
|
4.6
|
32.7
|
1.0
|
HA
|
A:GLU383
|
4.7
|
36.2
|
1.0
|
O
|
A:HOH766
|
4.7
|
19.4
|
1.0
|
CG2
|
A:THR68
|
4.8
|
23.7
|
1.0
|
CA
|
A:PRO381
|
4.8
|
28.0
|
1.0
|
CA
|
A:GLU383
|
5.0
|
30.2
|
1.0
|
|
Iodine binding site 2 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 2 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_02.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 2 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I516
b:48.1
occ:0.83
|
HD21
|
A:ASN165
|
2.8
|
43.8
|
1.0
|
HA
|
A:ASN168
|
3.1
|
38.7
|
1.0
|
HZ2
|
A:LYS167
|
3.2
|
51.5
|
1.0
|
HG3
|
A:LYS167
|
3.5
|
39.9
|
1.0
|
H81
|
A:NAG511
|
3.5
|
76.5
|
1.0
|
ND2
|
A:ASN165
|
3.6
|
36.5
|
1.0
|
HB2
|
A:ASN168
|
3.6
|
39.5
|
1.0
|
HZ3
|
A:LYS167
|
3.8
|
51.5
|
1.0
|
O
|
A:HOH718
|
3.8
|
25.7
|
1.0
|
O
|
A:LYS167
|
3.8
|
35.1
|
1.0
|
H83
|
A:NAG511
|
3.8
|
76.5
|
1.0
|
NZ
|
A:LYS167
|
3.9
|
42.9
|
1.0
|
CA
|
A:ASN168
|
3.9
|
32.3
|
1.0
|
HD22
|
A:ASN165
|
4.0
|
43.8
|
1.0
|
O
|
A:HOH650
|
4.1
|
31.6
|
1.0
|
C8
|
A:NAG511
|
4.1
|
63.7
|
1.0
|
CB
|
A:ASN168
|
4.2
|
32.9
|
1.0
|
C
|
A:LYS167
|
4.2
|
34.2
|
1.0
|
N
|
A:ASN168
|
4.2
|
33.2
|
1.0
|
HZ1
|
A:LYS167
|
4.3
|
51.5
|
1.0
|
CG
|
A:LYS167
|
4.5
|
33.2
|
1.0
|
C7
|
A:NAG511
|
4.5
|
64.4
|
1.0
|
CG
|
A:ASN165
|
4.6
|
36.3
|
1.0
|
CG
|
A:ASN168
|
4.6
|
34.9
|
1.0
|
OD1
|
A:ASN165
|
4.6
|
37.5
|
1.0
|
O7
|
A:NAG511
|
4.6
|
64.2
|
1.0
|
H
|
A:GLU169
|
4.7
|
49.0
|
1.0
|
O
|
A:HOH803
|
4.8
|
51.7
|
1.0
|
H
|
A:ASN168
|
4.8
|
39.9
|
1.0
|
HG2
|
A:LYS167
|
4.9
|
39.9
|
1.0
|
HD2
|
A:LYS167
|
4.9
|
43.6
|
1.0
|
H82
|
A:NAG511
|
5.0
|
76.5
|
1.0
|
HD21
|
A:ASN168
|
5.0
|
45.6
|
1.0
|
ND2
|
A:ASN168
|
5.0
|
38.0
|
1.0
|
|
Iodine binding site 3 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 3 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_03.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 3 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I517
b:42.2
occ:0.68
|
H
|
A:GLU276
|
3.0
|
58.9
|
1.0
|
HA
|
A:PHE275
|
3.2
|
47.5
|
1.0
|
HE2
|
A:LYS106
|
3.4
|
49.9
|
1.0
|
HD2
|
A:LYS104
|
3.5
|
57.3
|
1.0
|
HD2
|
A:PHE275
|
3.5
|
45.3
|
1.0
|
HB3
|
A:LYS104
|
3.6
|
56.9
|
1.0
|
HG3
|
A:GLU276
|
3.6
|
59.0
|
1.0
|
HG2
|
A:GLU276
|
3.7
|
59.0
|
1.0
|
N
|
A:GLU276
|
3.8
|
49.1
|
1.0
|
CD2
|
A:PHE275
|
3.9
|
37.7
|
1.0
|
CA
|
A:PHE275
|
4.1
|
39.6
|
1.0
|
O
|
A:GLU276
|
4.1
|
49.2
|
1.0
|
CG
|
A:GLU276
|
4.1
|
49.1
|
1.0
|
HZ3
|
A:LYS106
|
4.2
|
48.7
|
1.0
|
CE
|
A:LYS106
|
4.3
|
41.6
|
1.0
|
HZ1
|
A:LYS106
|
4.3
|
48.7
|
1.0
|
CD
|
A:LYS104
|
4.3
|
47.7
|
1.0
|
HD3
|
A:LYS104
|
4.3
|
57.3
|
1.0
|
CE2
|
A:PHE275
|
4.4
|
36.1
|
1.0
|
HE2
|
A:PHE275
|
4.4
|
43.3
|
1.0
|
CG
|
A:PHE275
|
4.5
|
37.6
|
1.0
|
C
|
A:PHE275
|
4.5
|
37.4
|
1.0
|
NZ
|
A:LYS106
|
4.5
|
40.6
|
1.0
|
HA
|
A:LYS104
|
4.5
|
54.7
|
1.0
|
CB
|
A:LYS104
|
4.5
|
47.5
|
1.0
|
O
|
A:GLU274
|
4.6
|
55.4
|
1.0
|
HB2
|
A:PHE275
|
4.6
|
47.6
|
1.0
|
CB
|
A:PHE275
|
4.6
|
39.7
|
1.0
|
CA
|
A:GLU276
|
4.8
|
48.5
|
1.0
|
O
|
A:LYS104
|
4.8
|
44.6
|
1.0
|
HD3
|
A:LYS106
|
4.8
|
50.5
|
1.0
|
CG
|
A:LYS104
|
4.8
|
48.1
|
1.0
|
HE3
|
A:LYS106
|
4.9
|
49.9
|
1.0
|
C
|
A:GLU276
|
4.9
|
48.7
|
1.0
|
HG3
|
A:LYS104
|
4.9
|
57.7
|
1.0
|
CA
|
A:LYS104
|
5.0
|
45.6
|
1.0
|
|
Iodine binding site 4 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 4 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_04.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 4 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I518
b:76.0
occ:0.53
|
HD3
|
A:ARG204
|
3.1
|
43.7
|
1.0
|
HH11
|
A:ARG204
|
3.5
|
52.5
|
1.0
|
HE2
|
A:LYS167
|
3.5
|
48.1
|
1.0
|
HE3
|
A:LYS167
|
3.6
|
48.1
|
1.0
|
HE2
|
A:TYR205
|
3.7
|
38.2
|
1.0
|
HD3
|
A:LYS167
|
3.7
|
43.6
|
1.0
|
HD2
|
A:ARG204
|
3.8
|
43.7
|
1.0
|
HA
|
A:THR201
|
3.8
|
33.8
|
1.0
|
CD
|
A:ARG204
|
3.9
|
36.5
|
1.0
|
CE
|
A:LYS167
|
4.0
|
40.1
|
1.0
|
HB3
|
A:SER200
|
4.0
|
39.3
|
1.0
|
HB3
|
A:ARG204
|
4.0
|
41.5
|
1.0
|
HB2
|
A:ARG204
|
4.2
|
41.5
|
1.0
|
NH1
|
A:ARG204
|
4.2
|
43.7
|
1.0
|
CD
|
A:LYS167
|
4.3
|
36.3
|
1.0
|
HG1
|
A:THR201
|
4.4
|
36.4
|
1.0
|
OG1
|
A:THR201
|
4.5
|
30.3
|
1.0
|
CE2
|
A:TYR205
|
4.5
|
31.8
|
1.0
|
CB
|
A:ARG204
|
4.5
|
34.6
|
1.0
|
O
|
A:SER200
|
4.5
|
30.1
|
1.0
|
O
|
A:HOH737
|
4.6
|
30.3
|
1.0
|
CA
|
A:THR201
|
4.6
|
28.2
|
1.0
|
O
|
A:HOH637
|
4.6
|
35.1
|
1.0
|
C
|
A:SER200
|
4.7
|
30.7
|
1.0
|
OE2
|
A:GLU197
|
4.7
|
33.3
|
1.0
|
HH12
|
A:ARG204
|
4.7
|
52.5
|
1.0
|
N
|
A:THR201
|
4.7
|
29.2
|
1.0
|
HH
|
A:TYR205
|
4.7
|
44.6
|
1.0
|
CG
|
A:ARG204
|
4.7
|
34.4
|
1.0
|
I
|
A:IOD539
|
4.8
|
0.2
|
0.6
|
HB2
|
A:SER200
|
4.8
|
39.3
|
1.0
|
CB
|
A:SER200
|
4.8
|
32.7
|
1.0
|
HD2
|
A:TYR205
|
4.8
|
38.8
|
1.0
|
NE
|
A:ARG204
|
4.9
|
42.6
|
1.0
|
HD2
|
A:LYS167
|
5.0
|
43.6
|
1.0
|
CZ
|
A:ARG204
|
5.0
|
44.9
|
1.0
|
|
Iodine binding site 5 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 5 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_05.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 5 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I519
b:66.4
occ:0.57
|
HG
|
A:SER103
|
2.6
|
52.3
|
1.0
|
HH
|
A:TYR98
|
2.8
|
50.7
|
1.0
|
HG21
|
A:VAL105
|
3.0
|
52.6
|
1.0
|
HH21
|
A:ARG117
|
3.3
|
51.2
|
1.0
|
HD21
|
A:ASN100
|
3.4
|
61.4
|
1.0
|
OG
|
A:SER103
|
3.4
|
43.6
|
1.0
|
HB
|
A:VAL105
|
3.6
|
52.9
|
1.0
|
HE2
|
A:TYR98
|
3.6
|
44.5
|
1.0
|
OH
|
A:TYR98
|
3.6
|
42.3
|
1.0
|
CG2
|
A:VAL105
|
3.7
|
43.9
|
1.0
|
HG23
|
A:VAL105
|
3.8
|
52.6
|
1.0
|
ND2
|
A:ASN100
|
3.9
|
51.1
|
1.0
|
HG11
|
A:VAL105
|
3.9
|
53.2
|
1.0
|
HB3
|
A:ASN100
|
4.0
|
53.5
|
1.0
|
NH2
|
A:ARG117
|
4.0
|
42.7
|
1.0
|
HB2
|
A:SER103
|
4.1
|
54.4
|
1.0
|
HB3
|
A:SER103
|
4.1
|
54.4
|
1.0
|
CB
|
A:VAL105
|
4.1
|
44.1
|
1.0
|
CB
|
A:SER103
|
4.1
|
45.4
|
1.0
|
H2
|
A:NAG503
|
4.1
|
75.7
|
1.0
|
HH22
|
A:ARG117
|
4.1
|
51.2
|
1.0
|
O7
|
A:NAG503
|
4.2
|
71.6
|
1.0
|
CE2
|
A:TYR98
|
4.3
|
37.0
|
1.0
|
HB2
|
A:ASN100
|
4.3
|
53.5
|
1.0
|
O
|
A:HOH617
|
4.4
|
47.2
|
1.0
|
CZ
|
A:TYR98
|
4.5
|
38.8
|
1.0
|
CB
|
A:ASN100
|
4.5
|
44.6
|
1.0
|
O5
|
A:NAG503
|
4.5
|
57.1
|
1.0
|
HG22
|
A:VAL105
|
4.5
|
52.6
|
1.0
|
CG1
|
A:VAL105
|
4.5
|
44.3
|
1.0
|
CG
|
A:ASN100
|
4.6
|
46.1
|
1.0
|
C1
|
A:NAG503
|
4.7
|
49.2
|
1.0
|
C2
|
A:NAG503
|
4.9
|
63.1
|
1.0
|
HE
|
A:ARG117
|
4.9
|
52.0
|
1.0
|
|
Iodine binding site 6 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 6 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_06.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 6 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I520
b:71.5
occ:0.58
|
H
|
A:ASN267
|
2.8
|
79.6
|
1.0
|
HD2
|
A:PRO266
|
2.9
|
75.2
|
1.0
|
HB2
|
A:ASN267
|
3.0
|
86.5
|
1.0
|
HB3
|
A:PHE265
|
3.0
|
65.0
|
1.0
|
O
|
A:ALA299
|
3.4
|
79.0
|
1.0
|
N
|
A:ASN267
|
3.6
|
66.3
|
1.0
|
HB2
|
A:ALA303
|
3.7
|
53.0
|
1.0
|
CD
|
A:PRO266
|
3.8
|
62.6
|
1.0
|
HA
|
A:ALA303
|
3.8
|
55.0
|
1.0
|
HB1
|
A:ALA299
|
3.9
|
87.6
|
1.0
|
N
|
A:PRO266
|
3.9
|
63.5
|
1.0
|
HA
|
A:PHE265
|
3.9
|
67.4
|
1.0
|
CB
|
A:PHE265
|
3.9
|
54.1
|
1.0
|
CB
|
A:ASN267
|
3.9
|
72.1
|
1.0
|
H81
|
A:NAG513
|
3.9
|
0.1
|
1.0
|
HB1
|
A:ALA303
|
4.0
|
53.0
|
1.0
|
O
|
A:HOH607
|
4.0
|
47.4
|
1.0
|
HD21
|
A:ASN267
|
4.0
|
96.7
|
1.0
|
H83
|
A:NAG513
|
4.0
|
0.1
|
1.0
|
H
|
A:PHE268
|
4.0
|
61.0
|
1.0
|
C
|
A:PHE265
|
4.1
|
59.7
|
1.0
|
CB
|
A:ALA303
|
4.2
|
44.2
|
1.0
|
CA
|
A:PHE265
|
4.2
|
56.2
|
1.0
|
CA
|
A:ASN267
|
4.2
|
68.8
|
1.0
|
HD3
|
A:PRO266
|
4.3
|
75.2
|
1.0
|
C8
|
A:NAG513
|
4.3
|
85.1
|
1.0
|
C
|
A:ALA299
|
4.4
|
75.5
|
1.0
|
O7
|
A:NAG513
|
4.4
|
85.2
|
1.0
|
N
|
A:PHE268
|
4.4
|
50.9
|
1.0
|
HA
|
A:ALA299
|
4.4
|
91.9
|
1.0
|
HB2
|
A:PRO266
|
4.4
|
79.2
|
1.0
|
CA
|
A:ALA303
|
4.5
|
45.8
|
1.0
|
C7
|
A:NAG513
|
4.5
|
84.9
|
1.0
|
HB3
|
A:ASN267
|
4.5
|
86.5
|
1.0
|
C
|
A:PRO266
|
4.5
|
67.3
|
1.0
|
HB2
|
A:PHE265
|
4.6
|
65.0
|
1.0
|
CG
|
A:PHE265
|
4.6
|
51.1
|
1.0
|
ND2
|
A:ASN267
|
4.6
|
80.6
|
1.0
|
HB2
|
A:PHE268
|
4.6
|
54.7
|
1.0
|
C
|
A:ASN267
|
4.6
|
66.8
|
1.0
|
CA
|
A:PRO266
|
4.7
|
66.2
|
1.0
|
CB
|
A:ALA299
|
4.7
|
73.0
|
1.0
|
CG
|
A:ASN267
|
4.7
|
77.6
|
1.0
|
O
|
A:PHE265
|
4.8
|
58.3
|
1.0
|
CA
|
A:ALA299
|
4.8
|
76.6
|
1.0
|
CG
|
A:PRO266
|
4.8
|
65.8
|
1.0
|
HG2
|
A:PRO266
|
4.8
|
79.0
|
1.0
|
CB
|
A:PRO266
|
4.9
|
66.0
|
1.0
|
HB3
|
A:PHE268
|
4.9
|
54.7
|
1.0
|
HD1
|
A:PHE265
|
5.0
|
60.7
|
1.0
|
HD23
|
A:LEU300
|
5.0
|
61.1
|
1.0
|
HA
|
A:LEU300
|
5.0
|
61.4
|
1.0
|
|
Iodine binding site 7 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 7 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_07.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 7 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I521
b:58.8
occ:0.48
|
HZ1
|
A:LYS312
|
3.0
|
57.3
|
1.0
|
HE2
|
A:LYS312
|
3.3
|
53.6
|
1.0
|
OD1
|
A:ASN323
|
3.5
|
58.5
|
1.0
|
C
|
A:ASN324
|
3.5
|
34.9
|
1.0
|
HA
|
A:PRO325
|
3.5
|
42.8
|
1.0
|
N
|
A:ASN324
|
3.6
|
35.8
|
1.0
|
N
|
A:PRO325
|
3.6
|
34.4
|
1.0
|
H
|
A:ASN324
|
3.7
|
42.9
|
1.0
|
NZ
|
A:LYS312
|
3.7
|
47.7
|
1.0
|
HD3
|
A:PRO325
|
3.7
|
41.6
|
1.0
|
HA
|
A:ASN324
|
3.7
|
41.1
|
1.0
|
HZ3
|
A:LYS312
|
3.8
|
57.3
|
1.0
|
O
|
A:ASN324
|
3.8
|
35.5
|
1.0
|
HA
|
A:ASN323
|
3.8
|
61.8
|
1.0
|
O
|
A:HOH786
|
3.8
|
41.8
|
1.0
|
HG3
|
A:PRO325
|
3.8
|
44.0
|
1.0
|
CA
|
A:ASN324
|
3.8
|
34.2
|
1.0
|
CE
|
A:LYS312
|
3.9
|
44.7
|
1.0
|
C
|
A:ASN323
|
4.0
|
50.4
|
1.0
|
CD
|
A:PRO325
|
4.1
|
34.7
|
1.0
|
CA
|
A:PRO325
|
4.1
|
35.6
|
1.0
|
HE3
|
A:LYS312
|
4.1
|
53.6
|
1.0
|
CG
|
A:ASN323
|
4.3
|
58.1
|
1.0
|
CA
|
A:ASN323
|
4.4
|
51.5
|
1.0
|
CG
|
A:PRO325
|
4.4
|
36.7
|
1.0
|
HZ2
|
A:LYS312
|
4.5
|
57.3
|
1.0
|
O
|
A:ASN323
|
4.5
|
50.8
|
1.0
|
CB
|
A:PRO325
|
4.8
|
36.7
|
1.0
|
HB3
|
A:PRO325
|
4.9
|
44.1
|
1.0
|
HD2
|
A:PRO325
|
5.0
|
41.6
|
1.0
|
CB
|
A:ASN323
|
5.0
|
53.5
|
1.0
|
|
Iodine binding site 8 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 8 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_08.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 8 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I522
b:50.7
occ:0.45
|
H
|
A:THR148
|
2.9
|
45.8
|
1.0
|
HG1
|
A:THR148
|
2.9
|
48.9
|
1.0
|
HA
|
A:VAL147
|
3.1
|
36.3
|
1.0
|
HB2
|
A:GLN116
|
3.2
|
62.4
|
1.0
|
HG3
|
A:GLN116
|
3.5
|
65.2
|
1.0
|
HG12
|
A:VAL147
|
3.5
|
35.2
|
1.0
|
HG23
|
A:THR148
|
3.6
|
45.9
|
1.0
|
O
|
A:HOH616
|
3.6
|
49.3
|
1.0
|
N
|
A:THR148
|
3.7
|
38.2
|
1.0
|
HB
|
A:VAL147
|
3.7
|
36.6
|
1.0
|
OG1
|
A:THR148
|
3.8
|
40.8
|
1.0
|
H83
|
A:NAG508
|
3.8
|
45.3
|
1.0
|
CA
|
A:VAL147
|
3.9
|
30.2
|
1.0
|
OE1
|
A:GLN116
|
4.1
|
60.3
|
1.0
|
CB
|
A:GLN116
|
4.1
|
52.0
|
1.0
|
CB
|
A:VAL147
|
4.1
|
30.5
|
1.0
|
CG
|
A:GLN116
|
4.1
|
54.3
|
1.0
|
CG1
|
A:VAL147
|
4.2
|
29.3
|
1.0
|
C
|
A:VAL147
|
4.3
|
29.2
|
1.0
|
CG2
|
A:THR148
|
4.3
|
38.2
|
1.0
|
C8
|
A:NAG508
|
4.4
|
37.8
|
1.0
|
H81
|
A:NAG508
|
4.4
|
45.3
|
1.0
|
CB
|
A:THR148
|
4.5
|
38.4
|
1.0
|
H82
|
A:NAG508
|
4.5
|
45.3
|
1.0
|
CD
|
A:GLN116
|
4.6
|
56.7
|
1.0
|
HG21
|
A:THR148
|
4.6
|
45.9
|
1.0
|
HB3
|
A:GLN116
|
4.6
|
62.4
|
1.0
|
O
|
A:ASN146
|
4.6
|
29.8
|
1.0
|
CA
|
A:THR148
|
4.7
|
36.7
|
1.0
|
HG11
|
A:VAL147
|
4.8
|
35.2
|
1.0
|
HA
|
A:GLN116
|
4.9
|
59.4
|
1.0
|
HG13
|
A:VAL147
|
4.9
|
35.2
|
1.0
|
HG2
|
A:GLN116
|
5.0
|
65.2
|
1.0
|
|
Iodine binding site 9 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 9 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_09.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_09_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 9 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I523
b:65.7
occ:0.45
|
HZ2
|
A:LYS104
|
2.8
|
63.7
|
1.0
|
HG3
|
A:LYS104
|
3.5
|
57.7
|
1.0
|
HG2
|
A:LYS104
|
3.6
|
57.7
|
1.0
|
NZ
|
A:LYS104
|
3.6
|
53.1
|
1.0
|
HZ1
|
A:LYS104
|
3.7
|
63.7
|
1.0
|
HE3
|
A:LYS104
|
3.8
|
58.8
|
1.0
|
CG
|
A:LYS104
|
3.9
|
48.1
|
1.0
|
I
|
A:IOD529
|
4.1
|
93.9
|
0.5
|
CE
|
A:LYS104
|
4.2
|
49.0
|
1.0
|
HZ3
|
A:LYS104
|
4.2
|
63.7
|
1.0
|
O
|
A:THR102
|
4.6
|
48.0
|
1.0
|
CD
|
A:LYS104
|
4.7
|
47.7
|
1.0
|
|
Iodine binding site 10 out
of 37 in 5tcd
Go back to
Iodine Binding Sites List in 5tcd
Iodine binding site 10 out
of 37 in the Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine
![](/pictures/I/pdb/tc/5tcd-I-sphere_10.jpg) Mono view
![](/pictures/I/pdb/tc/5tcd-I-sphere_10_stereo.jpg) Stereo pair view
|
A full contact list of Iodine with other atoms in the I binding
site number 10 of Human Alkaline Sphingomyelinase (ENPP7) in Complex with Phosphocholine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:I524
b:67.8
occ:0.38
|
HD13
|
A:LEU413
|
3.0
|
38.8
|
1.0
|
HB3
|
A:SER372
|
3.2
|
40.7
|
1.0
|
HD23
|
A:LEU394
|
3.4
|
36.2
|
1.0
|
HG3
|
A:ARG393
|
3.7
|
37.6
|
1.0
|
HG
|
A:SER372
|
3.7
|
46.0
|
1.0
|
HA
|
A:LEU394
|
3.8
|
36.3
|
1.0
|
O
|
A:HOH731
|
3.9
|
39.0
|
1.0
|
CD1
|
A:LEU413
|
4.0
|
32.3
|
1.0
|
OG
|
A:SER372
|
4.0
|
38.3
|
1.0
|
CB
|
A:SER372
|
4.1
|
33.9
|
1.0
|
HB3
|
A:LEU413
|
4.2
|
42.8
|
1.0
|
HD2
|
A:ARG393
|
4.2
|
38.2
|
1.0
|
HD12
|
A:LEU413
|
4.2
|
38.8
|
1.0
|
CD2
|
A:LEU394
|
4.3
|
30.2
|
1.0
|
O
|
A:ARG393
|
4.4
|
34.4
|
1.0
|
HD11
|
A:LEU413
|
4.4
|
38.8
|
1.0
|
HD22
|
A:LEU413
|
4.5
|
41.5
|
1.0
|
CG
|
A:ARG393
|
4.5
|
31.3
|
1.0
|
HD21
|
A:LEU394
|
4.6
|
36.2
|
1.0
|
HB2
|
A:SER372
|
4.6
|
40.7
|
1.0
|
HD3
|
A:ARG393
|
4.7
|
38.2
|
1.0
|
HD22
|
A:LEU394
|
4.7
|
36.2
|
1.0
|
CD
|
A:ARG393
|
4.7
|
31.8
|
1.0
|
CA
|
A:LEU394
|
4.7
|
30.3
|
1.0
|
HA
|
A:SER372
|
4.8
|
43.2
|
1.0
|
HG2
|
A:ARG393
|
4.9
|
37.6
|
1.0
|
CG
|
A:LEU413
|
4.9
|
33.1
|
1.0
|
C
|
A:ARG393
|
4.9
|
33.6
|
1.0
|
CB
|
A:LEU413
|
4.9
|
35.7
|
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 Aug 11 21:52:38 2024
|