Phosphorus in PDB 1agn: X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Enzymatic activity of X-Ray Structure of Human Sigma Alcohol Dehydrogenase
All present enzymatic activity of X-Ray Structure of Human Sigma Alcohol Dehydrogenase:
1.1.1.1;
Protein crystallography data
The structure of X-Ray Structure of Human Sigma Alcohol Dehydrogenase, PDB code: 1agn
was solved by
T.D.Hurley,
P.Xie,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
3.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
86.300,
94.650,
121.660,
90.00,
100.03,
90.00
|
R / Rfree (%)
|
22.5 /
30.5
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
(pdb code 1agn). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 8 binding sites of Phosphorus where determined in the
X-Ray Structure of Human Sigma Alcohol Dehydrogenase, PDB code: 1agn:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Phosphorus binding site 1 out
of 8 in 1agn
Go back to
Phosphorus Binding Sites List in 1agn
Phosphorus binding site 1 out
of 8 in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of X-Ray Structure of Human Sigma Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P377
b:19.6
occ:1.00
|
PA
|
A:NAD377
|
0.0
|
19.6
|
1.0
|
O1A
|
A:NAD377
|
1.5
|
19.6
|
1.0
|
O2A
|
A:NAD377
|
1.5
|
19.6
|
1.0
|
O3
|
A:NAD377
|
1.6
|
19.6
|
1.0
|
O5B
|
A:NAD377
|
1.6
|
19.6
|
1.0
|
C5B
|
A:NAD377
|
2.6
|
19.6
|
1.0
|
PN
|
A:NAD377
|
2.9
|
19.6
|
1.0
|
O2N
|
A:NAD377
|
3.4
|
19.6
|
1.0
|
CA
|
A:GLY201
|
3.8
|
19.6
|
1.0
|
O1N
|
A:NAD377
|
3.8
|
19.6
|
1.0
|
C4B
|
A:NAD377
|
3.8
|
19.6
|
1.0
|
O5D
|
A:NAD377
|
3.9
|
19.6
|
1.0
|
NE
|
A:ARG47
|
4.2
|
19.6
|
1.0
|
C5D
|
A:NAD377
|
4.2
|
19.6
|
1.0
|
N
|
A:GLY202
|
4.2
|
19.6
|
1.0
|
CB
|
A:ARG47
|
4.2
|
19.6
|
1.0
|
C3B
|
A:NAD377
|
4.3
|
19.6
|
1.0
|
C
|
A:GLY201
|
4.6
|
19.6
|
1.0
|
CG
|
A:ARG47
|
4.7
|
19.6
|
1.0
|
NH2
|
A:ARG47
|
4.7
|
19.6
|
1.0
|
N
|
A:GLY201
|
4.8
|
19.6
|
1.0
|
CZ
|
A:ARG47
|
4.9
|
19.6
|
1.0
|
NH1
|
A:ARG369
|
4.9
|
19.6
|
1.0
|
O4B
|
A:NAD377
|
5.0
|
19.6
|
1.0
|
|
Phosphorus binding site 2 out
of 8 in 1agn
Go back to
Phosphorus Binding Sites List in 1agn
Phosphorus binding site 2 out
of 8 in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of X-Ray Structure of Human Sigma Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P377
b:19.6
occ:1.00
|
PN
|
A:NAD377
|
0.0
|
19.6
|
1.0
|
O1N
|
A:NAD377
|
1.5
|
19.6
|
1.0
|
O2N
|
A:NAD377
|
1.5
|
19.6
|
1.0
|
O3
|
A:NAD377
|
1.5
|
19.6
|
1.0
|
O5D
|
A:NAD377
|
1.6
|
19.6
|
1.0
|
C5D
|
A:NAD377
|
2.7
|
19.6
|
1.0
|
PA
|
A:NAD377
|
2.9
|
19.6
|
1.0
|
CB
|
A:ARG47
|
3.4
|
19.6
|
1.0
|
O2A
|
A:NAD377
|
3.5
|
19.6
|
1.0
|
O5B
|
A:NAD377
|
3.7
|
19.6
|
1.0
|
O1A
|
A:NAD377
|
3.9
|
19.6
|
1.0
|
CG2
|
A:VAL203
|
4.0
|
19.6
|
1.0
|
C4D
|
A:NAD377
|
4.0
|
19.6
|
1.0
|
NH1
|
A:ARG369
|
4.0
|
19.6
|
1.0
|
N
|
A:ARG47
|
4.2
|
19.6
|
1.0
|
O4D
|
A:NAD377
|
4.2
|
19.6
|
1.0
|
N
|
A:VAL203
|
4.3
|
19.6
|
1.0
|
NH2
|
A:ARG369
|
4.4
|
19.6
|
1.0
|
CB
|
A:VAL203
|
4.4
|
19.6
|
1.0
|
N
|
A:GLY202
|
4.4
|
19.6
|
1.0
|
CG
|
A:ARG47
|
4.4
|
19.6
|
1.0
|
CA
|
A:ARG47
|
4.5
|
19.6
|
1.0
|
C5B
|
A:NAD377
|
4.6
|
19.6
|
1.0
|
C6N
|
A:NAD377
|
4.7
|
19.6
|
1.0
|
CZ
|
A:ARG369
|
4.7
|
19.6
|
1.0
|
C2D
|
A:NAD377
|
4.7
|
19.6
|
1.0
|
C3D
|
A:NAD377
|
4.8
|
19.6
|
1.0
|
SG
|
A:CYS46
|
4.9
|
19.6
|
1.0
|
CA
|
A:GLY201
|
5.0
|
19.6
|
1.0
|
|
Phosphorus binding site 3 out
of 8 in 1agn
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Phosphorus Binding Sites List in 1agn
Phosphorus binding site 3 out
of 8 in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of X-Ray Structure of Human Sigma Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P377
b:15.4
occ:1.00
|
PA
|
B:NAD377
|
0.0
|
15.4
|
1.0
|
O2A
|
B:NAD377
|
1.5
|
15.4
|
1.0
|
O1A
|
B:NAD377
|
1.5
|
15.4
|
1.0
|
O5B
|
B:NAD377
|
1.5
|
15.4
|
1.0
|
O3
|
B:NAD377
|
1.6
|
15.4
|
1.0
|
C5B
|
B:NAD377
|
2.5
|
15.4
|
1.0
|
PN
|
B:NAD377
|
2.8
|
15.4
|
1.0
|
O5D
|
B:NAD377
|
3.1
|
15.4
|
1.0
|
O2N
|
B:NAD377
|
3.4
|
15.4
|
1.0
|
C4B
|
B:NAD377
|
3.5
|
15.4
|
1.0
|
O1N
|
B:NAD377
|
4.0
|
15.4
|
1.0
|
C3B
|
B:NAD377
|
4.0
|
15.4
|
1.0
|
CA
|
B:GLY201
|
4.0
|
15.4
|
1.0
|
CB
|
B:ARG47
|
4.1
|
15.4
|
1.0
|
C5D
|
B:NAD377
|
4.1
|
15.4
|
1.0
|
NE
|
B:ARG47
|
4.3
|
15.4
|
1.0
|
CG
|
B:ARG47
|
4.4
|
15.4
|
1.0
|
CD1
|
B:LEU362
|
4.5
|
15.4
|
1.0
|
N
|
B:GLY202
|
4.7
|
15.4
|
1.0
|
O4B
|
B:NAD377
|
4.8
|
15.4
|
1.0
|
N
|
B:GLY201
|
4.8
|
15.4
|
1.0
|
C
|
B:GLY201
|
4.9
|
15.4
|
1.0
|
NH2
|
B:ARG47
|
5.0
|
15.4
|
1.0
|
CD
|
B:ARG47
|
5.0
|
15.4
|
1.0
|
O3B
|
B:NAD377
|
5.0
|
15.4
|
1.0
|
|
Phosphorus binding site 4 out
of 8 in 1agn
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Phosphorus Binding Sites List in 1agn
Phosphorus binding site 4 out
of 8 in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of X-Ray Structure of Human Sigma Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P377
b:15.4
occ:1.00
|
PN
|
B:NAD377
|
0.0
|
15.4
|
1.0
|
O1N
|
B:NAD377
|
1.5
|
15.4
|
1.0
|
O2N
|
B:NAD377
|
1.5
|
15.4
|
1.0
|
O3
|
B:NAD377
|
1.5
|
15.4
|
1.0
|
O5D
|
B:NAD377
|
1.6
|
15.4
|
1.0
|
C5D
|
B:NAD377
|
2.7
|
15.4
|
1.0
|
PA
|
B:NAD377
|
2.8
|
15.4
|
1.0
|
O5B
|
B:NAD377
|
3.3
|
15.4
|
1.0
|
CB
|
B:ARG47
|
3.7
|
15.4
|
1.0
|
C4D
|
B:NAD377
|
3.7
|
15.4
|
1.0
|
O4D
|
B:NAD377
|
3.7
|
15.4
|
1.0
|
O1A
|
B:NAD377
|
3.7
|
15.4
|
1.0
|
O2A
|
B:NAD377
|
3.8
|
15.4
|
1.0
|
CG2
|
B:VAL203
|
4.0
|
15.4
|
1.0
|
C3D
|
B:NAD377
|
4.1
|
15.4
|
1.0
|
NH1
|
B:ARG369
|
4.2
|
15.4
|
1.0
|
N
|
B:VAL203
|
4.3
|
15.4
|
1.0
|
CB
|
B:VAL203
|
4.4
|
15.4
|
1.0
|
N
|
B:GLY202
|
4.4
|
15.4
|
1.0
|
C2D
|
B:NAD377
|
4.5
|
15.4
|
1.0
|
N
|
B:ARG47
|
4.5
|
15.4
|
1.0
|
C5B
|
B:NAD377
|
4.5
|
15.4
|
1.0
|
CG
|
B:ARG47
|
4.6
|
15.4
|
1.0
|
CA
|
B:ARG47
|
4.7
|
15.4
|
1.0
|
C1D
|
B:NAD377
|
4.8
|
15.4
|
1.0
|
O
|
B:VAL268
|
4.9
|
15.4
|
1.0
|
CA
|
B:GLY201
|
4.9
|
15.4
|
1.0
|
CA
|
B:VAL203
|
5.0
|
15.4
|
1.0
|
|
Phosphorus binding site 5 out
of 8 in 1agn
Go back to
Phosphorus Binding Sites List in 1agn
Phosphorus binding site 5 out
of 8 in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 5 of X-Ray Structure of Human Sigma Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P377
b:25.9
occ:1.00
|
PA
|
C:NAD377
|
0.0
|
25.9
|
1.0
|
O2A
|
C:NAD377
|
1.5
|
25.9
|
1.0
|
O1A
|
C:NAD377
|
1.5
|
25.9
|
1.0
|
O3
|
C:NAD377
|
1.5
|
25.9
|
1.0
|
O5B
|
C:NAD377
|
1.6
|
25.9
|
1.0
|
C5B
|
C:NAD377
|
2.6
|
25.9
|
1.0
|
PN
|
C:NAD377
|
2.7
|
25.9
|
1.0
|
O2N
|
C:NAD377
|
3.2
|
25.9
|
1.0
|
C4B
|
C:NAD377
|
3.7
|
25.9
|
1.0
|
O1N
|
C:NAD377
|
3.8
|
25.9
|
1.0
|
O5D
|
C:NAD377
|
3.8
|
25.9
|
1.0
|
C5D
|
C:NAD377
|
3.9
|
25.9
|
1.0
|
CB
|
C:ARG47
|
3.9
|
25.9
|
1.0
|
NE
|
C:ARG47
|
4.0
|
25.9
|
1.0
|
CA
|
C:GLY201
|
4.0
|
25.9
|
1.0
|
N
|
C:GLY202
|
4.2
|
25.9
|
1.0
|
CG
|
C:ARG47
|
4.4
|
25.9
|
1.0
|
NH2
|
C:ARG47
|
4.4
|
25.9
|
1.0
|
C3B
|
C:NAD377
|
4.5
|
25.9
|
1.0
|
C
|
C:GLY201
|
4.6
|
25.9
|
1.0
|
CZ
|
C:ARG47
|
4.7
|
25.9
|
1.0
|
CD
|
C:ARG47
|
4.8
|
25.9
|
1.0
|
O4B
|
C:NAD377
|
4.8
|
25.9
|
1.0
|
N
|
C:GLY201
|
4.9
|
25.9
|
1.0
|
|
Phosphorus binding site 6 out
of 8 in 1agn
Go back to
Phosphorus Binding Sites List in 1agn
Phosphorus binding site 6 out
of 8 in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 6 of X-Ray Structure of Human Sigma Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:P377
b:25.9
occ:1.00
|
PN
|
C:NAD377
|
0.0
|
25.9
|
1.0
|
O1N
|
C:NAD377
|
1.5
|
25.9
|
1.0
|
O2N
|
C:NAD377
|
1.5
|
25.9
|
1.0
|
O3
|
C:NAD377
|
1.6
|
25.9
|
1.0
|
O5D
|
C:NAD377
|
1.6
|
25.9
|
1.0
|
C5D
|
C:NAD377
|
2.6
|
25.9
|
1.0
|
PA
|
C:NAD377
|
2.7
|
25.9
|
1.0
|
O2A
|
C:NAD377
|
3.1
|
25.9
|
1.0
|
O5B
|
C:NAD377
|
3.5
|
25.9
|
1.0
|
CB
|
C:ARG47
|
3.8
|
25.9
|
1.0
|
CG2
|
C:VAL203
|
3.8
|
25.9
|
1.0
|
C4D
|
C:NAD377
|
3.9
|
25.9
|
1.0
|
O1A
|
C:NAD377
|
4.0
|
25.9
|
1.0
|
N
|
C:VAL203
|
4.0
|
25.9
|
1.0
|
O4D
|
C:NAD377
|
4.2
|
25.9
|
1.0
|
N
|
C:GLY202
|
4.2
|
25.9
|
1.0
|
CB
|
C:VAL203
|
4.2
|
25.9
|
1.0
|
NH1
|
C:ARG369
|
4.3
|
25.9
|
1.0
|
C2D
|
C:NAD377
|
4.4
|
25.9
|
1.0
|
C3D
|
C:NAD377
|
4.6
|
25.9
|
1.0
|
N
|
C:ARG47
|
4.6
|
25.9
|
1.0
|
CG
|
C:ARG47
|
4.6
|
25.9
|
1.0
|
CA
|
C:GLY202
|
4.7
|
25.9
|
1.0
|
CA
|
C:VAL203
|
4.8
|
25.9
|
1.0
|
C6N
|
C:NAD377
|
4.8
|
25.9
|
1.0
|
CA
|
C:ARG47
|
4.8
|
25.9
|
1.0
|
C
|
C:GLY202
|
4.9
|
25.9
|
1.0
|
C
|
C:GLY201
|
4.9
|
25.9
|
1.0
|
C5B
|
C:NAD377
|
4.9
|
25.9
|
1.0
|
NH2
|
C:ARG369
|
5.0
|
25.9
|
1.0
|
C1D
|
C:NAD377
|
5.0
|
25.9
|
1.0
|
|
Phosphorus binding site 7 out
of 8 in 1agn
Go back to
Phosphorus Binding Sites List in 1agn
Phosphorus binding site 7 out
of 8 in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 7 of X-Ray Structure of Human Sigma Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:P377
b:14.9
occ:1.00
|
PA
|
D:NAD377
|
0.0
|
14.9
|
1.0
|
O2A
|
D:NAD377
|
1.5
|
14.9
|
1.0
|
O1A
|
D:NAD377
|
1.5
|
14.9
|
1.0
|
O5B
|
D:NAD377
|
1.6
|
14.9
|
1.0
|
O3
|
D:NAD377
|
1.6
|
14.9
|
1.0
|
C5B
|
D:NAD377
|
2.8
|
14.9
|
1.0
|
PN
|
D:NAD377
|
2.9
|
14.9
|
1.0
|
O5D
|
D:NAD377
|
3.6
|
14.9
|
1.0
|
O2N
|
D:NAD377
|
3.6
|
14.9
|
1.0
|
C4B
|
D:NAD377
|
3.8
|
14.9
|
1.0
|
O1N
|
D:NAD377
|
4.1
|
14.9
|
1.0
|
CA
|
D:GLY201
|
4.1
|
14.9
|
1.0
|
C3B
|
D:NAD377
|
4.1
|
14.9
|
1.0
|
NE
|
D:ARG47
|
4.1
|
14.9
|
1.0
|
CB
|
D:ARG47
|
4.3
|
14.9
|
1.0
|
CD1
|
D:LEU362
|
4.4
|
14.9
|
1.0
|
N
|
D:GLY202
|
4.4
|
14.9
|
1.0
|
NH2
|
D:ARG47
|
4.5
|
14.9
|
1.0
|
CG
|
D:ARG47
|
4.8
|
14.9
|
1.0
|
CZ
|
D:ARG47
|
4.8
|
14.9
|
1.0
|
C
|
D:GLY201
|
4.8
|
14.9
|
1.0
|
C5D
|
D:NAD377
|
4.9
|
14.9
|
1.0
|
|
Phosphorus binding site 8 out
of 8 in 1agn
Go back to
Phosphorus Binding Sites List in 1agn
Phosphorus binding site 8 out
of 8 in the X-Ray Structure of Human Sigma Alcohol Dehydrogenase
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 8 of X-Ray Structure of Human Sigma Alcohol Dehydrogenase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:P377
b:14.9
occ:1.00
|
PN
|
D:NAD377
|
0.0
|
14.9
|
1.0
|
O1N
|
D:NAD377
|
1.5
|
14.9
|
1.0
|
O2N
|
D:NAD377
|
1.5
|
14.9
|
1.0
|
O5D
|
D:NAD377
|
1.6
|
14.9
|
1.0
|
O3
|
D:NAD377
|
1.6
|
14.9
|
1.0
|
C5D
|
D:NAD377
|
2.5
|
14.9
|
1.0
|
PA
|
D:NAD377
|
2.9
|
14.9
|
1.0
|
O5B
|
D:NAD377
|
3.2
|
14.9
|
1.0
|
CB
|
D:ARG47
|
3.7
|
14.9
|
1.0
|
CG2
|
D:VAL203
|
3.8
|
14.9
|
1.0
|
O2A
|
D:NAD377
|
3.8
|
14.9
|
1.0
|
C4D
|
D:NAD377
|
3.8
|
14.9
|
1.0
|
O1A
|
D:NAD377
|
4.0
|
14.9
|
1.0
|
N
|
D:GLY202
|
4.1
|
14.9
|
1.0
|
N
|
D:VAL203
|
4.2
|
14.9
|
1.0
|
NH1
|
D:ARG369
|
4.3
|
14.9
|
1.0
|
N
|
D:ARG47
|
4.3
|
14.9
|
1.0
|
C5B
|
D:NAD377
|
4.4
|
14.9
|
1.0
|
NH2
|
D:ARG369
|
4.5
|
14.9
|
1.0
|
CB
|
D:VAL203
|
4.5
|
14.9
|
1.0
|
C3D
|
D:NAD377
|
4.6
|
14.9
|
1.0
|
CA
|
D:ARG47
|
4.7
|
14.9
|
1.0
|
CG
|
D:ARG47
|
4.7
|
14.9
|
1.0
|
CZ
|
D:ARG369
|
4.7
|
14.9
|
1.0
|
CA
|
D:GLY202
|
4.7
|
14.9
|
1.0
|
O4D
|
D:NAD377
|
4.8
|
14.9
|
1.0
|
CA
|
D:GLY201
|
4.9
|
14.9
|
1.0
|
C
|
D:GLY201
|
4.9
|
14.9
|
1.0
|
CA
|
D:VAL203
|
5.0
|
14.9
|
1.0
|
|
Reference:
P.Xie,
S.H.Parsons,
D.C.Speckhard,
W.F.Bosron,
T.D.Hurley.
X-Ray Structure of Human Class IV Sigmasigma Alcohol Dehydrogenase. Structural Basis For Substrate Specificity. J.Biol.Chem. V. 272 18558 1997.
ISSN: ISSN 0021-9258
PubMed: 9228021
DOI: 10.1074/JBC.272.30.18558
Page generated: Fri Sep 25 12:52:33 2020
|