Phosphorus in PDB 1ad3: Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide
Enzymatic activity of Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide
All present enzymatic activity of Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide:
1.2.1.5;
Protein crystallography data
The structure of Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide, PDB code: 1ad3
was solved by
Z.-J.Liu,
J.Rose,
B.C.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
8.00 /
2.60
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.950,
170.950,
47.160,
90.00,
110.25,
90.00
|
R / Rfree (%)
|
17.7 /
27.9
|
Phosphorus Binding Sites:
The binding sites of Phosphorus atom in the Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide
(pdb code 1ad3). This binding sites where shown within
5.0 Angstroms radius around Phosphorus atom.
In total 4 binding sites of Phosphorus where determined in the
Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide, PDB code: 1ad3:
Jump to Phosphorus binding site number:
1;
2;
3;
4;
Phosphorus binding site 1 out
of 4 in 1ad3
Go back to
Phosphorus Binding Sites List in 1ad3
Phosphorus binding site 1 out
of 4 in the Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 1 of Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P600
b:20.0
occ:1.00
|
PA
|
A:NAD600
|
0.0
|
20.0
|
1.0
|
O1A
|
A:NAD600
|
1.5
|
20.0
|
1.0
|
O2A
|
A:NAD600
|
1.5
|
20.0
|
1.0
|
O3
|
A:NAD600
|
1.6
|
20.0
|
1.0
|
O5B
|
A:NAD600
|
1.6
|
20.0
|
1.0
|
C5B
|
A:NAD600
|
2.6
|
20.0
|
1.0
|
PN
|
A:NAD600
|
2.9
|
20.0
|
1.0
|
O1N
|
A:NAD600
|
3.4
|
20.0
|
1.0
|
O2N
|
A:NAD600
|
3.5
|
20.0
|
1.0
|
CE1
|
A:HIS289
|
3.9
|
18.0
|
1.0
|
C4B
|
A:NAD600
|
4.0
|
20.0
|
1.0
|
HE2
|
A:HIS289
|
4.1
|
15.0
|
1.0
|
HE1
|
A:TRP113
|
4.1
|
15.0
|
1.0
|
O5D
|
A:NAD600
|
4.1
|
20.0
|
1.0
|
CG2
|
A:VAL141
|
4.3
|
2.6
|
1.0
|
NE2
|
A:HIS289
|
4.4
|
17.3
|
1.0
|
O
|
A:HOH617
|
4.5
|
20.8
|
1.1
|
CZ
|
A:ARG288
|
4.5
|
65.0
|
1.0
|
NH1
|
A:ARG288
|
4.5
|
65.0
|
1.0
|
C3B
|
A:NAD600
|
4.6
|
20.0
|
1.0
|
HH11
|
A:ARG288
|
4.7
|
15.0
|
1.0
|
NE
|
A:ARG288
|
4.7
|
65.0
|
1.0
|
NE1
|
A:TRP113
|
4.7
|
11.4
|
1.0
|
HD21
|
A:ASN286
|
4.7
|
15.0
|
1.0
|
HH12
|
A:ARG288
|
4.8
|
15.0
|
1.0
|
C5D
|
A:NAD600
|
4.9
|
20.0
|
1.0
|
NH2
|
A:ARG288
|
4.9
|
65.0
|
1.0
|
O4B
|
A:NAD600
|
4.9
|
20.0
|
1.0
|
CD1
|
A:TRP113
|
5.0
|
10.4
|
1.0
|
|
Phosphorus binding site 2 out
of 4 in 1ad3
Go back to
Phosphorus Binding Sites List in 1ad3
Phosphorus binding site 2 out
of 4 in the Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 2 of Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:P600
b:20.0
occ:1.00
|
PN
|
A:NAD600
|
0.0
|
20.0
|
1.0
|
O1N
|
A:NAD600
|
1.5
|
20.0
|
1.0
|
O2N
|
A:NAD600
|
1.5
|
20.0
|
1.0
|
O5D
|
A:NAD600
|
1.6
|
20.0
|
1.0
|
O3
|
A:NAD600
|
1.6
|
20.0
|
1.0
|
C5D
|
A:NAD600
|
2.7
|
20.0
|
1.0
|
PA
|
A:NAD600
|
2.9
|
20.0
|
1.0
|
O5B
|
A:NAD600
|
3.0
|
20.0
|
1.0
|
HE1
|
A:TRP113
|
3.3
|
15.0
|
1.0
|
HE2
|
A:HIS289
|
3.3
|
15.0
|
1.0
|
C5B
|
A:NAD600
|
3.5
|
20.0
|
1.0
|
O1A
|
A:NAD600
|
3.8
|
20.0
|
1.0
|
O2A
|
A:NAD600
|
4.0
|
20.0
|
1.0
|
C4D
|
A:NAD600
|
4.0
|
20.0
|
1.0
|
NE2
|
A:HIS289
|
4.0
|
17.3
|
1.0
|
C2N
|
A:NAD600
|
4.2
|
20.0
|
1.0
|
NE1
|
A:TRP113
|
4.2
|
11.4
|
1.0
|
CE1
|
A:HIS289
|
4.2
|
18.0
|
1.0
|
O4D
|
A:NAD600
|
4.3
|
20.0
|
1.0
|
C2D
|
A:NAD600
|
4.4
|
20.0
|
1.0
|
C4B
|
A:NAD600
|
4.5
|
20.0
|
1.0
|
HH12
|
A:ARG288
|
4.5
|
15.0
|
1.0
|
C3D
|
A:NAD600
|
4.6
|
20.0
|
1.0
|
HH22
|
A:ARG288
|
4.6
|
15.0
|
1.0
|
C1D
|
A:NAD600
|
4.6
|
20.0
|
1.0
|
N7N
|
A:NAD600
|
4.7
|
20.0
|
1.0
|
N1N
|
A:NAD600
|
4.7
|
20.0
|
1.0
|
NH1
|
A:ARG288
|
4.9
|
65.0
|
1.0
|
CD1
|
A:TRP113
|
4.9
|
10.4
|
1.0
|
NH2
|
A:ARG288
|
4.9
|
65.0
|
1.0
|
O
|
A:HOH617
|
5.0
|
20.8
|
1.1
|
HG
|
A:SER188
|
5.0
|
15.0
|
1.0
|
|
Phosphorus binding site 3 out
of 4 in 1ad3
Go back to
Phosphorus Binding Sites List in 1ad3
Phosphorus binding site 3 out
of 4 in the Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 3 of Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P600
b:20.0
occ:1.00
|
PA
|
B:NAD600
|
0.0
|
20.0
|
1.0
|
O1A
|
B:NAD600
|
1.5
|
20.0
|
1.0
|
O2A
|
B:NAD600
|
1.5
|
20.0
|
1.0
|
O3
|
B:NAD600
|
1.6
|
20.0
|
1.0
|
O5B
|
B:NAD600
|
1.6
|
20.0
|
1.0
|
C5B
|
B:NAD600
|
2.6
|
20.0
|
1.0
|
PN
|
B:NAD600
|
2.9
|
20.0
|
1.0
|
O1N
|
B:NAD600
|
3.3
|
20.0
|
1.0
|
O2N
|
B:NAD600
|
3.5
|
20.0
|
1.0
|
CE1
|
B:HIS289
|
3.9
|
23.7
|
1.0
|
C4B
|
B:NAD600
|
4.0
|
20.0
|
1.0
|
O5D
|
B:NAD600
|
4.2
|
20.0
|
1.0
|
HE1
|
B:TRP113
|
4.2
|
15.0
|
1.0
|
HE2
|
B:HIS289
|
4.2
|
15.0
|
1.0
|
CG2
|
B:VAL141
|
4.3
|
10.3
|
1.0
|
NE2
|
B:HIS289
|
4.4
|
13.8
|
1.0
|
NH1
|
B:ARG288
|
4.5
|
42.4
|
1.0
|
CZ
|
B:ARG288
|
4.6
|
45.3
|
1.0
|
HH11
|
B:ARG288
|
4.6
|
15.0
|
1.0
|
C3B
|
B:NAD600
|
4.6
|
20.0
|
1.0
|
HH12
|
B:ARG288
|
4.7
|
15.0
|
1.0
|
NE1
|
B:TRP113
|
4.8
|
15.4
|
1.0
|
NE
|
B:ARG288
|
4.8
|
44.3
|
1.0
|
C5D
|
B:NAD600
|
4.9
|
20.0
|
1.0
|
O4B
|
B:NAD600
|
4.9
|
20.0
|
1.0
|
NH2
|
B:ARG288
|
5.0
|
54.6
|
1.0
|
ND1
|
B:HIS289
|
5.0
|
25.7
|
1.0
|
HD21
|
B:ASN286
|
5.0
|
15.0
|
1.0
|
|
Phosphorus binding site 4 out
of 4 in 1ad3
Go back to
Phosphorus Binding Sites List in 1ad3
Phosphorus binding site 4 out
of 4 in the Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide
Mono view
Stereo pair view
|
A full contact list of Phosphorus with other atoms in the P binding
site number 4 of Class 3 Aldehyde Dehydrogenase Complex with Nicotinamide- Adenine-Dinucleotide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:P600
b:20.0
occ:1.00
|
PN
|
B:NAD600
|
0.0
|
20.0
|
1.0
|
O1N
|
B:NAD600
|
1.5
|
20.0
|
1.0
|
O2N
|
B:NAD600
|
1.5
|
20.0
|
1.0
|
O5D
|
B:NAD600
|
1.6
|
20.0
|
1.0
|
O3
|
B:NAD600
|
1.6
|
20.0
|
1.0
|
C5D
|
B:NAD600
|
2.7
|
20.0
|
1.0
|
PA
|
B:NAD600
|
2.9
|
20.0
|
1.0
|
O5B
|
B:NAD600
|
2.9
|
20.0
|
1.0
|
HE2
|
B:HIS289
|
3.2
|
15.0
|
1.0
|
HE1
|
B:TRP113
|
3.4
|
15.0
|
1.0
|
C5B
|
B:NAD600
|
3.6
|
20.0
|
1.0
|
O1A
|
B:NAD600
|
3.8
|
20.0
|
1.0
|
C4D
|
B:NAD600
|
3.9
|
20.0
|
1.0
|
NE2
|
B:HIS289
|
4.0
|
13.8
|
1.0
|
O2A
|
B:NAD600
|
4.0
|
20.0
|
1.0
|
O4D
|
B:NAD600
|
4.1
|
20.0
|
1.0
|
C2N
|
B:NAD600
|
4.2
|
20.0
|
1.0
|
CE1
|
B:HIS289
|
4.2
|
23.7
|
1.0
|
C2D
|
B:NAD600
|
4.3
|
20.0
|
1.0
|
NE1
|
B:TRP113
|
4.3
|
15.4
|
1.0
|
HH12
|
B:ARG288
|
4.5
|
15.0
|
1.0
|
C3D
|
B:NAD600
|
4.5
|
20.0
|
1.0
|
HG
|
B:SER188
|
4.5
|
15.0
|
1.0
|
C4B
|
B:NAD600
|
4.5
|
20.0
|
1.0
|
C1D
|
B:NAD600
|
4.6
|
20.0
|
1.0
|
HH22
|
B:ARG288
|
4.7
|
15.0
|
1.0
|
N1N
|
B:NAD600
|
4.7
|
20.0
|
1.0
|
N7N
|
B:NAD600
|
4.7
|
20.0
|
1.0
|
NH1
|
B:ARG288
|
4.8
|
42.4
|
1.0
|
OG
|
B:SER188
|
5.0
|
24.7
|
1.0
|
|
Reference:
Z.J.Liu,
Y.J.Sun,
J.Rose,
Y.J.Chung,
C.D.Hsiao,
W.R.Chang,
I.Kuo,
J.Perozich,
R.Lindahl,
J.Hempel,
B.C.Wang.
The First Structure of An Aldehyde Dehydrogenase Reveals Novel Interactions Between Nad and the Rossmann Fold. Nat.Struct.Biol. V. 4 317 1997.
ISSN: ISSN 1072-8368
PubMed: 9095201
DOI: 10.1038/NSB0497-317
Page generated: Fri Sep 25 12:45:19 2020
|