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

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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

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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

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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

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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

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