Phosphorus in PDB 1afs: Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone

Enzymatic activity of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone

All present enzymatic activity of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone:
1.1.1.50;

Protein crystallography data

The structure of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone, PDB code: 1afs was solved by M.J.Bennett, R.H.Albert, J.M.Jez, H.Ma, T.M.Penning, M.Lewis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 96.400, 157.100, 49.000, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.2

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone (pdb code 1afs). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 6 binding sites of Phosphorus where determined in the Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone, PDB code: 1afs:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6;

Phosphorus binding site 1 out of 6 in 1afs

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Phosphorus binding site 1 out of 6 in the Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P324

b:30.1
occ:1.00
 PA A:NAP324 0.0 30.1 1.0
O2A A:NAP324 1.5 32.6 1.0
O1A A:NAP324 1.5 30.6 1.0
O5B A:NAP324 1.6 32.7 1.0
O3 A:NAP324 1.6 26.6 1.0
C5B A:NAP324 2.6 31.7 1.0
PN A:NAP324 3.0 22.9 1.0
O A:HOH332 3.3 18.7 1.0
O1N A:NAP324 3.5 31.3 1.0
CA A:SER221 3.7 34.2 1.0
O5D A:NAP324 3.7 28.1 1.0
N A:SER221 3.8 28.9 1.0
C4B A:NAP324 3.8 32.6 1.0
CA A:CYS217 3.9 13.9 1.0
C5D A:NAP324 3.9 22.5 1.0
C A:SER221 4.0 36.2 1.0
O2N A:NAP324 4.1 33.6 1.0
N A:LEU219 4.2 17.2 1.0
O4B A:NAP324 4.2 29.7 1.0
CB A:LEU219 4.3 21.5 1.0
N A:CYS217 4.3 13.2 1.0
N A:THR218 4.3 15.7 1.0
C A:CYS217 4.4 15.1 1.0
O A:SER221 4.4 37.9 1.0
N A:SER222 4.5 37.8 1.0
CA A:LEU219 4.6 21.6 1.0
C A:LEU219 4.8 24.9 1.0
CG A:LEU219 4.8 25.0 1.0
N A:GLY220 4.8 27.9 1.0
C A:GLY220 5.0 28.9 1.0
CB A:SER221 5.0 32.8 1.0

Phosphorus binding site 2 out of 6 in 1afs

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Phosphorus binding site 2 out of 6 in the Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P324

b:22.9
occ:1.00
 PN A:NAP324 0.0 22.9 1.0
O2N A:NAP324 1.5 33.6 1.0
O1N A:NAP324 1.5 31.3 1.0
O3 A:NAP324 1.6 26.6 1.0
O5D A:NAP324 1.6 28.1 1.0
C5D A:NAP324 2.7 22.5 1.0
PA A:NAP324 3.0 30.1 1.0
O2A A:NAP324 3.6 32.6 1.0
O5B A:NAP324 3.6 32.7 1.0
O A:HOH342 3.6 25.3 1.0
C5B A:NAP324 3.8 31.7 1.0
N A:SER222 3.9 37.8 1.0
C4D A:NAP324 3.9 16.8 1.0
NH1 A:ARG270 4.0 32.3 1.0
O1A A:NAP324 4.1 30.6 1.0
CA A:SER221 4.1 34.2 1.0
CB A:SER222 4.2 47.3 1.0
OG A:SER222 4.2 53.9 1.0
C3D A:NAP324 4.2 17.3 1.0
C A:SER221 4.3 36.2 1.0
O4D A:NAP324 4.5 17.5 1.0
O A:HOH332 4.6 18.7 1.0
CA A:SER222 4.6 45.7 1.0
CB A:SER221 4.7 32.8 1.0
C6N A:NAP324 4.7 16.6 1.0
O3D A:NAP324 4.8 18.8 1.0
SG A:CYS217 4.8 21.3 1.0
OG1 A:THR24 4.8 24.5 1.0
CA A:CYS217 4.8 13.9 1.0
N A:CYS217 4.8 13.2 1.0
CB A:ARG270 5.0 21.1 1.0

Phosphorus binding site 3 out of 6 in 1afs

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Phosphorus binding site 3 out of 6 in the Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P324

b:33.5
occ:1.00
 P2B A:NAP324 0.0 33.5 1.0
O2X A:NAP324 1.5 42.0 1.0
O1X A:NAP324 1.5 34.9 1.0
O2B A:NAP324 1.6 29.3 1.0
O3X A:NAP324 1.6 31.4 1.0
C2B A:NAP324 2.7 34.0 1.0
NE A:ARG276 3.6 41.8 1.0
NH2 A:ARG276 3.6 40.6 1.0
C3B A:NAP324 3.7 33.3 1.0
C1B A:NAP324 3.8 31.3 1.0
O3B A:NAP324 3.9 40.5 1.0
OG A:SER271 3.9 25.8 1.0
CZ A:ARG276 4.0 44.2 1.0
N A:PHE272 4.1 26.1 1.0
CA A:SER271 4.1 20.1 1.0
N9A A:NAP324 4.2 31.7 1.0
CB A:SER271 4.3 19.7 1.0
C8A A:NAP324 4.5 32.9 1.0
CB A:ASN273 4.5 33.2 1.0
N A:ASN273 4.6 29.1 1.0
C A:SER271 4.6 22.2 1.0
CD A:ARG276 4.6 34.2 1.0
C4A A:NAP324 4.8 30.3 1.0
O A:ARG270 4.9 23.8 1.0
C4B A:NAP324 5.0 32.6 1.0
O4B A:NAP324 5.0 29.7 1.0

Phosphorus binding site 4 out of 6 in 1afs

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Phosphorus binding site 4 out of 6 in the Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P324

b:24.2
occ:1.00
 PA B:NAP324 0.0 24.2 1.0
O1A B:NAP324 1.5 21.1 1.0
O2A B:NAP324 1.5 16.2 1.0
O5B B:NAP324 1.6 19.1 1.0
O3 B:NAP324 1.6 25.7 1.0
C5B B:NAP324 2.6 19.6 1.0
PN B:NAP324 3.1 18.1 1.0
O B:HOH333 3.4 12.6 1.0
O1N B:NAP324 3.5 18.1 1.0
CA B:SER221 3.7 29.1 1.0
O5D B:NAP324 3.7 20.6 1.0
N B:SER221 3.8 24.6 1.0
C4B B:NAP324 3.8 20.0 1.0
CA B:CYS217 3.9 14.7 1.0
C5D B:NAP324 4.0 14.2 1.0
C B:SER221 4.0 32.8 1.0
O2N B:NAP324 4.1 29.4 1.0
N B:LEU219 4.2 14.0 1.0
O4B B:NAP324 4.2 20.0 1.0
CB B:LEU219 4.3 13.1 1.0
N B:CYS217 4.3 12.9 1.0
N B:THR218 4.3 9.4 1.0
O B:SER221 4.4 33.7 1.0
C B:CYS217 4.4 14.1 1.0
N B:SER222 4.5 36.2 1.0
CA B:LEU219 4.6 16.2 1.0
C B:LEU219 4.8 20.9 1.0
CG B:LEU219 4.8 19.5 1.0
N B:GLY220 4.8 20.9 1.0
C B:GLY220 4.9 23.0 1.0
CB B:SER221 5.0 28.1 1.0

Phosphorus binding site 5 out of 6 in 1afs

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Phosphorus binding site 5 out of 6 in the Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P324

b:18.1
occ:1.00
 PN B:NAP324 0.0 18.1 1.0
O1N B:NAP324 1.5 18.1 1.0
O2N B:NAP324 1.5 29.4 1.0
O5D B:NAP324 1.6 20.6 1.0
O3 B:NAP324 1.6 25.7 1.0
C5D B:NAP324 2.7 14.2 1.0
PA B:NAP324 3.1 24.2 1.0
O2A B:NAP324 3.6 16.2 1.0
O B:HOH343 3.6 33.2 1.0
O5B B:NAP324 3.6 19.1 1.0
C5B B:NAP324 3.8 19.6 1.0
N B:SER222 3.9 36.2 1.0
C4D B:NAP324 3.9 8.8 1.0
NH1 B:ARG270 4.0 24.1 1.0
CA B:SER221 4.1 29.1 1.0
O1A B:NAP324 4.1 21.1 1.0
OG B:SER222 4.2 49.1 1.0
C3D B:NAP324 4.2 6.6 1.0
CB B:SER222 4.2 43.2 1.0
C B:SER221 4.3 32.8 1.0
O4D B:NAP324 4.5 10.9 1.0
O B:HOH333 4.6 12.6 1.0
CA B:SER222 4.6 41.1 1.0
C6N B:NAP324 4.7 7.7 1.0
O3D B:NAP324 4.7 7.9 1.0
CB B:SER221 4.7 28.1 1.0
SG B:CYS217 4.7 18.6 1.0
OG1 B:THR24 4.8 19.5 1.0
N B:CYS217 4.9 12.9 1.0
CA B:CYS217 4.9 14.7 1.0
CB B:ARG270 5.0 13.9 1.0

Phosphorus binding site 6 out of 6 in 1afs

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Phosphorus binding site 6 out of 6 in the Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Recombinant Rat Liver 3-Alpha-Hydroxysteroid Dehydrogenase (3-Alpha-Hsd) Complexed with Nadp and Testosterone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P324

b:17.3
occ:1.00
 P2B B:NAP324 0.0 17.3 1.0
O1X B:NAP324 1.5 21.2 1.0
O2X B:NAP324 1.5 19.3 1.0
O2B B:NAP324 1.6 17.0 1.0
O3X B:NAP324 1.6 17.0 1.0
C2B B:NAP324 2.7 18.9 1.0
NE B:ARG276 3.6 34.6 1.0
NH2 B:ARG276 3.6 35.5 1.0
O B:HOH355 3.6 32.9 1.0
C3B B:NAP324 3.7 20.9 1.0
C1B B:NAP324 3.8 18.8 1.0
O3B B:NAP324 3.9 33.1 1.0
O B:HOH353 3.9 15.4 1.0
OG B:SER271 3.9 17.1 1.0
CZ B:ARG276 4.0 37.5 1.0
N B:PHE272 4.1 19.0 1.0
CA B:SER271 4.1 16.8 1.0
N9A B:NAP324 4.1 22.1 1.0
CB B:SER271 4.3 17.8 1.0
C8A B:NAP324 4.5 24.4 1.0
CB B:ASN273 4.5 30.3 1.0
N B:ASN273 4.6 21.1 1.0
C B:SER271 4.6 16.5 1.0
CD B:ARG276 4.6 24.1 1.0
C4A B:NAP324 4.8 23.0 1.0
O B:HOH352 4.9 26.2 1.0
O B:ARG270 4.9 16.4 1.0
C4B B:NAP324 5.0 20.0 1.0
O4B B:NAP324 5.0 20.0 1.0

Reference:

M.J.Bennett, R.H.Albert, J.M.Jez, H.Ma, T.M.Penning, M.Lewis. Steroid Recognition and Regulation of Hormone Action: Crystal Structure of Testosterone and Nadp+ Bound to 3 Alpha-Hydroxysteroid/Dihydrodiol Dehydrogenase. Structure V. 5 799 1997.
ISSN: ISSN 0969-2126
PubMed: 9261071
DOI: 10.1016/S0969-2126(97)00234-7
Page generated: Fri Sep 25 12:48:44 2020

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