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Manganese in PDB 5a3u: Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid:
1.14.11.2; 1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid, PDB code: 5a3u was solved by R.Chowdhury, V.Gomez-Perez, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.73 / 3.30
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 154.939, 154.939, 85.401, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 22.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid (pdb code 5a3u). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid, PDB code: 5a3u:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5a3u

Go back to Manganese Binding Sites List in 5a3u
Manganese binding site 1 out of 3 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1420

b:50.6
occ:1.00
 OD1 A:ASP315 2.1 39.5 1.0
NAM A:R8J1421 2.3 97.2 1.0
NE2 A:HIS313 2.3 42.9 1.0
NE2 A:HIS374 2.3 48.6 1.0
NAK A:R8J1421 2.4 0.3 1.0
NAT A:R8J1421 3.0 0.3 1.0
CE1 A:HIS313 3.0 41.8 1.0
CAP A:R8J1421 3.1 1.0 1.0
CE1 A:HIS374 3.1 47.5 1.0
CG A:ASP315 3.2 39.4 1.0
CD2 A:HIS313 3.4 44.2 1.0
CAI A:R8J1421 3.4 94.5 1.0
CD2 A:HIS374 3.4 49.3 1.0
CAH A:R8J1421 3.4 1.0 1.0
OD2 A:ASP315 3.5 39.1 1.0
ND1 A:HIS313 4.2 42.5 1.0
CAR A:R8J1421 4.2 0.5 1.0
ND1 A:HIS374 4.2 47.1 1.0
CAQ A:R8J1421 4.4 94.1 1.0
CG A:HIS313 4.4 42.4 1.0
CAF A:R8J1421 4.4 0.6 1.0
CG A:HIS374 4.4 47.9 1.0
CB A:ASP315 4.5 37.7 1.0
CAO A:R8J1421 4.6 94.0 1.0
CA A:ASP315 4.7 37.0 1.0
N A:ASP315 4.7 37.0 1.0

Manganese binding site 2 out of 3 in 5a3u

Go back to Manganese Binding Sites List in 5a3u
Manganese binding site 2 out of 3 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1405

b:52.6
occ:1.00
 NAM B:R8J1406 2.1 0.1 1.0
OD1 B:ASP315 2.3 57.4 1.0
NE2 B:HIS313 2.4 48.5 1.0
NAK B:R8J1406 2.5 76.8 1.0
CE1 B:HIS374 2.5 51.6 1.0
NAT B:R8J1406 2.8 97.5 1.0
NE2 B:HIS374 2.9 51.7 1.0
CAP B:R8J1406 3.0 82.4 1.0
CE1 B:HIS313 3.1 45.9 1.0
CAI B:R8J1406 3.1 0.6 1.0
CG B:ASP315 3.2 56.6 1.0
OD2 B:ASP315 3.4 52.5 1.0
CD2 B:HIS313 3.5 49.7 1.0
CAH B:R8J1406 3.6 72.2 1.0
ND1 B:HIS374 3.7 47.8 1.0
CAR B:R8J1406 4.0 0.3 1.0
CAQ B:R8J1406 4.1 0.3 1.0
CD2 B:HIS374 4.2 48.2 1.0
ND1 B:HIS313 4.3 43.2 1.0
CAF B:R8J1406 4.4 75.5 1.0
CG B:HIS313 4.5 45.0 1.0
CG B:HIS374 4.5 47.2 1.0
CB B:ASP315 4.6 59.2 1.0
CAO B:R8J1406 4.8 68.0 1.0
CA B:ASP315 4.9 59.6 1.0
N B:ASP315 5.0 57.3 1.0

Manganese binding site 3 out of 3 in 5a3u

Go back to Manganese Binding Sites List in 5a3u
Manganese binding site 3 out of 3 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 6-(5-Oxo-4-(1H- 1,2,3-Triazol-1-Yl)-2,5-Dihydro-1H-Pyrazol-1-Yl)Nicotinic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1406

b:76.4
occ:1.00
 NAK C:R8J1407 1.9 0.4 1.0
NE2 C:HIS374 2.5 47.9 1.0
OD1 C:ASP315 2.5 47.2 1.0
CAP C:R8J1407 2.7 0.5 1.0
NAT C:R8J1407 2.7 0.2 1.0
NAM C:R8J1407 2.8 0.6 1.0
NE2 C:HIS313 2.9 54.4 1.0
CAH C:R8J1407 3.0 1.0 1.0
CE1 C:HIS313 3.1 52.4 1.0
CD2 C:HIS374 3.3 43.3 1.0
CG C:ASP315 3.4 43.0 1.0
CE1 C:HIS374 3.5 49.3 1.0
CAR C:R8J1407 3.6 0.7 1.0
CAI C:R8J1407 3.6 0.9 1.0
OD2 C:ASP315 3.7 39.7 1.0
CAF C:R8J1407 4.0 0.7 1.0
CD2 C:HIS313 4.1 54.2 1.0
CAQ C:R8J1407 4.1 0.8 1.0
CAO C:R8J1407 4.2 0.1 1.0
ND1 C:HIS313 4.3 50.6 1.0
OAB C:R8J1407 4.3 0.4 1.0
CG C:HIS374 4.4 45.3 1.0
ND1 C:HIS374 4.5 48.4 1.0
CAE C:R8J1407 4.6 0.1 1.0
CG C:HIS313 4.8 51.8 1.0
CB C:ASP315 4.8 42.8 1.0

Reference:

M.C.Chan, O.Atasoylu, E.Hodson, A.Tumber, I.K.H.Leung, R.Chowdhury, V.Gomez-Perez, M.Demetriades, A.M.Rydzik, J.Holt-Martyn, Y.Tian, T.Bishop, T.D.W.Claridge, A.Kawamura, C.W.Pugh, P.J.Ratcliffe, C.J.Schofield. Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain. Plos One V. 10 32004 2015.
ISSN: ESSN 1932-6203
PubMed: 26147748
DOI: 10.1371/JOURNAL.PONE.0132004
Page generated: Sat Oct 5 23:20:35 2024

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