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Manganese in PDB 6zbn: Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4), PDB code: 6zbn was solved by W.D.Figg Jr, M.A.Mcdonough, Y.Nakashima, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.062, 75.472, 127.555, 90, 95.04, 90
R / Rfree (%) 20.5 / 23

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4) (pdb code 6zbn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4), PDB code: 6zbn:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6zbn

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Manganese binding site 1 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4)


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 Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:40.4
occ:1.00
 N10 A:QEE501 2.1 44.1 1.0
OD1 A:ASP315 2.2 42.0 1.0
NE2 A:HIS374 2.2 37.3 1.0
N13 A:QEE501 2.2 46.1 1.0
NE2 A:HIS313 2.3 41.1 1.0
O A:HOH616 2.4 40.2 1.0
N12 A:QEE501 2.9 41.0 1.0
C11 A:QEE501 2.9 51.2 1.0
CE1 A:HIS374 3.0 40.4 1.0
HE1 A:HIS374 3.0 48.7 1.0
CE1 A:HIS313 3.1 42.0 1.0
CG A:ASP315 3.1 44.7 1.0
C09 A:QEE501 3.1 48.4 1.0
HE1 A:HIS313 3.1 50.7 1.0
H091 A:QEE501 3.2 58.4 1.0
CD2 A:HIS374 3.3 42.8 1.0
OD2 A:ASP315 3.4 41.0 1.0
CD2 A:HIS313 3.4 44.8 1.0
C14 A:QEE501 3.4 43.5 1.0
HD2 A:HIS374 3.6 51.6 1.0
HD2 A:HIS313 3.6 54.1 1.0
H141 A:QEE501 3.8 52.5 1.0
O A:HOH647 4.0 42.1 1.0
C21 A:QEE501 4.2 47.5 1.0
ND1 A:HIS374 4.2 37.4 1.0
ND1 A:HIS313 4.2 44.3 1.0
C23 A:QEE501 4.3 48.2 1.0
HZ A:PHE366 4.3 49.6 1.0
HA A:ASP315 4.3 46.0 1.0
HZ2 A:TRP389 4.4 43.0 1.0
CG A:HIS374 4.4 38.3 1.0
C08 A:QEE501 4.4 40.9 1.0
CG A:HIS313 4.4 42.3 1.0
C15 A:QEE501 4.4 48.5 1.0
CB A:ASP315 4.5 41.3 1.0
CA A:ASP315 4.8 38.2 1.0
HG21 A:THR325 4.8 45.8 1.0
H A:ASP315 4.8 48.0 1.0
C24 A:QEE501 4.9 46.9 1.0
HD1 A:HIS374 4.9 43.4 1.0
HB3 A:ASP315 4.9 49.9 1.0
N A:ASP315 4.9 39.7 1.0
H231 A:QEE501 4.9 58.1 1.0
HD1 A:HIS313 5.0 53.4 1.0

Manganese binding site 2 out of 6 in 6zbn

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Manganese binding site 2 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4)


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 Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:50.3
occ:1.00
 OD1 B:ASP315 2.2 46.0 1.0
N13 B:QEE501 2.2 43.5 1.0
N10 B:QEE501 2.2 51.6 1.0
NE2 B:HIS374 2.2 51.7 1.0
O B:HOH617 2.2 53.6 1.0
NE2 B:HIS313 2.2 45.6 1.0
N12 B:QEE501 2.9 50.5 1.0
C11 B:QEE501 2.9 51.6 1.0
CE1 B:HIS313 3.1 46.5 1.0
CG B:ASP315 3.1 49.3 1.0
HE1 B:HIS313 3.2 54.4 1.0
C09 B:QEE501 3.2 48.9 1.0
CE1 B:HIS374 3.2 54.6 1.0
CD2 B:HIS374 3.2 49.3 1.0
H091 B:QEE501 3.3 59.0 1.0
CD2 B:HIS313 3.3 48.4 1.0
HE1 B:HIS374 3.3 65.8 1.0
C14 B:QEE501 3.3 49.5 1.0
HD2 B:HIS374 3.4 59.5 1.0
OD2 B:ASP315 3.4 47.3 1.0
HD2 B:HIS313 3.6 58.3 1.0
H141 B:QEE501 3.7 59.6 1.0
C21 B:QEE501 4.1 48.0 1.0
O B:HOH623 4.1 44.5 1.0
ND1 B:HIS313 4.2 50.7 1.0
HZ2 B:TRP389 4.3 54.1 1.0
C23 B:QEE501 4.3 51.8 1.0
ND1 B:HIS374 4.3 46.6 1.0
HA B:ASP315 4.3 59.5 1.0
C15 B:QEE501 4.4 47.3 1.0
CG B:HIS374 4.4 49.9 1.0
CG B:HIS313 4.4 51.0 1.0
HZ B:PHE366 4.4 54.1 1.0
C08 B:QEE501 4.5 49.1 1.0
CB B:ASP315 4.5 47.3 1.0
H B:ASP315 4.8 54.3 1.0
CA B:ASP315 4.8 49.4 1.0
HG21 B:THR325 4.8 59.2 1.0
N B:ASP315 4.9 45.0 1.0
C24 B:QEE501 4.9 45.5 1.0
H231 B:QEE501 4.9 62.4 1.0
HD1 B:HIS313 5.0 61.2 1.0
HB3 B:ASP315 5.0 57.1 1.0

Manganese binding site 3 out of 6 in 6zbn

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Manganese binding site 3 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4)


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 Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn503

b:36.9
occ:1.00
 N13 C:QEE501 2.1 36.9 1.0
OD1 C:ASP315 2.1 37.1 1.0
O C:HOH614 2.2 36.9 1.0
NE2 C:HIS374 2.2 37.7 1.0
N10 C:QEE501 2.2 36.9 1.0
NE2 C:HIS313 2.2 38.7 1.0
N12 C:QEE501 2.8 37.3 1.0
C11 C:QEE501 2.9 36.9 1.0
CE1 C:HIS313 3.1 42.8 1.0
CE1 C:HIS374 3.1 49.6 1.0
CG C:ASP315 3.2 38.6 1.0
HE1 C:HIS313 3.2 51.7 1.0
C09 C:QEE501 3.2 36.9 1.0
HE1 C:HIS374 3.2 59.8 1.0
CD2 C:HIS374 3.3 45.2 1.0
C14 C:QEE501 3.3 38.3 1.0
CD2 C:HIS313 3.3 45.9 1.0
H091 C:QEE501 3.3 44.6 1.0
HD2 C:HIS374 3.5 54.5 1.0
OD2 C:ASP315 3.5 35.9 1.0
HD2 C:HIS313 3.5 55.3 1.0
H141 C:QEE501 3.6 46.2 1.0
C21 C:QEE501 4.1 43.2 1.0
H31 C:GOL502 4.1 70.0 1.0
HZ C:PHE366 4.2 57.5 1.0
ND1 C:HIS313 4.2 48.5 1.0
O C:HOH642 4.3 36.9 1.0
ND1 C:HIS374 4.3 47.1 1.0
HA C:ASP315 4.3 51.6 1.0
C23 C:QEE501 4.3 51.3 1.0
C15 C:QEE501 4.3 36.9 1.0
HZ2 C:TRP389 4.3 51.5 1.0
CG C:HIS374 4.4 46.7 1.0
CG C:HIS313 4.4 42.7 1.0
C08 C:QEE501 4.5 41.6 1.0
CB C:ASP315 4.5 40.3 1.0
CA C:ASP315 4.8 42.7 1.0
HG21 C:THR325 4.8 45.6 1.0
H32 C:GOL502 4.9 70.0 1.0
H C:ASP315 4.9 53.2 1.0
C3 C:GOL502 4.9 58.1 1.0
H231 C:QEE501 4.9 61.8 1.0
C24 C:QEE501 4.9 46.4 1.0
HD1 C:HIS313 5.0 58.5 1.0
N C:ASP315 5.0 44.1 1.0
HD11 C:ILE327 5.0 55.2 1.0

Manganese binding site 4 out of 6 in 6zbn

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Manganese binding site 4 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn502

b:48.6
occ:1.00
 O D:HOH601 2.1 48.8 1.0
OD1 D:ASP315 2.2 47.3 1.0
N13 D:QEE501 2.2 51.0 1.0
NE2 D:HIS313 2.2 47.9 1.0
NE2 D:HIS374 2.2 51.2 1.0
N10 D:QEE501 2.2 37.2 1.0
N12 D:QEE501 2.9 48.0 1.0
C11 D:QEE501 3.0 39.0 1.0
CE1 D:HIS313 3.0 48.7 1.0
CE1 D:HIS374 3.1 55.1 1.0
HE1 D:HIS313 3.1 57.0 1.0
CG D:ASP315 3.2 49.8 1.0
C09 D:QEE501 3.2 47.8 1.0
CD2 D:HIS313 3.2 48.0 1.0
CD2 D:HIS374 3.2 52.0 1.0
HE1 D:HIS374 3.3 66.4 1.0
H091 D:QEE501 3.3 57.7 1.0
C14 D:QEE501 3.3 50.4 1.0
HD2 D:HIS374 3.4 60.9 1.0
HD2 D:HIS313 3.4 57.9 1.0
OD2 D:ASP315 3.5 48.2 1.0
H141 D:QEE501 3.7 60.7 1.0
C21 D:QEE501 4.1 52.8 1.0
ND1 D:HIS313 4.2 47.9 1.0
O D:HOH618 4.2 46.0 1.0
ND1 D:HIS374 4.3 50.9 1.0
HZ2 D:TRP389 4.3 62.6 1.0
CG D:HIS313 4.3 46.5 1.0
C23 D:QEE501 4.3 46.0 1.0
HA D:ASP315 4.3 61.7 1.0
HZ D:PHE366 4.3 64.9 1.0
C15 D:QEE501 4.4 56.3 1.0
CG D:HIS374 4.4 51.8 1.0
C08 D:QEE501 4.5 47.3 1.0
CB D:ASP315 4.5 50.0 1.0
CA D:ASP315 4.8 51.2 1.0
HG21 D:THR325 4.8 65.7 1.0
H D:ASP315 4.9 60.6 1.0
HD1 D:HIS313 4.9 56.2 1.0
C24 D:QEE501 5.0 48.3 1.0
H231 D:QEE501 5.0 55.4 1.0
N D:ASP315 5.0 50.2 1.0

Manganese binding site 5 out of 6 in 6zbn

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Manganese binding site 5 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn502

b:51.1
occ:1.00
 N13 E:QEE501 2.1 55.6 1.0
N10 E:QEE501 2.1 54.3 1.0
NE2 E:HIS374 2.2 56.3 1.0
OD1 E:ASP315 2.2 57.5 1.0
NE2 E:HIS313 2.3 57.3 1.0
O E:HOH601 2.3 53.3 1.0
N12 E:QEE501 2.8 50.4 1.0
C11 E:QEE501 2.9 52.3 1.0
CE1 E:HIS374 3.0 56.9 1.0
CE1 E:HIS313 3.1 57.5 1.0
HE1 E:HIS374 3.1 68.5 1.0
C09 E:QEE501 3.1 52.1 1.0
CG E:ASP315 3.1 58.3 1.0
HE1 E:HIS313 3.2 67.6 1.0
CD2 E:HIS374 3.2 56.2 1.0
H091 E:QEE501 3.2 62.9 1.0
C14 E:QEE501 3.3 48.5 1.0
CD2 E:HIS313 3.3 60.4 1.0
OD2 E:ASP315 3.4 59.9 1.0
HD2 E:HIS374 3.5 66.0 1.0
HD2 E:HIS313 3.6 72.8 1.0
H141 E:QEE501 3.7 58.5 1.0
C21 E:QEE501 4.1 48.1 1.0
ND1 E:HIS374 4.2 55.8 1.0
O E:HOH614 4.2 56.5 1.0
C23 E:QEE501 4.2 49.2 1.0
ND1 E:HIS313 4.3 56.7 1.0
HZ2 E:TRP389 4.3 71.8 1.0
CG E:HIS374 4.3 55.9 1.0
C15 E:QEE501 4.3 56.3 1.0
HZ E:PHE366 4.4 75.7 1.0
HA E:ASP315 4.4 72.0 1.0
CG E:HIS313 4.4 55.9 1.0
C08 E:QEE501 4.4 47.4 1.0
CB E:ASP315 4.5 57.1 1.0
H E:ASP315 4.8 70.2 1.0
CA E:ASP315 4.9 59.8 1.0
C24 E:QEE501 4.9 52.6 1.0
H231 E:QEE501 4.9 59.3 1.0
HG21 E:THR325 4.9 75.9 1.0
HD1 E:HIS374 4.9 65.6 1.0
HD11 E:ILE327 4.9 80.4 1.0
HB3 E:ASP315 5.0 67.1 1.0
N E:ASP315 5.0 58.3 1.0
HD1 E:HIS313 5.0 66.6 1.0

Manganese binding site 6 out of 6 in 6zbn

Go back to Manganese Binding Sites List in 6zbn
Manganese binding site 6 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with Tert-Butyl 6-(5- Hydroxy-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-1-Yl)Nicotinate (IOX4) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn502

b:65.9
occ:1.00
 O F:HOH605 2.2 54.9 1.0
OD1 F:ASP315 2.2 55.9 1.0
N13 F:QEE501 2.2 53.6 1.0
NE2 F:HIS374 2.2 51.8 1.0
NE2 F:HIS313 2.2 52.7 1.0
N10 F:QEE501 2.3 57.6 1.0
N12 F:QEE501 2.9 43.5 1.0
C11 F:QEE501 3.0 42.8 1.0
CE1 F:HIS313 3.0 43.0 1.0
CE1 F:HIS374 3.1 42.8 1.0
HE1 F:HIS313 3.1 50.2 1.0
CG F:ASP315 3.2 50.9 1.0
HE1 F:HIS374 3.2 50.0 1.0
CD2 F:HIS374 3.2 45.3 1.0
C09 F:QEE501 3.2 50.5 1.0
CD2 F:HIS313 3.3 43.4 1.0
H091 F:QEE501 3.3 60.9 1.0
C14 F:QEE501 3.4 43.1 1.0
HD2 F:HIS374 3.4 54.6 1.0
OD2 F:ASP315 3.5 55.2 1.0
HD2 F:HIS313 3.6 50.6 1.0
H141 F:QEE501 3.7 52.0 1.0
C21 F:QEE501 4.2 52.1 1.0
ND1 F:HIS313 4.2 49.6 1.0
ND1 F:HIS374 4.2 48.3 1.0
O F:HOH616 4.2 55.0 1.0
HZ F:PHE366 4.3 57.5 1.0
HA F:ASP315 4.3 63.0 1.0
CG F:HIS374 4.3 48.5 1.0
CG F:HIS313 4.3 43.9 1.0
C23 F:QEE501 4.4 51.6 1.0
C15 F:QEE501 4.4 48.0 1.0
HZ2 F:TRP389 4.4 65.9 1.0
C08 F:QEE501 4.5 53.2 1.0
CB F:ASP315 4.5 52.5 1.0
HG21 F:THR325 4.8 65.4 1.0
CA F:ASP315 4.8 52.3 1.0
H F:ASP315 4.8 57.9 1.0
HD1 F:HIS313 4.9 59.9 1.0
N F:ASP315 5.0 48.0 1.0
HD11 F:ILE327 5.0 58.7 1.0
C24 F:QEE501 5.0 50.5 1.0
HD1 F:HIS374 5.0 58.2 1.0

Reference:

W.D.Figg Jr, Y.Nakashima, M.A.Mcdonough, J.P.Holt-Martyn, A.Krajnc, C.J.Schofield. Co-Crystal Structure of PHD2 with Molidustat and IOX4 Chemmedchem 2021.
ISSN: ESSN 1860-7187
DOI: 10.1002/CMDC.202100133
Page generated: Sun Oct 6 07:58:12 2024

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