Manganese in PDB 7q5v: Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542), PDB code: 7q5v was solved by W.D.Figg Jr, M.A.Mcdonough, R.Chowdhury, Y.Nakashima, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.88 / 1.17
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 130.914, 38.322, 42.88, 90, 90, 90
R / Rfree (%) 15.7 / 17.9

Other elements in 7q5v:

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Magnesium (Mg) 3 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542) (pdb code 7q5v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542), PDB code: 7q5v:

Manganese binding site 1 out of 1 in 7q5v

Go back to Manganese Binding Sites List in 7q5v
Manganese binding site 1 out of 1 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542)


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 N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:9.3
occ:1.00
 OD1 A:ASP315 2.1 9.9 1.0
O1 A:OGA502 2.2 13.8 1.0
NE2 A:HIS374 2.2 9.8 1.0
O2' A:OGA502 2.2 12.5 1.0
NE2 A:HIS313 2.2 9.4 1.0
O A:HOH654 2.2 11.6 1.0
C2 A:OGA502 2.7 15.7 1.0
C1 A:OGA502 2.8 16.5 1.0
CE1 A:HIS313 3.0 9.5 1.0
CE1 A:HIS374 3.1 9.8 1.0
CG A:ASP315 3.2 9.4 1.0
HE1 A:HIS313 3.2 11.4 1.0
CD2 A:HIS374 3.2 9.7 1.0
CD2 A:HIS313 3.2 9.9 1.0
HE1 A:HIS374 3.3 11.7 1.0
HD2 A:HIS374 3.4 11.6 1.0
HG3 B:PRO531 3.4 14.1 1.0
HD2 A:HIS313 3.5 11.8 1.0
OD2 A:ASP315 3.5 10.1 1.0
N1 A:OGA502 4.0 17.4 1.0
HZ A:PHE366 4.0 13.3 1.0
O2 A:OGA502 4.0 17.5 1.0
HD3 B:PRO531 4.1 13.1 1.0
ND1 A:HIS313 4.2 10.7 1.0
HZ2 A:TRP389 4.2 13.7 1.0
ND1 A:HIS374 4.2 10.5 1.0
O A:HOH717 4.3 14.9 1.0
HA A:ASP315 4.3 11.8 1.0
CG B:PRO531 4.3 11.8 1.0
CG A:HIS374 4.3 10.1 1.0
CG A:HIS313 4.3 11.2 1.0
H4C2 A:OGA502 4.4 21.6 1.0
CB A:ASP315 4.5 10.0 1.0
C4 A:OGA502 4.6 18.0 1.0
HE2 A:TYR310 4.6 12.4 1.0
H4C1 A:OGA502 4.6 21.6 1.0
CD B:PRO531 4.6 10.9 1.0
H1 A:OGA502 4.7 20.9 1.0
CE2 A:TYR310 4.8 10.3 1.0
CA A:ASP315 4.8 9.8 1.0
HG2 B:PRO531 4.8 14.1 1.0
HG21 A:THR325 4.8 12.2 1.0
CZ A:PHE366 4.9 11.1 1.0
HD2 B:PRO531 4.9 13.1 1.0
HB3 B:PRO531 4.9 13.5 1.0
HE1 A:PHE366 4.9 13.5 1.0
HD1 A:HIS313 4.9 12.8 1.0
N A:ASP315 5.0 9.4 1.0
H A:ASP315 5.0 11.3 1.0

Reference:

W.D.Figg Jr, M.A.Mcdonough, R.Chowdhury, Y.Nakashima, C.J.Schofield. Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with N-Oxalylglycine (Nog) and Hif-2 Alpha Codd (523-542) To Be Published.
Page generated: Fri Apr 7 12:20:21 2023

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