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Magnesium in PDB 7q5x: Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542)

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

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) 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 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542), PDB code: 7q5x 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) 42.75 / 1.21
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 130.454, 38.175, 42.751, 90, 90, 90
R / Rfree (%) 15.7 / 17.6

Other elements in 7q5x:

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

Chlorine (Cl) 3 atoms
Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542) (pdb code 7q5x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542), PDB code: 7q5x:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7q5x

Go back to Magnesium Binding Sites List in 7q5x
Magnesium binding site 1 out of 3 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg515

b:47.9
occ:1.00
 H A:TRP258 2.4 15.1 1.0
HG1 A:THR257 2.6 22.8 1.0
HD1 A:TRP258 2.8 18.0 1.0
O2 A:FMT513 2.9 33.2 0.5
HB2 A:TRP258 3.2 15.5 1.0
OG1 A:THR257 3.2 19.0 1.0
HA A:THR257 3.2 16.4 1.0
N A:TRP258 3.2 12.6 1.0
C A:FMT513 3.3 31.2 0.5
O1 A:FMT513 3.5 30.3 0.5
O A:HOH669 3.5 43.1 1.0
O A:HOH628 3.6 49.8 1.0
CD1 A:TRP258 3.6 15.0 1.0
H A:FMT513 3.7 52.2 0.5
C A:FMT513 3.8 43.5 0.5
CB A:TRP258 3.9 12.9 1.0
CA A:THR257 3.9 13.7 1.0
O2 A:FMT513 3.9 42.8 0.5
H A:FMT513 4.0 37.5 0.5
C A:THR257 4.1 13.2 1.0
CA A:TRP258 4.1 12.7 1.0
CB A:THR257 4.1 15.5 1.0
CG A:TRP258 4.1 14.5 1.0
O A:TRP258 4.2 14.9 1.0
O1 A:FMT513 4.5 43.1 0.5
HD12 A:ILE256 4.5 25.1 0.7
HB A:THR257 4.5 18.6 1.0
C A:TRP258 4.6 12.8 1.0
HB3 A:TRP258 4.7 15.5 1.0
O2 A:FMT509 4.7 39.3 0.4
NE1 A:TRP258 4.7 16.5 1.0
O B:HOH701 4.8 40.3 1.0
HA A:TRP258 4.9 15.3 1.0
HE1 A:TRP258 5.0 19.8 1.0

Magnesium binding site 2 out of 3 in 7q5x

Go back to Magnesium Binding Sites List in 7q5x
Magnesium binding site 2 out of 3 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg516

b:45.0
occ:1.00
 HA2 A:GLY340 3.4 21.6 1.0
H A:GLY340 3.6 20.3 1.0
O A:LYS337 3.6 26.6 1.0
HE2 A:TYR380 3.6 29.6 1.0
HA3 A:GLY340 3.7 21.6 1.0
O A:HOH652 3.7 24.9 1.0
N A:GLY340 3.8 16.9 1.0
CA A:GLY340 3.8 18.0 1.0
O A:VAL338 3.9 23.9 0.5
O A:HOH637 3.9 19.0 1.0
O A:ALA336 3.9 20.0 1.0
HD2 A:TYR380 3.9 27.5 1.0
HA A:VAL338 4.1 23.8 0.5
C A:LYS337 4.2 22.6 1.0
C A:VAL338 4.3 20.0 0.5
O A:VAL338 4.3 23.9 0.5
CE2 A:TYR380 4.3 24.7 1.0
C A:VAL338 4.3 22.4 0.5
CD2 A:TYR380 4.5 22.9 1.0
HA A:VAL338 4.5 27.2 0.5
CA A:VAL338 4.6 19.8 0.5
HA A:LYS337 4.6 23.9 1.0
C A:SER339 4.7 16.7 1.0
N A:VAL338 4.7 19.3 0.5
N A:VAL338 4.7 20.5 0.5
CA A:VAL338 4.7 22.7 0.5
N A:SER339 4.8 18.3 1.0
O A:HOH660 4.8 18.3 1.0
CA A:LYS337 5.0 19.9 1.0

Magnesium binding site 3 out of 3 in 7q5x

Go back to Magnesium Binding Sites List in 7q5x
Magnesium binding site 3 out of 3 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 2-Oxoglutarate (2OG) and Hif-2 Alpha Codd (523-542) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg517

b:46.9
occ:1.00
 HD2 A:LYS234 3.7 34.0 1.0
HD21 A:LEU229 3.9 23.6 1.0
HE3 A:LYS234 3.9 43.0 1.0
HD22 A:LEU229 3.9 23.6 1.0
HG3 A:LYS234 4.0 28.8 1.0
O A:HOH669 4.0 43.1 1.0
HG2 A:GLU263 4.0 35.6 1.0
HD11 A:ILE259 4.0 25.1 1.0
HD13 A:ILE259 4.2 25.1 1.0
HD23 A:LEU229 4.2 23.6 1.0
CD2 A:LEU229 4.2 19.7 1.0
HG A:CYS266 4.3 30.5 1.0
HD12 A:ILE259 4.4 25.1 1.0
CD1 A:ILE259 4.4 20.9 1.0
CD A:LYS234 4.4 28.3 1.0
HB3 A:GLU263 4.5 36.1 1.0
CE A:LYS234 4.6 35.8 1.0
CG A:LYS234 4.6 24.0 1.0
HB3 A:LYS234 4.7 23.8 1.0
HZ2 A:LYS234 4.7 71.0 1.0
CG A:GLU263 4.8 29.7 1.0
O A:HOH716 4.9 43.9 1.0
HB2 A:GLU263 5.0 36.1 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 2_OXOGLUTARATE (2OG) and Hif-2 Alpha Codd (523-542) To Be Published.
Page generated: Thu Oct 3 04:58:18 2024

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