Magnesium in PDB 8q6e: Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide

Enzymatic activity of Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide

All present enzymatic activity of Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide:
1.14.11.29;

Protein crystallography data

The structure of Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide, PDB code: 8q6e was solved by G.Fiorini, W.D.Figg Jr, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.77 / 1.37
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 130.9, 38.12, 42.77, 90, 90, 90
R / Rfree (%) 18 / 20.5

Other elements in 8q6e:

The structure of Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide (pdb code 8q6e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide, PDB code: 8q6e:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 8q6e

Go back to Magnesium Binding Sites List in 8q6e
Magnesium binding site 1 out of 3 in the Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:26.4
occ:0.00
 H A:TRP258 2.4 23.4 1.0
HD1 A:TRP258 2.8 23.9 1.0
HG1 A:THR257 3.1 28.8 1.0
HA A:THR257 3.2 24.2 1.0
OG1 A:THR257 3.2 24.0 1.0
HB2 A:TRP258 3.2 23.2 1.0
N A:TRP258 3.2 19.5 1.0
O A:HOH637 3.3 33.9 1.0
O A:HOH643 3.5 37.9 1.0
CD1 A:TRP258 3.6 19.9 1.0
O A:HOH615 3.6 32.6 1.0
CA A:THR257 3.9 20.1 1.0
CB A:TRP258 3.9 19.3 1.0
C A:THR257 4.0 19.6 1.0
CA A:TRP258 4.1 18.6 1.0
CB A:THR257 4.1 24.9 1.0
CG A:TRP258 4.1 17.8 1.0
O A:TRP258 4.2 21.0 1.0
HD12 A:ILE256 4.5 36.6 1.0
HB A:THR257 4.6 29.9 1.0
C A:TRP258 4.6 17.4 1.0
HB3 A:TRP258 4.8 23.2 1.0
NE1 A:TRP258 4.8 20.5 1.0
HA A:TRP258 4.9 22.4 1.0
HE1 A:TRP258 5.0 24.6 1.0

Magnesium binding site 2 out of 3 in 8q6e

Go back to Magnesium Binding Sites List in 8q6e
Magnesium binding site 2 out of 3 in the Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:28.7
occ:0.00
 O A:VAL338 3.3 33.0 1.0
H A:GLY340 3.4 29.7 1.0
HA2 A:GLY340 3.4 33.0 1.0
HE2 A:TYR380 3.4 41.9 1.0
HD2 A:TYR380 3.4 37.4 1.0
HA3 A:GLY340 3.5 33.0 1.0
N A:GLY340 3.5 24.8 1.0
CA A:GLY340 3.6 27.4 1.0
C A:VAL338 3.7 29.3 1.0
O A:LYS337 3.8 33.2 1.0
O A:HOH723 3.9 29.1 1.0
CE2 A:TYR380 4.0 34.9 1.0
HA A:VAL338 4.0 33.6 1.0
CD2 A:TYR380 4.0 31.2 1.0
O A:ALA336 4.0 27.6 1.0
O A:HOH661 4.1 23.3 1.0
C A:SER339 4.2 26.3 1.0
C A:LYS337 4.3 32.4 1.0
CA A:VAL338 4.3 28.0 1.0
N A:SER339 4.3 24.4 1.0
N A:VAL338 4.5 28.1 1.0
CA A:SER339 4.7 24.2 1.0
HA A:SER339 4.7 29.1 1.0
H A:SER339 4.8 29.3 0.5
H A:SER339 4.8 29.3 0.5
O A:SER339 4.8 26.4 1.0
HA A:LYS337 5.0 33.3 1.0

Magnesium binding site 3 out of 3 in 8q6e

Go back to Magnesium Binding Sites List in 8q6e
Magnesium binding site 3 out of 3 in the Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Aerobic Crystal Structure of Hif Prolyl Hydroxylase 2 (PHD2 181-407) in Complex with Fe(III), 2-Oxoglutarate (2OG) and HIF2ALPHA-Codd Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:33.5
occ:0.00
 HE3 A:LYS234 3.4 47.5 1.0
HD2 A:LYS234 3.6 36.1 1.0
HD22 A:LEU229 3.9 28.9 1.0
HG3 A:LYS234 4.0 33.4 1.0
O A:HOH606 4.0 41.7 1.0
HG2 A:GLU263 4.0 38.3 1.0
HD21 A:LEU229 4.0 28.9 1.0
O A:HOH643 4.1 37.9 1.0
HD11 A:ILE259 4.2 31.1 1.0
HD13 A:ILE259 4.2 31.1 1.0
CE A:LYS234 4.2 39.5 1.0
CD A:LYS234 4.2 30.0 1.0
CD2 A:LEU229 4.3 24.1 1.0
HD23 A:LEU229 4.3 28.9 1.0
HD12 A:ILE259 4.5 31.1 1.0
CD1 A:ILE259 4.5 25.9 1.0
HG A:CYS266 4.6 37.7 1.0
CG A:LYS234 4.6 27.8 1.0
HB3 A:GLU263 4.6 35.4 1.0
HB3 A:LYS234 4.7 30.1 1.0
HZ3 A:LYS234 4.8 57.9 1.0
CG A:GLU263 4.9 31.9 1.0
HE2 A:LYS234 4.9 47.5 1.0
O A:HOH727 5.0 43.4 1.0

Reference:

G.Fiorini, W.D.Figg Jr, C.J.Schofield. Hif Prolyl Hydroxylase 2 in Complex with HIF2ALPHA-Codd To Be Published.
Page generated: Fri Oct 4 16:34:26 2024

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