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Magnesium 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
Manganese (Mn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where 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:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7q5v

Go back to Magnesium Binding Sites List in 7q5v
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg510

b:56.1
occ:1.00
 HB2 A:GLN243 2.6 50.7 1.0
O A:ASP246 2.7 26.7 0.5
O A:ASP246 2.8 20.7 0.5
O A:LYS244 3.0 55.2 1.0
HG3 A:GLN243 3.2 47.1 1.0
HG2 A:GLN243 3.3 47.1 1.0
CB A:GLN243 3.5 42.2 1.0
C A:LYS244 3.5 38.5 1.0
CG A:GLN243 3.5 39.3 1.0
C A:SER245 3.5 20.9 1.0
N A:ASP246 3.6 21.6 0.5
HA A:SER245 3.6 26.4 1.0
N A:ASP246 3.6 22.3 0.5
H A:ASP246 3.6 25.9 0.5
O A:HOH606 3.6 30.6 1.0
H A:ASP246 3.6 26.8 0.5
O A:HOH694 3.6 23.2 0.5
C A:ASP246 3.7 21.5 0.5
N A:SER245 3.7 24.0 1.0
C A:ASP246 3.7 25.1 0.5
CA A:SER245 3.8 22.0 1.0
O A:HOH819 3.9 21.6 1.0
O A:SER245 4.0 24.2 1.0
O A:HOH662 4.1 19.6 1.0
HB3 A:GLN243 4.1 50.7 1.0
N A:LYS244 4.1 24.7 1.0
C A:GLN243 4.2 21.6 1.0
H A:SER245 4.2 28.8 1.0
CA A:ASP246 4.2 20.9 0.5
CA A:ASP246 4.3 22.6 0.5
H A:LYS244 4.3 29.7 1.0
CA A:LYS244 4.4 33.7 1.0
CA A:GLN243 4.4 25.9 1.0
O A:HOH694 4.6 16.3 0.5
O A:HOH728 4.6 23.1 1.0
HA A:SER247 4.6 24.6 1.0
HA A:GLN243 4.6 31.1 1.0
HB2 A:ASP246 4.7 28.6 0.5
O A:GLN243 4.7 25.6 1.0
HA A:LYS244 4.7 40.4 1.0
N A:SER247 4.8 20.4 1.0
HB2 A:ASP246 4.9 46.2 0.5
HA A:ASP246 5.0 27.2 0.5
O A:HOH674 5.0 26.9 1.0
HA A:ASP246 5.0 25.1 0.5

Magnesium binding site 2 out of 3 in 7q5v

Go back to Magnesium Binding Sites List in 7q5v
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg511

b:39.4
occ:1.00
 OD1 A:ASN284 2.2 17.9 0.5
HA A:ASN284 2.4 30.7 0.5
HA A:ASN284 2.4 30.9 0.5
HB A:ILE292 2.7 18.5 1.0
O A:ILE280 2.8 13.8 0.6
O A:HOH780 2.8 15.3 0.5
O A:ILE280 2.8 13.7 0.4
HG23 A:ILE280 2.9 21.0 0.4
O A:HOH780 3.0 24.9 0.5
HG23 A:ILE280 3.1 13.6 0.6
CA A:ASN284 3.2 25.6 0.5
CA A:ASN284 3.2 25.7 0.5
HB2 A:ASN284 3.2 33.8 0.5
HG22 A:ILE280 3.2 13.6 0.6
CG A:ASN284 3.3 17.9 0.5
HD22 A:ASN284 3.3 39.7 0.5
O A:HOH642 3.4 19.1 1.0
HG22 A:ILE280 3.4 21.0 0.4
N A:ASN284 3.4 24.1 0.5
N A:ASN284 3.5 28.7 0.5
HA A:ARG281 3.5 15.2 0.6
HD12 A:ILE292 3.5 23.6 1.0
HA A:ARG281 3.5 14.8 0.4
CG2 A:ILE280 3.6 17.5 0.4
CG2 A:ILE280 3.6 11.3 0.6
CB A:ILE292 3.6 15.4 1.0
C A:ILE280 3.7 13.2 0.6
H A:ASN284 3.7 28.9 0.5
C A:ILE280 3.7 11.5 0.4
CB A:ASN284 3.7 28.2 0.5
H A:ASN284 3.7 34.4 0.5
CB A:ASN284 3.7 23.7 0.5
H A:ILE292 3.8 16.6 1.0
C A:CYS283 3.9 19.5 1.0
O A:ILE292 4.0 21.9 1.0
HB2 A:CYS283 4.1 22.2 1.0
H A:GLY285 4.1 32.8 1.0
HG21 A:ILE280 4.1 21.0 0.4
ND2 A:ASN284 4.1 33.1 0.5
HB3 A:ASN284 4.2 28.4 0.5
O A:CYS283 4.2 21.3 1.0
HG21 A:ILE280 4.2 13.6 0.6
HG13 A:ILE292 4.2 22.8 1.0
CA A:ARG281 4.3 12.3 0.4
HG22 A:ILE292 4.3 25.1 1.0
CA A:ARG281 4.3 12.7 0.6
CG1 A:ILE292 4.3 19.0 1.0
O A:ARG281 4.3 12.5 0.4
N A:ARG281 4.3 13.9 0.4
CD1 A:ILE292 4.3 19.7 1.0
N A:ARG281 4.4 10.9 0.6
CG2 A:ILE292 4.4 20.9 1.0
HG21 A:ILE292 4.4 25.1 1.0
C A:ASN284 4.4 21.4 0.5
C A:ASN284 4.4 22.7 0.5
ND2 A:ASN284 4.4 16.3 0.5
CA A:ILE292 4.4 14.4 1.0
N A:ILE292 4.5 13.8 1.0
CG A:ASN284 4.5 28.7 0.5
HB3 A:ASN284 4.5 33.8 0.5
H A:CYS283 4.5 22.2 1.0
HB2 A:ASN284 4.5 28.4 0.5
HA A:ILE280 4.6 15.3 0.6
C A:ARG281 4.6 15.8 0.4
N A:GLY285 4.6 27.4 1.0
CA A:ILE280 4.6 12.8 0.6
HA A:ILE280 4.6 16.1 0.4
CA A:ILE280 4.6 13.4 0.4
HD21 A:ASN284 4.6 19.5 0.5
HD12 A:LEU287 4.6 21.8 1.0
C A:ILE292 4.6 17.7 1.0
CB A:ILE280 4.7 13.9 0.4
C A:ARG281 4.7 11.9 0.6
CB A:ILE280 4.7 12.2 0.6
CA A:CYS283 4.8 22.9 1.0
CB A:CYS283 4.8 18.5 1.0
O A:ARG281 4.8 15.1 0.6
HD21 A:ASN284 4.8 39.7 0.5
N A:CYS283 4.9 18.5 1.0
O A:HOH711 4.9 24.4 1.0
HD13 A:ILE292 4.9 23.6 1.0
HD11 A:ILE292 4.9 23.6 1.0

Magnesium binding site 3 out of 3 in 7q5v

Go back to Magnesium Binding Sites List in 7q5v
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg binding site number 3 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
B:Mg602

b:42.0
occ:1.00
 O B:HOH721 2.3 30.6 1.0
O B:GLN541 2.8 15.2 1.0
H B:GLN541 2.9 17.6 1.0
O A:HOH823 3.1 45.4 1.0
HB2 B:GLN541 3.2 22.7 1.0
N B:GLN541 3.5 14.7 1.0
CE1 B:PHE540 3.5 18.7 0.5
CZ B:PHE540 3.6 19.3 0.5
C B:GLN541 3.7 13.6 1.0
HE1 B:PHE540 3.8 22.5 0.5
CE1 B:PHE540 3.8 20.2 0.5
HZ B:PHE540 3.8 23.1 0.5
CD1 B:PHE540 3.8 21.6 0.5
CA B:GLN541 3.9 15.4 1.0
HE1 B:PHE540 3.9 24.3 0.5
CB B:GLN541 3.9 18.9 1.0
CD1 B:PHE540 4.0 13.9 0.5
CE2 B:PHE540 4.0 14.7 0.5
CZ B:PHE540 4.0 16.6 0.5
HA B:PHE540 4.1 18.7 0.5
CG B:PHE540 4.2 18.0 0.5
HD1 B:PHE540 4.2 16.6 0.5
CD2 B:PHE540 4.2 22.0 0.5
HD1 B:PHE540 4.2 25.9 0.5
HZ B:PHE540 4.3 19.9 0.5
HA B:PHE540 4.3 17.5 0.5
CG B:PHE540 4.3 14.3 0.5
CE2 B:PHE540 4.4 15.6 0.5
HE2 B:PHE540 4.4 17.6 0.5
C B:PHE540 4.5 13.6 0.5
HG2 B:GLN541 4.5 25.0 1.0
CD2 B:PHE540 4.5 14.2 0.5
C B:PHE540 4.5 13.2 0.5
HB3 B:GLN541 4.6 22.7 1.0
CA B:PHE540 4.8 15.6 0.5
HD2 B:PHE540 4.8 26.4 0.5
CG B:GLN541 4.8 20.8 1.0
CA B:PHE540 4.8 14.6 0.5
HA B:GLN541 4.8 18.4 1.0
HE2 B:PHE540 4.9 18.7 0.5
N B:LEU542 5.0 13.6 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: Thu Oct 3 04:58:05 2024

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