Atomistry » Magnesium » PDB 7pxh-7q7f » 7q5v
Atomistry »
  Magnesium »
    PDB 7pxh-7q7f »
      7q5v »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy