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Magnesium in PDB 1dbr: Hypoxanthine Guanine Xanthine

Protein crystallography data

The structure of Hypoxanthine Guanine Xanthine, PDB code: 1dbr was solved by M.A.Schumacher, D.Carter, D.Roos, B.Ullman, R.G.Brennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.150, 109.220, 79.740, 90.00, 111.80, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hypoxanthine Guanine Xanthine (pdb code 1dbr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hypoxanthine Guanine Xanthine, PDB code: 1dbr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1dbr

Go back to Magnesium Binding Sites List in 1dbr
Magnesium binding site 1 out of 4 in the Hypoxanthine Guanine Xanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hypoxanthine Guanine Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg232

b:36.1
occ:1.00
OE1 A:GLU146 2.7 35.3 1.0
O A:HOH323 2.7 30.2 1.0
OD1 A:ASP147 2.8 35.4 1.0
O A:ILE148 3.4 22.3 1.0
O A:HOH239 3.4 32.8 1.0
CD A:GLU146 3.6 48.0 1.0
CG A:ASP147 3.7 39.9 1.0
OD2 A:ASP147 3.7 48.1 1.0
OE2 A:GLU146 3.8 39.0 1.0
CG2 A:ILE148 4.3 25.1 1.0
C A:ILE148 4.5 26.8 1.0
N A:ILE148 4.6 19.7 1.0
N A:ASP147 5.0 21.0 1.0

Magnesium binding site 2 out of 4 in 1dbr

Go back to Magnesium Binding Sites List in 1dbr
Magnesium binding site 2 out of 4 in the Hypoxanthine Guanine Xanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hypoxanthine Guanine Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg232

b:31.3
occ:1.00
OE1 B:GLU146 2.2 2.8 1.0
OD1 B:ASP147 2.5 25.9 1.0
CD B:GLU146 3.2 26.2 1.0
CG B:ASP147 3.5 28.7 1.0
OE2 B:GLU146 3.6 21.4 1.0
OD2 B:ASP147 3.8 34.4 1.0
N B:ASP147 4.2 14.9 1.0
CA B:GLY80 4.4 13.1 1.0
O B:ILE148 4.4 19.1 1.0
CG B:GLU146 4.5 20.2 1.0
N B:SER81 4.5 17.4 1.0
C B:GLY80 4.6 20.2 1.0
O B:HOH300 4.7 90.4 1.0
CG2 B:ILE77 4.7 18.6 1.0
O B:ILE77 4.7 25.8 1.0
CB B:GLU146 4.7 13.6 1.0
CA B:GLU146 4.7 10.5 1.0
CB B:ILE77 4.7 16.6 1.0
N B:ILE148 4.8 25.9 1.0
CB B:ASP147 4.8 12.9 1.0
CB B:SER81 4.8 22.0 1.0

Magnesium binding site 3 out of 4 in 1dbr

Go back to Magnesium Binding Sites List in 1dbr
Magnesium binding site 3 out of 4 in the Hypoxanthine Guanine Xanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hypoxanthine Guanine Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg232

b:63.7
occ:1.00
OD1 C:ASP147 2.7 56.6 1.0
OE1 C:GLU146 3.1 58.7 1.0
CG C:ASP147 3.5 54.1 1.0
OD2 C:ASP147 3.7 65.1 1.0
CA C:GLY80 3.9 53.5 1.0
O C:HOH233 3.9 100.0 1.0
CD C:GLU146 4.0 50.6 1.0
OE2 C:GLU146 4.2 48.5 1.0
C C:GLY80 4.2 60.8 1.0
OG C:SER81 4.3 65.4 1.0
O C:GLY80 4.5 59.1 1.0
N C:GLY80 4.5 53.2 1.0
CG2 C:ILE77 4.8 28.9 1.0
N C:SER81 4.8 60.3 1.0
CB C:ASP147 4.9 23.4 1.0
O C:ILE77 4.9 35.4 1.0
N C:ASP147 4.9 20.3 1.0

Magnesium binding site 4 out of 4 in 1dbr

Go back to Magnesium Binding Sites List in 1dbr
Magnesium binding site 4 out of 4 in the Hypoxanthine Guanine Xanthine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hypoxanthine Guanine Xanthine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg232

b:76.3
occ:1.00
OE1 D:GLU146 2.0 57.0 1.0
OD1 D:ASP147 2.5 79.2 1.0
CD D:GLU146 2.6 63.8 1.0
OE2 D:GLU146 2.7 64.8 1.0
CG D:ASP147 3.6 53.4 1.0
OD2 D:ASP147 3.8 57.3 1.0
O D:ILE148 3.9 24.9 1.0
CG D:GLU146 3.9 37.0 1.0
CB D:GLU146 4.3 31.1 1.0
OG D:SER81 4.4 23.6 1.0
N D:ASP147 4.4 23.7 1.0
CG2 D:ILE77 4.5 39.3 1.0
N D:ILE148 4.8 23.6 1.0
CB D:ILE77 4.8 40.6 1.0
CA D:GLU146 4.8 29.4 1.0
CB D:ASP147 4.9 23.9 1.0

Reference:

M.A.Schumacher, D.Carter, D.S.Ross, B.Ullman, R.G.Brennan. Crystal Structures of Toxoplasma Gondii Hgxprtase Reveal the Catalytic Role of A Long Flexible Loop. Nat.Struct.Biol. V. 3 881 1996.
ISSN: ISSN 1072-8368
PubMed: 8836106
DOI: 10.1038/NSB1096-881
Page generated: Mon Dec 14 05:50:19 2020

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