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Magnesium in PDB 1d6n: Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding

Enzymatic activity of Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding

All present enzymatic activity of Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding:
2.4.2.8;

Protein crystallography data

The structure of Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding, PDB code: 1d6n was solved by G.K.Balendiran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 129.560, 65.850, 51.460, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding (pdb code 1d6n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding, PDB code: 1d6n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1d6n

Go back to Magnesium Binding Sites List in 1d6n
Magnesium binding site 1 out of 2 in the Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg313

b:2.0
occ:1.00
 O2 A:PRP312 2.0 2.0 1.0
O3 A:PRP312 2.2 2.0 1.0
O A:HOH989 2.3 2.0 1.0
O1B A:PRP312 2.5 2.0 1.0
O A:HOH990 2.6 2.0 1.0
OD2 A:ASP134 2.7 2.0 1.0
C3 A:PRP312 2.8 2.0 1.0
C2 A:PRP312 2.8 2.0 1.0
OE2 A:GLU133 3.0 2.0 1.0
N A:ASP134 3.3 2.0 1.0
CD A:GLU133 3.4 2.0 1.0
CG A:ASP134 3.4 2.0 1.0
CG A:GLU133 3.8 2.0 1.0
N A:ILE135 3.9 2.0 1.0
CA A:GLU133 3.9 2.0 1.0
CB A:GLU133 3.9 2.0 1.0
O3A A:PRP312 4.0 4.4 1.0
O A:ILE135 4.0 2.0 1.0
PB A:PRP312 4.0 4.1 1.0
C A:GLU133 4.0 2.0 1.0
CB A:ASP134 4.0 2.0 1.0
C4 A:PRP312 4.1 2.0 1.0
OE1 A:GLU133 4.1 2.2 1.0
OD1 A:ASP134 4.1 2.0 1.0
CA A:ASP134 4.1 2.0 1.0
C1 A:PRP312 4.2 2.0 1.0
O2B A:PRP312 4.2 2.8 1.0
O1A A:PRP312 4.2 2.0 1.0
CG2 A:ILE135 4.3 2.0 1.0
PA A:PRP312 4.4 4.0 1.0
C A:ASP134 4.5 2.0 1.0
O1 A:PRP312 4.6 2.0 1.0
C A:ILE135 4.7 2.0 1.0
O4 A:PRP312 4.8 2.0 1.0
CA A:ILE135 4.8 2.0 1.0
CB A:VAL66 4.9 2.0 1.0
CG1 A:VAL66 4.9 2.0 1.0
C5 A:PRP312 5.0 2.0 1.0

Magnesium binding site 2 out of 2 in 1d6n

Go back to Magnesium Binding Sites List in 1d6n
Magnesium binding site 2 out of 2 in the Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg315

b:2.0
occ:1.00
 O2 B:PRP314 1.8 2.0 1.0
O B:HOH991 2.2 2.0 1.0
O B:HOH992 2.3 2.0 1.0
O3 B:PRP314 2.4 2.0 1.0
OE2 B:GLU133 2.5 2.0 1.0
C2 B:PRP314 2.7 2.0 1.0
OD2 B:ASP134 2.8 2.0 1.0
C3 B:PRP314 2.8 2.0 1.0
CD B:GLU133 2.9 2.0 1.0
CG B:GLU133 3.3 2.0 1.0
CG1 B:VAL66 3.3 2.0 1.0
OE1 B:GLU133 3.7 2.2 1.0
CG B:ASP134 3.9 2.0 1.0
CB B:VAL66 4.0 2.0 1.0
C1 B:PRP314 4.1 2.0 1.0
O B:LEU67 4.1 2.0 1.0
C4 B:PRP314 4.2 2.0 1.0
OD1 B:ASP134 4.3 2.0 1.0
CB B:GLU133 4.3 2.0 1.0
O1 B:PRP314 4.6 2.0 1.0
O B:VAL66 4.6 2.0 1.0
O4 B:PRP314 4.8 2.0 1.0
C B:VAL66 4.9 2.0 1.0
O B:ILE135 4.9 2.0 1.0
N B:ASP134 4.9 2.0 1.0
CG2 B:VAL66 5.0 2.0 1.0
PA B:PRP314 5.0 4.0 1.0

Reference:

G.K.Balendiran, J.A.Molina, Y.Xu, J.Torres-Martinez, R.Stevens, P.J.Focia, A.E.Eakin, J.C.Sacchettini, S.P.Craig Iii. Ternary Complex Structure of Human Hgprtase, Prpp, MG2+, and the Inhibitor Hpp Reveals the Involvement of the Flexible Loop in Substrate Binding. Protein Sci. V. 8 1023 1999.
ISSN: ISSN 0961-8368
PubMed: 10338013
Page generated: Tue Aug 13 02:36:16 2024

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