Magnesium in PDB 1dy3: Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue.

All present enzymatic activity of Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue.:
2.7.6.3;

The structure of Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue., PDB code: 1dy3 was solved by D.K.Stammers, A.Achari, D.O.Somers, P.K.Bryant, J.Rosemond, D.L.Scott, J.N.Champness, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.0 / 2.0
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	40.960, 69.010, 115.490, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / n/a

The binding sites of Magnesium atom in the Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue. (pdb code 1dy3). 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 of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue., PDB code: 1dy3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:17.3 occ:1.00 O2B A:ATP200 2.4 15.1 1.0 OD2 A:ASP97 2.4 17.0 1.0 OD2 A:ASP95 2.5 9.3 1.0 O A:HOH2141 2.6 14.8 1.0 O1G A:ATP200 2.6 14.0 1.0 O16 A:87Y201 2.6 20.0 1.0 CG A:ASP97 3.2 13.8 1.0 OD1 A:ASP97 3.4 11.4 1.0 PB A:ATP200 3.5 17.7 1.0 CG A:ASP95 3.5 12.8 1.0 PG A:ATP200 3.6 15.0 1.0 MG A:MG203 3.6 23.6 1.0 O3B A:ATP200 3.7 15.8 1.0 NH1 A:ARG121 3.8 11.5 1.0 OD1 A:ASP95 3.9 11.6 1.0 C15 A:87Y201 4.0 16.8 1.0 O1B A:ATP200 4.1 20.6 1.0 O A:HOH2085 4.1 10.0 1.0 O3G A:ATP200 4.2 16.2 1.0 O A:HOH2084 4.2 11.8 1.0 CE1 A:HIS115 4.3 16.0 1.0 NH1 A:ARG92 4.3 13.4 1.0 N10 A:87Y201 4.5 12.7 1.0 CE A:MET124 4.5 15.7 1.0 CB A:ASP97 4.6 8.2 1.0 C12 A:87Y201 4.7 13.5 1.0 O A:HOH2136 4.7 18.3 1.0 O A:HOH2055 4.7 17.4 1.0 O3A A:ATP200 4.8 15.2 1.0 CB A:ASP95 4.8 5.4 1.0 O2G A:ATP200 4.9 13.5 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:23.6 occ:1.00 OD1 A:ASP97 2.3 11.4 1.0 O2B A:ATP200 2.4 15.1 1.0 OD1 A:ASP95 2.4 11.6 1.0 O A:HOH2068 2.4 9.9 1.0 O1A A:ATP200 2.5 11.5 1.0 O A:HOH2136 2.5 18.3 1.0 CG A:ASP95 3.3 12.8 1.0 CG A:ASP97 3.3 13.8 1.0 PA A:ATP200 3.3 17.5 1.0 OD2 A:ASP95 3.5 9.3 1.0 PB A:ATP200 3.5 17.7 1.0 MG A:MG202 3.6 17.3 1.0 OD2 A:ASP97 3.7 17.0 1.0 O3A A:ATP200 3.7 15.2 1.0 O5' A:ATP200 3.8 20.5 1.0 NH2 A:ARG84 3.9 38.0 1.0 O A:LEU96 4.2 10.9 1.0 OE2 A:GLU77 4.2 13.9 1.0 O1B A:ATP200 4.3 20.6 1.0 NH1 A:ARG82 4.3 13.1 1.0 O A:HOH2140 4.4 16.2 1.0 C5' A:ATP200 4.4 21.2 1.0 C2 A:ATP200 4.5 15.3 1.0 O3G A:ATP200 4.5 16.2 1.0 C A:LEU96 4.5 10.6 1.0 N3 A:ATP200 4.6 14.9 1.0 CB A:ASP97 4.6 8.2 1.0 O2A A:ATP200 4.6 14.2 1.0 CB A:ASP95 4.7 5.4 1.0 CA A:ASP97 4.7 7.7 1.0 O3B A:ATP200 4.7 15.8 1.0 N A:LEU96 4.7 9.6 1.0 NH2 A:ARG82 4.7 17.8 1.0 N A:ASP97 4.7 8.7 1.0 O1G A:ATP200 4.9 14.0 1.0 PG A:ATP200 5.0 15.0 1.0 CA A:ASP95 5.0 8.2 1.0

D.K.Stammers, A.Achari, D.O.Somers, P.K.Bryant, J.Rosemond, D.L.Scott, J.N.Champness. 2.0A X-Ray Structure of the Ternary Complex of 7,8-Dihydro-6-Hydroxymethylpterinpyrophosphokinase From Escherichia Coli with Atp and A Substrate Analogue Febs Lett. V. 456 49 1999.
ISSN: ISSN 0014-5793
PubMed: 10452528
DOI: 10.1016/S0014-5793(99)00860-1