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Magnesium in PDB 1eqm: Crystal Structure of Binary Complex of 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase with Adenosine-5'- Diphosphate

Enzymatic activity of Crystal Structure of Binary Complex of 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase with Adenosine-5'- Diphosphate

All present enzymatic activity of Crystal Structure of Binary Complex of 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase with Adenosine-5'- Diphosphate:
2.7.6.3;

Protein crystallography data

The structure of Crystal Structure of Binary Complex of 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase with Adenosine-5'- Diphosphate, PDB code: 1eqm was solved by B.Xiao, J.Blaszczyk, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 79.140, 52.800, 36.640, 90.00, 103.43, 90.00
R / Rfree (%) 19 / 26.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Binary Complex of 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase with Adenosine-5'- Diphosphate (pdb code 1eqm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Binary Complex of 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase with Adenosine-5'- Diphosphate, PDB code: 1eqm:

Magnesium binding site 1 out of 1 in 1eqm

Go back to Magnesium Binding Sites List in 1eqm
Magnesium binding site 1 out of 1 in the Crystal Structure of Binary Complex of 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase with Adenosine-5'- Diphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Binary Complex of 6-Hydroxymethyl-7,8- Dihydropterin Pyrophosphokinase with Adenosine-5'- Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg161

b:27.9
occ:1.00
 O1B A:ADP171 2.0 42.6 0.5
O1B A:ADP171 2.1 48.4 0.5
O3B A:ADP171 2.2 45.4 0.5
OE2 A:GLU77 2.6 14.5 1.0
PB A:ADP171 2.6 45.2 0.5
O A:HOH419 2.7 27.6 1.0
O A:LEU96 2.8 17.1 1.0
PB A:ADP171 3.0 48.1 0.5
O3B A:ADP171 3.1 27.8 0.5
O3A A:ADP171 3.3 49.0 0.5
O3A A:ADP171 3.3 37.9 0.5
CD A:GLU77 3.6 18.0 1.0
O A:HOH418 3.6 16.7 1.0
C A:LEU96 3.6 17.9 1.0
N A:LEU96 3.6 10.5 1.0
O A:HOH420 3.7 19.2 1.0
OD1 A:ASP97 3.8 27.8 1.0
OE1 A:GLU77 3.8 17.3 1.0
O2B A:ADP171 3.9 50.5 0.5
OD2 A:ASP97 4.0 26.4 1.0
CG A:ASP97 4.0 23.4 1.0
NH2 A:ARG92 4.1 36.7 1.0
CA A:LEU96 4.3 13.4 1.0
C A:ASP95 4.3 13.2 1.0
O2B A:ADP171 4.3 35.5 0.5
CA A:ASP95 4.3 14.4 1.0
C2 A:ADP171 4.3 12.2 0.5
CB A:ASP95 4.5 19.8 1.0
N A:ASP97 4.5 16.8 1.0
N3 A:ADP171 4.5 15.8 0.5
C5' A:ADP171 4.6 25.8 0.5
C2 A:ADP171 4.6 13.4 0.5
N3 A:ADP171 4.6 15.5 0.5
C5' A:ADP171 4.6 26.1 0.5
PA A:ADP171 4.7 40.8 0.5
O5' A:ADP171 4.7 32.5 0.5
CA A:ASP97 4.7 15.1 1.0
CZ A:ARG92 4.8 36.2 1.0
OD1 A:ASP95 4.8 35.6 1.0
PA A:ADP171 4.8 26.7 0.5
CG A:GLU77 4.9 12.5 1.0
O5' A:ADP171 5.0 22.6 0.5

Reference:

B.Xiao, G.Shi, J.Gao, J.Blaszczyk, Q.Liu, X.Ji, H.Yan. Unusual Conformational Changes in 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase As Revealed By X-Ray Crystallography and uc(Nmr). J.Biol.Chem. V. 276 40274 2001.
ISSN: ISSN 0021-9258
PubMed: 11546767
Page generated: Sat Aug 9 20:47:51 2025

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