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Magnesium in PDB 2aky: High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer

Enzymatic activity of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer

All present enzymatic activity of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer:
2.7.4.3;

Protein crystallography data

The structure of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer, PDB code: 2aky was solved by U.Abele, G.E.Schulz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.000, 40.400, 45.500, 110.70, 108.80, 64.70
R / Rfree (%) 17.6 / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer (pdb code 2aky). 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 High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer, PDB code: 2aky:

Magnesium binding site 1 out of 1 in 2aky

Go back to Magnesium Binding Sites List in 2aky
Magnesium binding site 1 out of 1 in the High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:14.5
occ:1.00
 H2 A:HOH503 1.8 0.0 1.0
H2 A:HOH505 1.9 0.0 1.0
H1 A:HOH505 2.2 0.0 1.0
O2B A:AP5301 2.3 12.6 1.0
O A:HOH506 2.4 14.5 1.0
O2G A:AP5301 2.4 11.6 1.0
O A:HOH505 2.4 14.7 1.0
O A:HOH503 2.4 16.4 1.0
H1 A:HOH506 2.6 0.0 1.0
H2 A:HOH587 2.9 0.0 1.0
H2 A:HOH506 3.1 0.0 1.0
H1 A:HOH503 3.2 0.0 1.0
PG A:AP5301 3.5 13.0 1.0
PB A:AP5301 3.5 11.5 1.0
HH12 A:ARG165 3.5 0.0 1.0
H A:GLY18 3.6 0.0 1.0
O A:HOH587 3.6 31.1 1.0
HH12 A:ARG132 3.6 0.0 1.0
O3B A:AP5301 3.6 14.9 1.0
H1 A:HOH587 3.9 0.0 1.0
N A:GLY18 4.0 10.4 1.0
O3G A:AP5301 4.0 10.2 1.0
CA A:GLY18 4.1 5.8 1.0
O A:HOH516 4.1 20.8 1.0
O3A A:AP5301 4.2 10.2 1.0
HH11 A:ARG165 4.2 0.0 1.0
NH1 A:ARG165 4.3 8.7 1.0
HH22 A:ARG40 4.3 0.0 1.0
NH1 A:ARG132 4.3 16.7 1.0
O1E A:AP5301 4.4 11.3 1.0
O A:HOH527 4.4 26.0 1.0
HH11 A:ARG132 4.4 0.0 1.0
H2 A:HOH516 4.5 0.0 1.0
O2A A:AP5301 4.5 12.1 1.0
OD2 A:ASP89 4.6 16.5 1.0
H1 A:HOH516 4.6 0.0 1.0
H1 A:HOH527 4.6 0.0 1.0
O1B A:AP5301 4.6 12.1 1.0
O A:HOH551 4.6 33.6 1.0
OD1 A:ASP89 4.6 16.2 1.0
O2E A:AP5301 4.7 11.5 1.0
PE A:AP5301 4.7 11.6 1.0
O1G A:AP5301 4.8 12.1 1.0
O3D A:AP5301 4.8 16.3 1.0
HH21 A:ARG40 4.8 0.0 1.0
PA A:AP5301 4.9 11.6 1.0
NH2 A:ARG40 4.9 18.7 1.0
H2 A:HOH525 4.9 0.0 1.0
H2 A:HOH527 4.9 0.0 1.0

Reference:

U.Abele, G.E.Schulz. High-Resolution Structures of Adenylate Kinase From Yeast Ligated with Inhibitor AP5A, Showing the Pathway of Phosphoryl Transfer. Protein Sci. V. 4 1262 1995.
ISSN: ISSN 0961-8368
PubMed: 7670369
Page generated: Sun Aug 10 09:47:29 2025

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