Magnesium in PDB 8rj6: E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis.

All present enzymatic activity of E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis.:
2.7.4.3;

The structure of E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis., PDB code: 8rj6 was solved by S.Tischlik, P.Ronge, M.Wolf-Watz, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.05 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	56.153, 77.7, 59.279, 90, 94.99, 90
R / Rfree (%)	18.4 / 22.6

The binding sites of Magnesium atom in the E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis. (pdb code 8rj6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis., PDB code: 8rj6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:44.8 occ:1.00 O2G A:ATP301 1.9 39.1 0.6 O A:HOH401 2.0 41.4 1.0 O1B A:ATP301 2.0 37.9 0.6 O A:HOH409 2.1 41.0 1.0 O3B A:ADP302 2.1 36.5 0.4 O A:HOH429 2.2 42.5 1.0 O A:HOH437 2.2 44.4 1.0 PG A:ATP301 3.0 49.2 0.6 PB A:ADP302 3.2 31.8 0.4 PB A:ATP301 3.2 31.7 0.6 O1B A:ADP302 3.3 31.7 0.4 O1G A:ATP301 3.4 57.6 0.6 O3B A:ATP301 3.5 31.9 0.6 N A:GLY14 4.1 34.8 1.0 OD2 A:ASP84 4.1 38.0 1.0 O2B A:ATP301 4.1 35.3 0.6 OD1 A:ASP84 4.1 42.6 1.0 O2B A:ADP302 4.2 32.5 0.4 O A:HOH485 4.2 51.5 1.0 O2A A:ATP301 4.2 34.7 0.6 O3P A:AMP303 4.3 50.4 1.0 CA A:GLY14 4.3 31.2 1.0 O3G A:ATP301 4.4 34.0 0.6 O A:HOH432 4.4 36.7 0.4 O2P A:AMP303 4.4 57.7 1.0 O3A A:ADP302 4.4 38.0 0.4 O1A A:ADP302 4.4 35.0 0.4 O3A A:ATP301 4.4 36.6 0.6 O A:HOH430 4.5 33.8 1.0 CG A:ASP84 4.5 35.6 1.0 NH1 A:ARG156 4.6 48.0 1.0 O A:HOH432 4.7 30.1 0.4 PA A:ATP301 4.8 37.1 0.6 P A:AMP303 4.8 49.6 1.0 NH1 A:ARG123 4.8 50.3 1.0 PA A:ADP302 4.8 36.6 0.4 CB A:LYS13 5.0 35.5 1.0

Magnesium binding site 2 out of 2 in the E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Adenylate Kinase in Complex with Atp and Amp and MG2+ As A Result of Enzymatic AP4A Hydrolysis. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:41.0 occ:1.00 O B:HOH405 2.0 45.5 1.0 O B:HOH421 2.1 33.6 1.0 O B:HOH433 2.2 39.2 1.0 O2B B:ADP301 2.2 29.9 1.0 O B:HOH449 2.3 49.3 1.0 O B:HOH440 2.3 42.2 1.0 PB B:ADP301 3.3 29.6 1.0 O3B B:ADP301 3.4 28.9 1.0 OD1 B:ASP84 4.1 40.8 1.0 OD2 B:ASP84 4.1 38.9 1.0 N B:GLY14 4.2 33.0 1.0 O2P B:AMP302 4.2 50.1 1.0 O2A B:ADP301 4.2 31.5 1.0 O1B B:ADP301 4.2 29.1 1.0 O3P B:AMP302 4.3 36.7 1.0 CA B:GLY14 4.3 30.4 1.0 O3A B:ADP301 4.4 30.5 1.0 O B:HOH476 4.4 44.8 1.0 O B:HOH417 4.5 32.7 1.0 CG B:ASP84 4.5 49.5 1.0 P B:AMP302 4.5 39.8 1.0 O B:HOH484 4.5 45.7 1.0 O1P B:AMP302 4.5 45.9 1.0 NH1 B:ARG123 4.7 29.7 1.0 NH2 B:ARG156 4.7 37.5 0.6 PA B:ADP301 4.8 31.7 1.0

A.T.Abdul Raafik, S.Tischlik, T.M.Nagy, C.Phoeurk, L.Schierholtz, J.Aden, P.Rogne, M.Drescher, K.Nam, S.A.Sauer-Eriksson, M.Wolf-Watz. Magnesium Induced Structural Preorganization in the Active Site of Adenylate Kinase. Sci Adv 2024.
ISSN: ESSN 2375-2548