Magnesium in PDB 8rj4: E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis

Enzymatic activity of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis

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

Protein crystallography data

The structure of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis, PDB code: 8rj4 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) 44.71 / 2.11
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.385, 76.29, 93.391, 90, 110.76, 90
R / Rfree (%) 19.1 / 25.3

Other elements in 8rj4:

The structure of E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Adenylate Kinase in Complex with Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis (pdb code 8rj4). 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 Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis, PDB code: 8rj4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8rj4

Go back to Magnesium Binding Sites List in 8rj4
Magnesium binding site 1 out of 2 in the E. Coli Adenylate Kinase in Complex with Two Adp Molecules 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 Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:39.6
occ:1.00
 O A:HOH434 2.2 28.4 1.0
O A:HOH431 2.2 34.0 1.0
O3B A:ADP302 2.2 44.8 1.0
O A:HOH424 2.2 39.1 1.0
O2B A:ADP301 2.2 31.6 1.0
O A:HOH408 2.4 44.5 1.0
O3B A:ADP301 3.1 31.4 1.0
PB A:ADP301 3.1 34.4 1.0
PB A:ADP302 3.4 50.0 1.0
O1B A:ADP302 3.7 53.9 1.0
NH1 A:ARG156 3.8 45.1 1.0
O A:HOH481 3.9 30.1 0.5
NH1 A:ARG123 4.0 32.9 1.0
O2A A:ADP301 4.0 30.3 1.0
O2A A:ADP302 4.0 40.8 1.0
O1B A:ADP301 4.2 31.2 1.0
O3A A:ADP301 4.2 32.0 1.0
N A:GLY14 4.3 35.1 1.0
O3A A:ADP302 4.3 46.5 1.0
O1A A:ADP302 4.3 38.0 1.0
O2B A:ADP302 4.4 45.9 1.0
OD1 A:ASP84 4.4 40.7 1.0
PA A:ADP302 4.4 43.0 1.0
CA A:GLY14 4.4 33.5 1.0
OD2 A:ASP84 4.5 44.1 1.0
PA A:ADP301 4.6 32.8 1.0
CZ A:ARG123 4.9 37.8 1.0
CG A:ASP84 4.9 47.1 1.0
O1A A:ADP301 5.0 30.1 1.0
O A:HOH419 5.0 40.0 1.0

Magnesium binding site 2 out of 2 in 8rj4

Go back to Magnesium Binding Sites List in 8rj4
Magnesium binding site 2 out of 2 in the E. Coli Adenylate Kinase in Complex with Two Adp Molecules 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 Two Adp Molecules and MG2+ As A Result of Enzymatic AP4A Hydrolysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:50.5
occ:1.00
 O B:HOH497 2.0 42.2 0.8
O2B B:ADP301 2.2 25.6 1.0
O3B B:ADP302 2.3 32.7 1.0
O B:HOH421 2.3 38.3 1.0
O B:HOH403 2.8 38.1 1.0
O1B B:ADP301 2.9 29.9 1.0
PB B:ADP301 3.1 28.8 1.0
O B:HOH440 3.1 32.4 1.0
PB B:ADP302 3.7 39.8 1.0
NH1 B:ARG123 3.7 33.8 1.0
O1A B:ADP301 4.0 31.1 1.0
NH1 B:ARG156 4.0 39.5 1.0
O3A B:ADP302 4.1 39.7 1.0
O3A B:ADP301 4.1 30.8 1.0
O B:HOH488 4.2 39.4 1.0
O3B B:ADP301 4.2 33.2 1.0
O2A B:ADP302 4.3 32.5 1.0
O1A B:ADP302 4.3 41.3 1.0
O1B B:ADP302 4.3 36.5 1.0
O B:HOH504 4.4 48.5 1.0
PA B:ADP302 4.4 40.6 1.0
CZ B:ARG123 4.5 35.5 1.0
N B:GLY14 4.5 30.9 1.0
PA B:ADP301 4.6 29.4 1.0
CA B:GLY14 4.7 32.6 1.0
O2B B:ADP302 4.7 40.2 1.0
NH2 B:ARG123 4.9 41.8 1.0
O2A B:ADP301 5.0 26.2 1.0

Reference:

A.T.Abdul Raafik, S.Tischlik, T.M.Nagy, C.Phoeurk, L.Schierholtz, J.Aden, P.Rogne, M.Drescher, K.Nam, A.E.Sauer-Eriksson, M.Wolf-Watz. Magnesium Induced Structural Preorganization in the Active Site of Adenylate Kinase. Sci Adv 2024.
ISSN: ESSN 2375-2548
Page generated: Fri Oct 4 17:39:38 2024

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