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Magnesium in PDB 5g3z: Crystal Structure of Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound

Enzymatic activity of Crystal Structure of Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound

All present enzymatic activity of Crystal Structure of Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound, PDB code: 5g3z was solved by V.Nguyen, S.Kutter, J.English, D.Kern, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.50 / 1.89
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 66.617, 77.435, 38.628, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.3

Other elements in 5g3z:

The structure of Crystal Structure of Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound (pdb code 5g3z). 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 Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound, PDB code: 5g3z:

Magnesium binding site 1 out of 1 in 5g3z

Go back to Magnesium Binding Sites List in 5g3z
Magnesium binding site 1 out of 1 in the Crystal Structure of Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound


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 Adenylate Kinase Ancestor 3 with Zn, Mg and AP5A Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1218

b:19.4
occ:1.00
 O2D A:AP51217 2.3 11.8 1.0
O2G A:AP51217 2.4 16.0 1.0
O A:HOH2064 2.5 16.9 1.0
O A:HOH2065 2.5 27.3 1.0
O A:HOH2089 2.6 19.9 1.0
O A:HOH2036 2.7 28.4 1.0
PG A:AP51217 3.4 15.8 1.0
PD A:AP51217 3.5 14.3 1.0
N A:GLY14 3.7 13.4 1.0
O3B A:AP51217 3.8 16.7 1.0
O3G A:AP51217 3.8 14.1 1.0
CA A:GLY14 3.8 12.9 1.0
NH1 A:ARG127 4.4 14.0 1.0
O3D A:AP51217 4.4 14.0 1.0
NH1 A:ARG160 4.5 14.8 1.0
O2A A:AP51217 4.5 16.9 1.0
OD2 A:ASP84 4.5 19.6 1.0
OD1 A:ASP84 4.6 19.0 1.0
O3A A:AP51217 4.6 16.6 1.0
O1D A:AP51217 4.6 14.3 1.0
O2E A:AP51217 4.7 12.6 1.0
CB A:LYS13 4.7 15.6 1.0
C A:LYS13 4.8 12.9 1.0
O1G A:AP51217 4.8 15.4 1.0
PE A:AP51217 4.8 14.7 1.0
O A:HOH2018 4.8 35.5 1.0
O1A A:AP51217 4.9 15.0 1.0
PA A:AP51217 4.9 14.5 1.0
PB A:AP51217 5.0 18.1 1.0
CG A:ASP84 5.0 19.5 1.0
O1E A:AP51217 5.0 12.4 1.0

Reference:

V.Nguyen, C.Wilson, M.Hoemberger, J.B.Stiller, R.V.Agafonov, S.Kutter, J.English, D.L.Theobald, D.Kern. Evolutionary Drivers of Thermoadaptation in Enzyme Catalysis. Science V. 355 289 2017.
ISSN: ESSN 1095-9203
PubMed: 28008087
DOI: 10.1126/SCIENCE.AAH3717
Page generated: Tue Aug 12 08:23:26 2025

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