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Magnesium in PDB 5g41: Crystal Structure of Adenylate Kinase Ancestor 4 with Zn, Mg and AP5A Bound

Enzymatic activity of Crystal Structure of Adenylate Kinase Ancestor 4 with Zn, Mg and AP5A Bound

All present enzymatic activity of Crystal Structure of Adenylate Kinase Ancestor 4 with Zn, Mg and AP5A Bound:
2.7.4.3;

Protein crystallography data

The structure of Crystal Structure of Adenylate Kinase Ancestor 4 with Zn, Mg and AP5A Bound, PDB code: 5g41 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) 59.65 / 1.54
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 73.999, 73.999, 100.782, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 19.6

Other elements in 5g41:

The structure of Crystal Structure of Adenylate Kinase Ancestor 4 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 4 with Zn, Mg and AP5A Bound (pdb code 5g41). 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 4 with Zn, Mg and AP5A Bound, PDB code: 5g41:

Magnesium binding site 1 out of 1 in 5g41

Go back to Magnesium Binding Sites List in 5g41
Magnesium binding site 1 out of 1 in the Crystal Structure of Adenylate Kinase Ancestor 4 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 4 with Zn, Mg and AP5A Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1217

b:27.0
occ:0.60
 O1G A:AP51216 1.9 17.7 0.5
O A:HOH2014 2.1 30.9 1.0
O2D A:AP51216 2.2 22.7 1.0
O A:HOH2184 2.2 26.1 1.0
O A:HOH2013 2.2 22.6 0.5
O A:HOH2039 2.2 25.4 0.5
PB A:AP51216 2.2 23.1 0.5
O2B A:AP51216 2.2 26.8 0.5
O3B A:AP51216 2.2 22.9 0.5
O1B A:AP51216 2.3 27.6 0.5
PG A:AP51216 3.2 19.3 0.5
PD A:AP51216 3.2 20.5 1.0
O3G A:AP51216 3.3 21.8 0.5
PG A:AP51216 3.3 21.6 0.5
O3G A:AP51216 3.5 21.4 0.5
O3A A:AP51216 3.8 22.1 0.5
O2G A:AP51216 3.8 22.2 0.5
O3B A:AP51216 3.9 19.1 0.5
O1A A:AP51216 3.9 23.9 0.5
O3A A:AP51216 3.9 17.4 0.5
N A:GLY14 4.1 18.8 1.0
O A:HOH2045 4.2 31.6 1.0
O1D A:AP51216 4.2 20.9 1.0
PA A:AP51216 4.4 21.7 0.5
O A:HOH2044 4.4 32.5 1.0
CA A:GLY14 4.4 20.6 1.0
O2G A:AP51216 4.5 20.8 0.5
O3D A:AP51216 4.5 23.2 1.0
OD1 A:ASP84 4.5 23.1 1.0
OD2 A:ASP84 4.5 24.4 1.0
O1G A:AP51216 4.5 24.8 0.5
O2E A:AP51216 4.5 27.5 1.0
PB A:AP51216 4.6 18.8 0.5
O2A A:AP51216 4.6 21.8 0.5
NH1 A:ARG160 4.6 30.3 1.0
CE A:LYS13 4.7 22.4 0.5
CB A:LYS13 4.7 19.2 0.5
NH2 A:ARG36 4.8 32.0 1.0
O1A A:AP51216 4.9 28.2 0.5
PA A:AP51216 4.9 25.7 0.5
CG A:ASP84 4.9 21.1 1.0
CB A:LYS13 4.9 19.5 0.5
PE A:AP51216 4.9 22.5 1.0
NH1 A:ARG127 5.0 25.5 1.0
O A:HOH2040 5.0 25.2 1.0
O2B A:AP51216 5.0 22.4 0.5

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: Sun Sep 29 04:36:04 2024

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