Zinc in PDB 5g40: Crystal Structure of Adenylate Kinase Ancestor 4 with Zn and Amp-Adp Bound

All present enzymatic activity of Crystal Structure of Adenylate Kinase Ancestor 4 with Zn and Amp-Adp Bound:
2.7.4.3;

The structure of Crystal Structure of Adenylate Kinase Ancestor 4 with Zn and Amp-Adp Bound, PDB code: 5g40 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)	39.11 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.046, 70.127, 40.270, 90.00, 103.78, 90.00
R / Rfree (%)	15.8 / 23.4

The binding sites of Zinc atom in the Crystal Structure of Adenylate Kinase Ancestor 4 with Zn and Amp-Adp Bound (pdb code 5g40). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Adenylate Kinase Ancestor 4 with Zn and Amp-Adp Bound, PDB code: 5g40:

Zinc binding site 1 out of 1 in the Crystal Structure of Adenylate Kinase Ancestor 4 with Zn and Amp-Adp Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Adenylate Kinase Ancestor 4 with Zn and Amp-Adp Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1216 b:22.4 occ:1.00 OD1 A:ASP153 2.0 24.6 1.0 SG A:CYS133 2.2 25.6 1.0 SG A:CYS130 2.3 20.6 1.0 SG A:CYS150 2.3 21.8 1.0 CG A:ASP153 2.8 21.2 1.0 CB A:CYS130 3.1 16.6 1.0 CB A:CYS150 3.1 20.3 1.0 OD2 A:ASP153 3.2 31.2 1.0 CB A:CYS133 3.5 24.4 1.0 N A:CYS133 3.7 22.1 1.0 OG1 A:THR132 3.8 32.1 1.0 CA A:CYS133 4.1 22.3 1.0 CB A:ASP153 4.2 21.9 1.0 N A:ASP153 4.2 22.2 1.0 CB A:ALA135 4.4 18.3 1.0 CA A:CYS130 4.5 15.8 1.0 CB A:LYS152 4.5 27.0 1.0 N A:GLY155 4.6 22.0 1.0 CA A:CYS150 4.6 19.8 1.0 CA A:ASP153 4.6 22.7 1.0 N A:GLY134 4.6 21.8 1.0 C A:CYS133 4.6 22.1 1.0 N A:ALA135 4.7 19.7 1.0 C A:THR132 4.7 21.6 1.0 CA A:GLY155 4.9 22.7 1.0 C A:ASP153 5.0 24.2 1.0 N A:THR132 5.0 22.2 1.0

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