Magnesium in PDB 5tth: Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State

The structure of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State, PDB code: 5tth was solved by D.Elnatan, M.Betegon, Y.Liu, D.A.Agard, Northeast Structural Genomicsconsortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.00 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.086, 95.711, 126.558, 90.00, 134.59, 90.00
R / Rfree (%)	22.8 / 26.1

The structure of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Magnesium atom in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State (pdb code 5tth). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State, PDB code: 5tth:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:48.0 occ:1.00 F1 A:BEF902 1.8 65.0 1.0 OD1 A:ASN134 2.1 77.4 1.0 O2A A:ADP901 2.5 50.5 1.0 O2B A:ADP901 2.7 54.4 1.0 CG A:ASN134 3.0 74.7 1.0 BE A:BEF902 3.3 66.1 1.0 ND2 A:ASN134 3.4 74.4 1.0 OE1 A:GLU130 3.6 0.1 1.0 PB A:ADP901 3.7 57.0 1.0 O A:GLU130 3.8 72.6 1.0 PA A:ADP901 3.8 56.5 1.0 O3B A:ADP901 3.9 60.8 1.0 O3A A:ADP901 4.1 53.3 1.0 F3 A:BEF902 4.2 72.8 1.0 F2 A:BEF902 4.3 57.3 1.0 CA A:GLY219 4.3 67.1 1.0 CB A:ASN134 4.3 74.9 1.0 N A:ASN134 4.3 71.7 1.0 CB A:SER133 4.5 72.8 1.0 CA A:ASN134 4.6 74.1 1.0 O5' A:ADP901 4.6 57.0 1.0 CD A:GLU130 4.6 94.1 1.0 C A:GLU130 4.6 74.0 1.0 CA A:GLY214 4.7 77.2 1.0 N A:GLY219 4.8 68.9 1.0 C A:GLY219 4.8 65.6 1.0 OD2 A:ASP137 4.8 88.3 1.0 CA A:GLU130 4.8 75.8 1.0 C A:SER133 4.8 72.3 1.0 CB A:GLU130 4.9 80.8 1.0 N A:PHE220 5.0 66.6 1.0

Magnesium binding site 2 out of 2 in the Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Heterodimeric Spycatcher/Spytag-Fused Zebrafish TRAP1 in Atp/Adp- Hybrid State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg803 b:38.0 occ:1.00 OD1 B:ASN134 1.8 86.0 1.0 F1 B:BEF802 2.0 55.7 1.0 O2B B:ADP801 2.3 54.3 1.0 O2A B:ADP801 2.3 52.6 1.0 CG B:ASN134 2.7 87.6 1.0 ND2 B:ASN134 3.2 87.9 1.0 PB B:ADP801 3.3 54.6 1.0 BE B:BEF802 3.3 55.7 1.0 PA B:ADP801 3.6 50.9 1.0 O3B B:ADP801 3.7 55.2 1.0 O B:GLU130 3.7 82.5 1.0 O3A B:ADP801 3.8 50.2 1.0 OE1 B:GLU130 4.0 1.0 1.0 CB B:ASN134 4.1 89.1 1.0 N B:ASN134 4.2 85.5 1.0 F2 B:BEF802 4.2 55.7 1.0 O5' B:ADP801 4.3 47.7 1.0 CA B:ASN134 4.3 87.9 1.0 CA B:GLY219 4.4 90.1 1.0 F3 B:BEF802 4.5 58.3 1.0 O1B B:ADP801 4.7 55.3 1.0 CA B:GLY214 4.7 88.6 1.0 CB B:SER133 4.7 77.9 1.0 C B:GLU130 4.7 83.8 1.0 OD2 B:ASP137 4.8 0.1 1.0 C B:SER133 4.8 84.6 1.0 N B:GLY219 4.8 90.7 1.0 N B:PHE220 4.9 94.0 1.0 C B:GLY219 4.9 92.7 1.0 O1A B:ADP801 4.9 49.3 1.0

D.Elnatan, M.Betegon, Y.Liu, T.Ramelot, M.A.Kennedy, D.A.Agard. Symmetry Broken and Rebroken During the Atp Hydrolysis Cycle of the Mitochondrial HSP90 TRAP1. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28742020
DOI: 10.7554/ELIFE.25235