Magnesium in PDB 7exp: Crystal Structure of Zebrafish TRAP1 with Amppnp and Mitoq

The structure of Crystal Structure of Zebrafish TRAP1 with Amppnp and Mitoq, PDB code: 7exp was solved by H.Lee, N.G.Yoon, B.H.Kang, C.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.21 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.339, 96.522, 125.615, 90, 134.39, 90
R / Rfree (%)	19.5 / 24.1

The structure of Crystal Structure of Zebrafish TRAP1 with Amppnp and Mitoq also contains other interesting chemical elements:

Cobalt

(Co)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Zebrafish TRAP1 with Amppnp and Mitoq (pdb code 7exp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Zebrafish TRAP1 with Amppnp and Mitoq, PDB code: 7exp:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Zebrafish TRAP1 with Amppnp and Mitoq


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 Zebrafish TRAP1 with Amppnp and Mitoq within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:25.6 occ:1.00 O2G A:ANP801 2.0 40.8 1.0 O2B A:ANP801 2.0 28.2 1.0 O1A A:ANP801 2.0 29.1 1.0 OD1 A:ASN134 2.0 34.5 1.0 O A:HOH932 2.1 30.9 1.0 O A:HOH941 2.3 23.6 1.0 CG A:ASN134 3.0 35.6 1.0 PB A:ANP801 3.1 30.5 1.0 PA A:ANP801 3.1 34.6 1.0 O3A A:ANP801 3.3 33.2 1.0 PG A:ANP801 3.3 34.6 1.0 ND2 A:ASN134 3.4 36.8 1.0 N3B A:ANP801 3.7 42.3 1.0 O A:HOH910 3.8 28.1 1.0 O5' A:ANP801 3.9 31.6 1.0 O A:HOH912 4.0 26.2 1.0 O1G A:ANP801 4.1 34.3 1.0 OE1 A:GLU130 4.3 30.8 1.0 O1B A:ANP801 4.3 29.6 1.0 CA A:GLY219 4.3 28.9 1.0 O2A A:ANP801 4.4 33.2 1.0 CB A:ASN134 4.4 27.0 1.0 O3G A:ANP801 4.4 44.5 1.0 N A:GLY219 4.5 34.4 1.0 O A:GLU130 4.6 36.1 1.0 CA A:ASN134 4.6 24.6 1.0 N A:PHE220 4.6 22.3 1.0 N A:ASN134 4.7 24.7 1.0 O A:HOH923 4.8 26.9 1.0 C A:GLY219 4.8 29.9 1.0 OD2 A:ASP137 4.9 37.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Zebrafish TRAP1 with Amppnp and Mitoq


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Zebrafish TRAP1 with Amppnp and Mitoq within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:60.1 occ:1.00 O2B B:ANP801 1.9 67.2 1.0 O2G B:ANP801 2.0 80.7 1.0 O B:HOH950 2.0 53.4 1.0 OD1 B:ASN134 2.1 68.7 1.0 O B:HOH930 2.2 60.2 1.0 O1A B:ANP801 2.2 53.3 1.0 PB B:ANP801 2.9 48.3 1.0 O3A B:ANP801 3.1 80.1 1.0 CG B:ASN134 3.1 55.9 1.0 PA B:ANP801 3.1 54.6 1.0 PG B:ANP801 3.2 43.4 1.0 N3B B:ANP801 3.5 46.2 1.0 ND2 B:ASN134 3.5 45.7 1.0 O1G B:ANP801 3.7 40.7 1.0 O5' B:ANP801 3.9 57.2 1.0 O1B B:ANP801 4.2 44.3 1.0 OE1 B:GLU130 4.2 40.7 1.0 CA B:GLY219 4.3 33.5 1.0 O B:HOH926 4.3 41.8 1.0 O2A B:ANP801 4.4 63.1 1.0 CB B:ASN134 4.4 45.0 1.0 N B:GLY219 4.4 37.7 1.0 O3G B:ANP801 4.5 47.5 1.0 CA B:ASN134 4.6 41.7 1.0 O B:GLU130 4.6 44.5 1.0 N B:PHE220 4.6 42.4 1.0 CA B:GLY214 4.7 51.9 1.0 N B:ASN134 4.7 35.4 1.0 OD2 B:ASP137 4.8 48.8 1.0 C B:GLY219 4.8 42.2 1.0

N.G.Yoon, H.Lee, S.Y.Kim, S.Hu, D.Kim, S.Yang, K.B.Hong, J.H.Lee, S.Kang, B.G.Kim, K.Myung, C.Lee, B.H.Kang. Mitoquinone Inactivates Mitochondrial Chaperone TRAP1 By Blocking the Client Binding Site. J.Am.Chem.Soc. V. 143 19684 2021.
ISSN: ESSN 1520-5126
PubMed: 34758612
DOI: 10.1021/JACS.1C07099