Magnesium in PDB 5f5r: TRAP1N-Adpnp

The structure of TRAP1N-Adpnp, PDB code: 5f5r was solved by F.T.F.Tsai, S.Lee, N.Sung, J.Lee, C.Chang, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.41 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.570, 143.168, 103.011, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.3

The binding sites of Magnesium atom in the TRAP1N-Adpnp (pdb code 5f5r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the TRAP1N-Adpnp, PDB code: 5f5r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the TRAP1N-Adpnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of TRAP1N-Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:2.0 occ:1.00 O2A A:ANP300 2.0 2.0 1.0 OD1 A:ASN119 2.0 8.8 1.0 O1G A:ANP300 2.0 2.3 1.0 O1B A:ANP300 2.1 2.2 1.0 O A:HOH458 2.1 2.0 1.0 O A:HOH443 2.2 2.0 1.0 CG A:ASN119 3.0 10.6 1.0 PB A:ANP300 3.1 2.0 1.0 PA A:ANP300 3.2 2.4 1.0 PG A:ANP300 3.3 2.2 1.0 O3A A:ANP300 3.4 2.0 1.0 ND2 A:ASN119 3.5 9.4 1.0 N3B A:ANP300 3.7 2.0 1.0 O3G A:ANP300 3.9 2.1 1.0 O5' A:ANP300 3.9 2.0 1.0 O A:HOH471 4.1 2.0 1.0 O A:HOH455 4.2 6.4 1.0 OD2 A:ASP122 4.4 9.7 1.0 CB A:ASN119 4.4 9.1 1.0 OE1 A:GLU115 4.4 17.1 1.0 O A:HOH422 4.4 7.3 1.0 O A:GLU115 4.5 10.7 1.0 O1A A:ANP300 4.5 2.0 1.0 O2B A:ANP300 4.5 2.1 1.0 O2G A:ANP300 4.5 3.1 1.0 N A:ASN119 4.6 8.8 1.0 CA A:ASN119 4.6 8.8 1.0 CA A:GLY204 4.9 13.0 1.0

Magnesium binding site 2 out of 2 in the TRAP1N-Adpnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of TRAP1N-Adpnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:2.0 occ:1.00 OD1 B:ASN119 2.0 5.7 1.0 O2A B:ANP300 2.0 3.5 1.0 O1G B:ANP300 2.0 2.7 1.0 O1B B:ANP300 2.0 2.0 1.0 O B:HOH469 2.1 4.0 1.0 O B:HOH513 2.1 3.3 1.0 CG B:ASN119 3.0 5.8 1.0 PB B:ANP300 3.1 3.2 1.0 PA B:ANP300 3.2 3.1 1.0 PG B:ANP300 3.3 3.2 1.0 O3A B:ANP300 3.4 2.0 1.0 ND2 B:ASN119 3.5 6.1 1.0 N3B B:ANP300 3.7 2.2 1.0 O2G B:ANP300 3.9 4.5 1.0 O5' B:ANP300 3.9 2.1 1.0 O B:HOH453 4.0 2.2 1.0 O B:HOH440 4.2 2.5 1.0 O B:HOH444 4.3 5.5 1.0 OD2 B:ASP122 4.3 7.6 1.0 CB B:ASN119 4.3 6.6 1.0 O B:GLU115 4.4 7.2 1.0 OE1 B:GLU115 4.5 14.1 1.0 O1A B:ANP300 4.5 2.0 1.0 O2B B:ANP300 4.5 2.0 1.0 O3G B:ANP300 4.5 4.4 1.0 N B:ASN119 4.5 5.7 1.0 CA B:ASN119 4.5 5.6 1.0 CA B:GLY204 5.0 8.1 1.0 CB B:SER118 5.0 7.0 1.0

N.Sung, J.Lee, J.H.Kim, C.Chang, A.Joachimiak, S.Lee, F.T.Tsai. Mitochondrial HSP90 Is A Ligand-Activated Molecular Chaperone Coupling Atp Binding to Dimer Closure Through A Coiled-Coil Intermediate. Proc.Natl.Acad.Sci.Usa V. 113 2952 2016.
ISSN: ESSN 1091-6490
PubMed: 26929380
DOI: 10.1073/PNAS.1516167113