Magnesium in PDB 4j0b: Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3

The structure of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3, PDB code: 4j0b was solved by J.R.Partridge, L.A.Lavery, D.A.Agard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.82 / 2.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	177.779, 96.566, 124.977, 90.00, 134.29, 90.00
R / Rfree (%)	20.5 / 24.8

The structure of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 also contains other interesting chemical elements:

Fluorine	(F)	6 atoms
Cobalt	(Co)	4 atoms

The binding sites of Magnesium atom in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 (pdb code 4j0b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3, PDB code: 4j0b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg805 b:51.5 occ:1.00 F1 A:BEF804 1.8 41.2 1.0 O2B A:ADP803 2.0 51.5 1.0 O1A A:ADP803 2.1 47.5 1.0 O A:HOH960 2.1 41.1 1.0 O A:HOH917 2.1 40.7 1.0 OD1 A:ASN134 2.2 45.0 1.0 BE A:BEF804 3.1 34.2 1.0 PB A:ADP803 3.1 48.9 1.0 CG A:ASN134 3.2 45.9 1.0 O1B A:ADP803 3.3 43.4 1.0 PA A:ADP803 3.4 44.4 1.0 ND2 A:ASN134 3.6 46.3 1.0 O3A A:ADP803 3.6 47.5 1.0 O A:HOH970 3.6 35.2 1.0 OE1 A:GLU130 3.9 46.6 1.0 F2 A:BEF804 4.0 44.3 1.0 O A:HOH905 4.1 33.9 1.0 O5' A:ADP803 4.2 44.9 1.0 F3 A:BEF804 4.2 41.4 1.0 CA A:GLY214 4.3 50.8 1.0 O A:GLU130 4.4 48.6 1.0 O3B A:ADP803 4.4 46.5 1.0 CA A:GLY219 4.5 43.9 1.0 CB A:ASN134 4.5 46.8 1.0 O2A A:ADP803 4.6 39.3 1.0 O A:HOH918 4.6 40.2 1.0 N A:GLY219 4.7 44.7 1.0 OD2 A:ASP137 4.7 47.7 1.0 CA A:ASN134 4.8 46.2 1.0 N A:ASN134 4.8 45.7 1.0 N A:GLY214 4.9 51.1 1.0 C A:GLY219 5.0 45.0 1.0 N A:PHE220 5.0 48.0 1.0

Magnesium binding site 2 out of 2 in the Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Mitochondrial HSP90 (TRAP1) with Adp-BEF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg805 b:49.7 occ:1.00 F3 B:BEF804 1.8 52.6 1.0 O1A B:ADP803 2.0 51.6 1.0 O2B B:ADP803 2.0 52.4 1.0 O B:HOH919 2.1 52.9 1.0 O B:HOH906 2.1 53.5 1.0 OD1 B:ASN134 2.1 60.5 1.0 CG B:ASN134 3.1 61.1 1.0 PB B:ADP803 3.2 60.3 1.0 BE B:BEF804 3.2 77.1 1.0 PA B:ADP803 3.3 55.8 1.0 O1B B:ADP803 3.5 69.6 1.0 ND2 B:ASN134 3.5 61.7 1.0 O B:HOH933 3.6 44.1 1.0 O3A B:ADP803 3.6 57.4 1.0 F1 B:BEF804 4.0 57.4 1.0 O B:HOH903 4.0 44.8 1.0 OE1 B:GLU130 4.1 53.7 1.0 O5' B:ADP803 4.2 55.5 1.0 O B:GLU130 4.2 54.7 1.0 CA B:GLY219 4.3 50.7 1.0 F2 B:BEF804 4.3 58.1 1.0 CB B:ASN134 4.4 61.1 1.0 CA B:GLY214 4.4 56.3 1.0 O3B B:ADP803 4.5 54.4 1.0 O2A B:ADP803 4.6 55.2 1.0 N B:GLY219 4.6 51.2 1.0 CA B:ASN134 4.6 60.4 1.0 N B:ASN134 4.6 59.5 1.0 OD2 B:ASP137 4.8 61.5 1.0 C B:GLY219 4.9 52.1 1.0 N B:PHE220 4.9 57.3 1.0 O B:HOH948 4.9 51.3 1.0

L.A.Lavery, J.R.Partridge, T.A.Ramelot, D.Elnatan, M.A.Kennedy, D.A.Agard. Structural Asymmetry in the Closed State of Mitochondrial HSP90 (TRAP1) Supports A Two-Step Atp Hydrolysis Mechanism. Mol.Cell V. 53 330 2014.
ISSN: ISSN 1097-2765
PubMed: 24462206
DOI: 10.1016/J.MOLCEL.2013.12.023