Magnesium in PDB 7f50: X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp

The structure of X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp, PDB code: 7f50 was solved by T.Yokoyama, S.Fujii, Y.Nabeshima, M.Mizuguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.85 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.827, 61.968, 142.779, 90, 90, 90
R / Rfree (%)	18.6 / 22.7

The structure of X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp (pdb code 7f50). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp, PDB code: 7f50:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:28.1 occ:1.00 O A:HOH562 2.0 28.8 1.0 OD2 A:ASP10 2.0 22.2 1.0 O A:HOH609 2.1 28.0 1.0 O A:HOH621 2.1 32.1 1.0 O1B A:ANP404 2.2 22.4 1.0 CG A:ASP10 2.8 20.8 1.0 OD1 A:ASP10 3.1 26.5 1.0 O A:HOH601 3.4 25.5 1.0 PB A:ANP404 3.6 19.1 1.0 O2A A:ANP404 3.9 19.2 1.0 O A:HOH555 4.0 25.0 1.0 O A:HOH546 4.0 18.2 1.0 CB A:ASP10 4.1 15.1 1.0 O A:TYR15 4.2 18.6 1.0 O A:HOH597 4.2 19.3 1.0 N3B A:ANP404 4.3 18.3 1.0 CA A:GLY12 4.3 17.2 1.0 O A:HOH517 4.4 33.4 1.0 O3A A:ANP404 4.4 20.6 1.0 O A:ASP366 4.5 19.7 1.0 PA A:ANP404 4.5 19.1 1.0 O2B A:ANP404 4.5 19.3 1.0 N A:GLY12 4.7 18.0 1.0 O1A A:ANP404 4.7 20.5 1.0 O A:ASP10 4.8 17.5 1.0 C A:ASP10 5.0 17.3 1.0

Magnesium binding site 2 out of 2 in the X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Y149A Mutated HSP72-Nbd in Complex with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:31.4 occ:1.00 O A:HOH560 2.1 32.4 1.0 O A:HOH524 2.1 29.2 1.0 OD2 A:ASP206 2.1 29.3 1.0 O A:HOH658 2.1 31.4 1.0 O A:HOH697 2.1 37.2 1.0 OG1 A:THR204 2.3 28.2 1.0 CG A:ASP206 3.2 29.8 1.0 CB A:THR204 3.4 21.9 1.0 OD1 A:ASP206 3.7 27.8 1.0 O2G A:ANP404 4.0 25.8 1.0 O3G A:ANP404 4.0 30.8 1.0 CG2 A:THR204 4.1 23.5 1.0 OE1 A:GLU175 4.2 30.4 1.0 CB A:ASP206 4.5 23.7 1.0 OD2 A:ASP199 4.5 32.7 1.0 CA A:THR204 4.6 20.0 1.0 PG A:ANP404 4.7 26.6 1.0 C A:THR204 4.7 19.6 1.0 CG A:PRO147 4.8 17.4 1.0 O A:HOH743 4.8 41.2 1.0 O A:THR204 4.9 18.6 1.0 O A:HOH530 4.9 34.8 1.0 O A:HOH517 5.0 33.4 1.0

T.Yokoyama, S.Fujii, A.Ostermann, T.E.Schrader, Y.Nabeshima, M.Mizuguchi. Neutron Crystallographic Analysis of the Nucleotide-Binding Domain of HSP72 in Complex with Adp. Iucrj V. 9 562 2022.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252522006297