Magnesium in PDB 5bn8: Crystal Structure of Nucleotide-Free Human HSP70 Nbd.

The structure of Crystal Structure of Nucleotide-Free Human HSP70 Nbd., PDB code: 5bn8 was solved by D.Narayanan, R.A.Engh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.35 / 1.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.129, 63.700, 144.118, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 15.4

The structure of Crystal Structure of Nucleotide-Free Human HSP70 Nbd. also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Nucleotide-Free Human HSP70 Nbd. (pdb code 5bn8). 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 Nucleotide-Free Human HSP70 Nbd., PDB code: 5bn8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Nucleotide-Free Human HSP70 Nbd.


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 Nucleotide-Free Human HSP70 Nbd. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:27.6 occ:1.00 O4 A:PO4407 1.9 21.3 0.2 O4 A:PO4407 2.5 15.8 0.2 O4 A:PO4404 2.6 12.9 0.5 N A:GLY203 2.9 13.1 1.0 O1 A:PO4407 3.1 16.9 0.3 N A:THR204 3.1 13.7 1.0 OG1 A:THR204 3.2 16.6 1.0 P A:PO4407 3.2 15.3 0.6 O2 A:PO4407 3.3 15.1 0.2 N A:GLY202 3.3 14.4 1.0 P A:PO4407 3.4 14.5 0.2 P A:PO4404 3.6 12.4 0.6 CA A:GLY203 3.6 13.6 1.0 O1 A:PO4404 3.7 14.7 0.8 CB A:THR13 3.7 10.7 1.0 C A:GLY201 3.8 13.5 1.0 C A:GLY203 3.8 11.6 1.0 CA A:GLY201 3.8 15.1 1.0 C A:GLY202 3.9 12.3 1.0 CB A:THR204 3.9 14.7 1.0 OG1 A:THR13 4.0 12.7 1.0 CA A:THR204 4.0 13.0 1.0 CA A:GLY202 4.1 14.1 1.0 CG2 A:THR204 4.1 17.3 1.0 O2 A:PO4407 4.1 22.9 0.2 O A:THR204 4.1 12.8 1.0 O3 A:PO4404 4.2 15.0 0.8 O3 A:PO4407 4.2 24.2 0.1 O A:HOH706 4.3 21.1 1.0 O1 A:PO4407 4.4 15.0 0.7 O3 A:PO4407 4.4 17.3 0.2 CG2 A:THR14 4.5 13.6 1.0 CG2 A:THR13 4.6 13.1 1.0 C A:THR204 4.6 11.7 1.0 O A:GLY201 4.6 17.1 1.0 N A:THR14 4.7 10.8 1.0 N A:GLY201 4.7 12.9 1.0 OG1 A:THR14 4.7 19.0 1.0 N A:THR13 4.7 9.0 1.0 CA A:THR13 4.8 9.1 1.0 O2 A:PO4404 4.9 11.5 0.6 O A:GLY203 5.0 14.3 1.0 O A:HOH563 5.0 16.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Nucleotide-Free Human HSP70 Nbd.


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 Nucleotide-Free Human HSP70 Nbd. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:13.4 occ:0.83 O A:HOH569 2.0 14.7 1.0 O1 A:PO4404 2.1 14.7 0.8 O A:HOH563 2.1 16.1 1.0 O A:HOH528 2.1 13.5 0.8 O1 A:PO4407 2.1 15.0 0.7 O A:HOH589 2.2 17.2 1.0 O1 A:PO4407 3.2 16.9 0.3 P A:PO4404 3.3 12.4 0.6 P A:PO4407 3.5 14.5 0.2 O3 A:PO4404 3.5 15.0 0.8 O4 A:PO4407 3.5 15.8 0.2 O A:HOH549 4.0 19.1 1.0 O A:HOH825 4.0 34.9 1.0 O2 A:PO4404 4.1 11.5 0.6 OD2 A:ASP199 4.1 17.4 1.0 OD1 A:ASP199 4.1 13.6 1.0 OE2 A:GLU175 4.2 13.3 1.0 OD2 A:ASP10 4.2 12.1 1.0 O A:HOH706 4.2 21.1 1.0 OD1 A:ASP10 4.3 12.2 1.0 O2 A:PO4407 4.3 15.1 0.2 O4 A:PO4404 4.5 12.9 0.5 CG A:ASP199 4.5 13.1 1.0 O3 A:PO4407 4.6 17.3 0.2 CG A:ASP10 4.7 10.1 1.0 CD A:GLU175 4.7 12.5 1.0 P A:PO4407 4.7 15.3 0.6 CG1 A:VAL337 4.8 16.7 1.0 O2 A:PO4407 4.9 22.9 0.2 O A:HOH631 4.9 13.9 1.0

D.Narayanan, A.Pflug, T.Christopeit, P.Kyomuhendo, R.A.Engh. Nucleotide Binding to Variants of the HSP70-Nbd. To Be Published.