Magnesium in PDB 8tf0: Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36

The structure of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36, PDB code: 8tf0 was solved by N.L.S.Que, D.T.Gewirth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.89 / 2.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	96.282, 104.392, 172.284, 90, 90, 90
R / Rfree (%)	22.8 / 26

The structure of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 (pdb code 8tf0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36, PDB code: 8tf0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


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 GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:93.7 occ:1.00 OG B:SER66 2.0 92.1 1.0 N B:HIS67 2.1 137.1 0.4 N B:HIS67 2.1 133.8 0.6 ND1 B:HIS67 2.1 105.7 0.6 CG B:HIS67 2.1 107.4 0.4 OE2 B:GLU71 2.2 101.0 1.0 CD2 B:HIS67 2.3 105.8 0.4 ND1 B:HIS67 2.4 100.7 0.4 NE2 B:HIS67 2.5 104.3 0.4 CE1 B:HIS67 2.6 101.7 0.4 C B:SER66 2.7 113.6 1.0 CG B:HIS67 2.8 110.0 0.6 CB B:HIS67 2.9 112.0 0.6 CA B:HIS67 2.9 115.8 0.6 CA B:HIS67 3.0 111.6 0.4 CB B:SER66 3.0 92.1 1.0 CB B:HIS67 3.0 111.8 0.4 CA B:SER66 3.0 109.9 1.0 CD B:GLU71 3.0 100.6 1.0 N B:SER66 3.1 107.3 1.0 CE1 B:HIS67 3.2 102.2 0.6 OE1 B:GLU71 3.3 105.9 1.0 N B:MET68 3.5 112.0 1.0 C B:HIS67 3.6 109.9 0.6 O B:SER66 3.6 98.1 1.0 C B:HIS67 3.7 105.5 0.4 CD2 B:HIS67 4.0 99.5 0.6 NE2 B:HIS67 4.2 97.5 0.6 CG B:GLU71 4.3 106.7 1.0 OD1 A:ASP113 4.5 84.4 1.0 CA B:MET68 4.8 107.8 1.0 O B:HIS67 4.8 95.5 0.6 O B:HIS67 4.8 95.4 0.4 CB B:MET68 4.9 105.8 1.0 CG A:ASP113 5.0 79.3 1.0

Magnesium binding site 2 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


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 GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:75.0 occ:1.00 OE1 B:GLN194 3.2 94.2 1.0 O B:GLY185 3.8 113.5 1.0 CB B:GLU190 3.8 74.6 1.0 CA B:GLN186 3.9 99.4 1.0 CB B:GLN186 4.0 107.4 1.0 OE2 B:GLU190 4.3 98.3 1.0 CD B:GLN194 4.3 97.3 1.0 C B:GLU190 4.3 70.9 1.0 O B:GLU190 4.4 78.3 1.0 CD2 B:LEU191 4.5 58.0 1.0 N B:LEU191 4.5 67.3 1.0 CD B:GLU190 4.7 102.4 1.0 C B:GLY185 4.7 115.8 1.0 CA B:GLU190 4.7 83.7 1.0 N B:GLN186 4.8 109.1 1.0 CG B:LEU191 4.8 67.3 1.0 CG B:GLU190 4.8 83.0 1.0 C B:GLN186 4.9 91.3 1.0 CA B:LEU191 4.9 69.9 1.0 N B:SER187 4.9 83.7 1.0

Magnesium binding site 3 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:75.3 occ:1.00 OD2 B:ASP226 2.9 71.5 1.0 ND2 B:ASN228 2.9 66.7 1.0 O B:HOH530 3.1 73.9 1.0 CD B:GLU229 3.3 105.1 1.0 OE2 B:GLU229 3.4 99.9 1.0 CG B:GLU229 3.5 80.5 1.0 OE1 B:GLU229 3.7 97.6 1.0 CB B:ASN228 3.7 71.6 1.0 CG B:ASP226 3.7 69.5 1.0 CG B:ASN228 3.8 73.6 1.0 OD1 B:ASP226 3.8 61.1 1.0 N B:GLU229 4.5 64.3 1.0 CB B:GLU229 4.6 65.5 1.0 CA B:ASN228 4.9 62.7 1.0 C B:ASN228 5.0 71.0 1.0 OD1 B:ASN228 5.0 77.1 1.0

Magnesium binding site 4 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:56.3 occ:1.00 OE2 A:GLU71 1.9 86.1 1.0 N A:HIS67 1.9 78.0 1.0 CG A:HIS67 2.1 85.3 1.0 ND1 A:HIS67 2.1 91.0 1.0 OG A:SER66 2.5 68.7 1.0 CD2 A:HIS67 2.6 104.1 1.0 CA A:HIS67 2.6 91.3 1.0 CE1 A:HIS67 2.6 105.1 1.0 CD A:GLU71 2.8 81.1 1.0 CB A:HIS67 2.8 98.7 1.0 NE2 A:HIS67 2.9 118.5 1.0 C A:SER66 3.0 94.0 1.0 C A:HIS67 3.0 89.5 1.0 OE1 A:GLU71 3.0 94.6 1.0 CB A:SER66 3.4 68.6 1.0 N A:MET68 3.4 98.8 1.0 CA A:SER66 3.4 83.2 1.0 N A:SER66 3.5 92.1 1.0 MG A:MG407 3.7 84.3 1.0 O A:HIS67 3.7 64.0 1.0 O A:SER66 4.0 73.5 1.0 CG A:GLU71 4.1 70.6 1.0 CA A:MET68 4.5 71.3 1.0 CB A:MET68 4.5 71.0 1.0 OD1 B:ASP113 4.8 84.3 1.0

Magnesium binding site 5 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:80.2 occ:1.00 O4 A:SO4410 3.2 126.5 1.0 ND1 A:HIS146 3.8 77.2 1.0 CG A:HIS146 4.1 78.0 1.0 CE1 A:HIS146 4.3 78.4 1.0 CG2 A:THR246 4.3 51.6 1.0 CB A:HIS146 4.3 74.9 1.0 OG1 A:THR148 4.4 58.6 1.0 S A:SO4410 4.4 253.9 1.0 O2 A:SO4410 4.5 126.5 1.0 CD2 A:HIS146 4.7 68.8 1.0 OG1 A:THR246 4.8 66.8 1.0 NE2 A:HIS146 4.8 71.2 1.0

Magnesium binding site 6 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:88.7 occ:1.00 SD A:MET68 2.8 86.1 1.0 OG C:SER106 3.1 86.3 1.0 CE A:MET68 3.8 58.7 1.0 CE2 A:PHE76 3.9 69.9 1.0 CB C:SER106 4.0 55.0 1.0 CD1 C:ILE275 4.3 63.5 1.0 CG A:MET68 4.4 80.5 1.0 CB C:PHE274 4.6 81.3 1.0 CD2 A:PHE76 4.7 77.8 1.0 CZ A:PHE76 4.7 82.9 1.0 CA C:SER106 4.8 64.5 1.0 CD2 C:PHE274 5.0 92.8 1.0

Magnesium binding site 7 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:84.3 occ:1.00 CD2 A:HIS67 2.2 104.1 1.0 CG A:HIS67 3.1 85.3 1.0 NE2 A:HIS67 3.2 118.5 1.0 O A:HIS67 3.2 64.0 1.0 CE A:MET68 3.6 58.7 1.0 CB A:HIS67 3.6 98.7 1.0 MG A:MG401 3.7 56.3 1.0 OD1 C:ASP110 3.8 80.9 1.0 C A:HIS67 3.8 89.5 1.0 OE2 A:GLU71 4.1 86.1 1.0 ND1 A:HIS67 4.2 91.0 1.0 CE1 A:HIS67 4.3 105.1 1.0 ND2 B:ASN276 4.3 74.5 1.0 CB A:MET68 4.3 71.0 1.0 CA A:HIS67 4.3 91.3 1.0 N A:MET68 4.6 98.8 1.0 CG C:ASP110 4.7 75.6 1.0 SD A:MET68 4.7 86.1 1.0 OD2 C:ASP110 4.8 81.5 1.0 CG A:MET68 4.9 80.5 1.0 N A:HIS67 4.9 78.0 1.0

Magnesium binding site 8 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg404 b:89.9 occ:1.00 O D:HOH504 2.1 73.8 1.0 ND2 D:ASN239 3.9 62.3 1.0 CE D:LYS214 4.1 52.9 1.0 NZ D:LYS214 4.2 66.1 1.0 CG D:ASN239 5.0 57.8 1.0

Magnesium binding site 9 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg405 b:88.2 occ:1.00 O D:HOH511 2.8 78.6 1.0 NE1 D:TRP333 3.1 70.9 1.0 CE2 D:TRP333 4.0 75.4 1.0 CD1 D:TRP333 4.0 78.9 1.0 NZ D:LYS135 4.1 78.3 1.0 CZ2 D:TRP333 4.2 76.6 1.0 CE D:LYS135 4.4 76.6 1.0 CD D:LYS135 4.6 72.6 1.0

Magnesium binding site 10 out of 11 in the Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of GRP94 N-Terminal Domain Bound to the Purine Inhibitor Pu-H36 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg406 b:76.6 occ:1.00 O D:HOH506 2.7 59.1 1.0 NH2 D:ARG237 2.9 85.8 1.0 OG1 D:THR212 3.1 63.9 1.0 CB D:THR212 4.0 66.8 1.0 CZ D:ARG237 4.0 90.9 1.0 NH1 D:ARG237 4.1 90.7 1.0 CG2 D:THR212 4.2 47.6 1.0 CG2 D:THR246 4.9 39.6 1.0

N.L.S.Que, P.M.Seidler, W.J.Aw, G.Chiosis, D.T.Gewirth. Selective Inhibition of HSP90 Paralogs: Uncovering the Role of Helix 1 in GRP94-Selective Ligand Binding. Proteins 2024.
ISSN: ESSN 1097-0134
PubMed: 39473058
DOI: 10.1002/PROT.26756