Magnesium in PDB 4z1i: Crystal Structure of Human TRAP1 with Amppnp

The structure of Crystal Structure of Human TRAP1 with Amppnp, PDB code: 4z1i was solved by C.Lee, H.K.Park, J.H.Ryu, B.H.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.82 / 3.30
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	115.547, 115.547, 339.936, 90.00, 90.00, 120.00
R / Rfree (%)	22 / 28.5

The binding sites of Magnesium atom in the Crystal Structure of Human TRAP1 with Amppnp (pdb code 4z1i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human TRAP1 with Amppnp, PDB code: 4z1i:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human TRAP1 with Amppnp


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 Human TRAP1 with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:42.1 occ:1.00 O1G A:ANP801 2.1 100.0 1.0 OD1 A:ASN119 2.1 47.4 1.0 O1B A:ANP801 2.1 58.5 1.0 O1A A:ANP801 2.1 53.6 1.0 CG A:ASN119 3.2 47.0 1.0 PB A:ANP801 3.3 41.0 1.0 PA A:ANP801 3.3 53.3 1.0 PG A:ANP801 3.5 49.5 1.0 O3A A:ANP801 3.7 48.8 1.0 N3B A:ANP801 3.8 51.0 1.0 ND2 A:ASN119 3.9 46.3 1.0 O5' A:ANP801 4.0 37.7 1.0 OE1 A:GLU115 4.1 54.4 1.0 CA A:ASN119 4.3 45.5 1.0 N A:ASN119 4.4 43.9 1.0 CB A:ASN119 4.4 46.1 1.0 O2G A:ANP801 4.4 49.0 1.0 O A:GLU115 4.4 46.8 1.0 CA A:GLY199 4.4 60.0 1.0 O3G A:ANP801 4.4 52.9 1.0 O2B A:ANP801 4.5 40.0 1.0 O2A A:ANP801 4.6 53.4 1.0 OD2 A:ASP122 4.7 47.1 1.0 CA A:GLY204 4.7 45.6 1.0 N A:GLY199 4.9 58.5 1.0 N A:PHE205 5.0 43.0 1.0 CB A:SER118 5.0 43.7 1.0 C A:SER118 5.0 42.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human TRAP1 with Amppnp


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 Human TRAP1 with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:36.4 occ:1.00 ND2 B:ASN119 1.9 0.1 1.0 OD1 B:ASN119 2.1 0.3 1.0 O2B B:ANP801 2.1 0.2 1.0 O2G B:ANP801 2.1 0.5 1.0 O2A B:ANP801 2.1 44.5 1.0 CG B:ASN119 2.2 0.3 1.0 PB B:ANP801 3.1 46.8 1.0 PG B:ANP801 3.3 41.8 1.0 PA B:ANP801 3.4 43.3 1.0 N3B B:ANP801 3.6 22.9 1.0 O3A B:ANP801 3.6 13.6 1.0 CB B:ASN119 3.6 0.4 1.0 OE1 B:GLU115 4.0 42.9 1.0 CA B:GLY204 4.1 42.0 1.0 O B:GLU115 4.1 35.6 1.0 CA B:ASN119 4.2 93.0 1.0 O3G B:ANP801 4.2 36.5 1.0 N B:ASN119 4.3 76.6 1.0 O5' B:ANP801 4.4 52.6 1.0 O1A B:ANP801 4.4 43.3 1.0 O1G B:ANP801 4.4 41.7 1.0 O1B B:ANP801 4.4 46.5 1.0 N B:PHE205 4.5 41.6 1.0 C B:GLY204 4.6 41.7 1.0 N B:GLY204 4.7 42.6 1.0 CA B:GLY199 4.8 45.6 1.0 C B:GLU115 4.9 34.9 1.0 NH2 B:ARG402 4.9 79.6 1.0 CB B:SER118 5.0 54.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human TRAP1 with Amppnp


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 Human TRAP1 with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg802 b:98.3 occ:1.00 ND2 C:ASN119 1.9 0.9 1.0 O2G C:ANP801 2.1 0.6 1.0 O2A C:ANP801 2.1 74.7 1.0 O2B C:ANP801 2.1 0.6 1.0 O3A C:ANP801 2.1 70.7 1.0 OD1 C:ASN119 2.1 0.6 1.0 CG C:ASN119 2.3 0.0 1.0 PB C:ANP801 2.5 69.0 1.0 PG C:ANP801 2.5 70.5 1.0 PA C:ANP801 2.6 72.6 1.0 O1G C:ANP801 2.7 70.5 1.0 N3B C:ANP801 3.0 57.2 1.0 O5' C:ANP801 3.5 43.1 1.0 CB C:ASN119 3.8 45.2 1.0 O1A C:ANP801 3.8 71.8 1.0 O1B C:ANP801 3.9 68.8 1.0 CA C:GLY204 4.0 43.8 1.0 O3G C:ANP801 4.1 42.3 1.0 OE1 C:GLU115 4.1 51.8 1.0 N C:GLY204 4.2 35.6 1.0 N C:PHE205 4.4 43.7 1.0 C C:GLY204 4.6 43.5 1.0 CA C:ASN119 4.7 45.5 1.0 CA C:GLY199 4.7 54.3 1.0 C5' C:ANP801 4.8 43.3 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human TRAP1 with Amppnp


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 Human TRAP1 with Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg802 b:0.2 occ:1.00 ND2 D:ASN119 1.9 41.1 1.0 N3B D:ANP801 1.9 0.9 1.0 PB D:ANP801 1.9 58.8 1.0 O1A D:ANP801 2.1 64.4 1.0 O3A D:ANP801 2.1 87.7 1.0 PA D:ANP801 2.1 66.7 1.0 O1B D:ANP801 2.1 58.6 1.0 OD1 D:ASN119 2.1 41.4 1.0 O1G D:ANP801 2.1 0.7 1.0 O5' D:ANP801 2.1 67.1 1.0 CG D:ASN119 2.2 41.2 1.0 PG D:ANP801 2.7 65.6 1.0 O2B D:ANP801 3.4 61.6 1.0 C5' D:ANP801 3.6 57.5 1.0 O2G D:ANP801 3.6 55.5 1.0 O2A D:ANP801 3.6 69.6 1.0 CB D:ASN119 3.7 27.8 1.0 O3G D:ANP801 4.0 80.1 1.0 CA D:ASN119 4.6 41.0 1.0 C3' D:ANP801 4.6 56.8 1.0 C4' D:ANP801 4.6 57.9 1.0 N D:GLY204 4.6 46.8 1.0 CA D:GLY204 4.6 45.2 1.0 CA D:GLY199 4.7 50.5 1.0 N D:PHE205 4.8 42.4 1.0

C.Lee, H.K.Park, H.Jeong, J.Lim, A.J.Lee, K.Y.Cheon, C.S.Kim, A.P.Thomas, B.Bae, N.D.Kim, S.H.Kim, P.G.Suh, J.H.Ryu, B.H.Kang. Development of A Mitochondria-Targeted HSP90 Inhibitor Based on the Crystal Structures of Human TRAP1 J.Am.Chem.Soc. V. 137 4358 2015.
ISSN: ESSN 1520-5126
PubMed: 25785725
DOI: 10.1021/JA511893N