Magnesium in PDB 7edz: Crystal Structure of Human Ppcs in Complex with P-Hopan and Amppnp

All present enzymatic activity of Crystal Structure of Human Ppcs in Complex with P-Hopan and Amppnp:
6.3.2.51;

The structure of Crystal Structure of Human Ppcs in Complex with P-Hopan and Amppnp, PDB code: 7edz was solved by N.Sharma, K.J.Mostert, E.Strauss, R.Anand, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.72 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100, 100, 146.9, 90, 90.2, 90
R / Rfree (%)	17.7 / 20.6

The binding sites of Magnesium atom in the Crystal Structure of Human Ppcs in Complex with P-Hopan and Amppnp (pdb code 7edz). 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 Ppcs in Complex with P-Hopan and Amppnp, PDB code: 7edz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Ppcs in Complex with P-Hopan and 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 Ppcs in Complex with P-Hopan and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg403 b:28.1 occ:1.00 O1G D:ANP401 2.0 24.3 1.0 O2B D:ANP401 2.1 25.9 1.0 O1A D:ANP401 2.1 21.1 1.0 OD1 D:ASP183 2.1 26.8 1.0 O D:HOH511 2.2 25.3 1.0 O D:HOH505 2.2 21.0 1.0 CG D:ASP183 3.0 27.8 1.0 PB D:ANP401 3.1 25.3 1.0 PA D:ANP401 3.2 24.3 1.0 OD2 D:ASP183 3.3 27.7 1.0 PG D:ANP401 3.4 28.1 1.0 O3A D:ANP401 3.5 23.5 1.0 N3B D:ANP401 3.6 25.2 1.0 O5' D:ANP401 4.0 24.2 1.0 OAC D:J1O405 4.0 69.1 1.0 NZ D:LYS212 4.0 33.8 1.0 CAP D:J1O405 4.1 52.0 1.0 OAF D:J1O405 4.1 51.7 1.0 O2G D:ANP401 4.3 25.0 1.0 O3G D:ANP401 4.3 26.9 1.0 O D:VAL181 4.3 25.1 1.0 O2A D:ANP401 4.4 24.3 1.0 CB D:ASP183 4.5 24.8 1.0 O1B D:ANP401 4.5 28.3 1.0 C8 D:ANP401 4.6 23.4 1.0 CAL D:J1O405 4.9 35.4 1.0 N7 D:ANP401 4.9 25.4 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Ppcs in Complex with P-Hopan and 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 Ppcs in Complex with P-Hopan and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:24.6 occ:1.00 O2B C:ANP401 2.0 24.5 1.0 O2G C:ANP401 2.1 25.3 1.0 OD1 C:ASP183 2.1 26.2 1.0 O1A C:ANP401 2.1 22.4 1.0 O C:HOH516 2.2 27.2 1.0 O C:HOH507 2.2 20.1 1.0 CG C:ASP183 3.0 29.0 1.0 PB C:ANP401 3.1 25.7 1.0 PA C:ANP401 3.2 24.3 1.0 OD2 C:ASP183 3.4 26.4 1.0 PG C:ANP401 3.4 27.6 1.0 O3A C:ANP401 3.5 23.2 1.0 N3B C:ANP401 3.6 24.5 1.0 O5' C:ANP401 3.9 22.9 1.0 NZ C:LYS212 4.0 34.2 1.0 OAF C:J1O402 4.1 48.8 0.7 OAC C:J1O402 4.2 48.0 1.0 CAP C:J1O402 4.2 45.7 0.7 O3G C:ANP401 4.3 24.4 1.0 O1G C:ANP401 4.3 28.2 1.0 O C:VAL181 4.4 24.7 1.0 O1B C:ANP401 4.4 26.6 1.0 CB C:ASP183 4.4 25.5 1.0 O2A C:ANP401 4.4 24.2 1.0 C8 C:ANP401 4.6 24.0 1.0 N7 C:ANP401 4.9 26.0 1.0 O C:HOH552 4.9 29.1 1.0 CAL C:J1O402 5.0 33.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Ppcs in Complex with P-Hopan and 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 Ppcs in Complex with P-Hopan and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:24.9 occ:1.00 O2B B:ANP401 2.0 23.0 1.0 O2G B:ANP401 2.0 26.6 1.0 OD1 B:ASP183 2.0 25.8 1.0 O B:HOH534 2.1 26.8 1.0 O1A B:ANP401 2.1 25.1 1.0 O B:HOH504 2.2 20.5 1.0 CG B:ASP183 3.0 29.4 1.0 PB B:ANP401 3.0 25.8 1.0 PA B:ANP401 3.3 24.9 1.0 OD2 B:ASP183 3.4 29.0 1.0 PG B:ANP401 3.4 28.9 1.0 O3A B:ANP401 3.5 22.0 1.0 N3B B:ANP401 3.6 27.2 1.0 NZ A:LYS195 3.8 31.4 1.0 NZ B:LYS212 3.9 34.2 1.0 O5' B:ANP401 3.9 24.4 1.0 O A:HOH552 4.0 26.9 1.0 OAF B:J1O402 4.2 48.9 1.0 O3G B:ANP401 4.2 27.4 1.0 OAC B:J1O402 4.3 49.3 0.7 CAP B:J1O402 4.3 48.1 0.7 O1G B:ANP401 4.3 28.4 1.0 O B:VAL181 4.4 24.2 1.0 O1B B:ANP401 4.4 27.4 1.0 CB B:ASP183 4.4 26.2 1.0 CE A:LYS195 4.4 31.5 1.0 O2A B:ANP401 4.5 26.0 1.0 C8 B:ANP401 4.6 26.1 1.0 OG A:SER198 4.6 37.2 1.0 N7 B:ANP401 4.9 26.6 1.0 O B:HOH566 5.0 30.2 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Ppcs in Complex with P-Hopan and 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 Ppcs in Complex with P-Hopan and Amppnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:25.6 occ:1.00 O2G A:ANP401 2.0 26.0 1.0 O2B A:ANP401 2.0 24.6 1.0 OD1 A:ASP183 2.1 25.0 1.0 O1A A:ANP401 2.1 23.7 1.0 O A:HOH531 2.2 28.5 1.0 O A:HOH507 2.2 20.9 1.0 CG A:ASP183 3.0 29.6 1.0 PB A:ANP401 3.1 24.3 1.0 PA A:ANP401 3.2 24.3 1.0 PG A:ANP401 3.3 28.0 1.0 OD2 A:ASP183 3.4 28.6 1.0 O3A A:ANP401 3.4 23.0 1.0 N3B A:ANP401 3.6 24.1 1.0 NZ B:LYS195 3.8 34.7 1.0 O B:HOH538 3.9 30.5 1.0 NZ A:LYS212 4.0 29.3 1.0 O5' A:ANP401 4.0 23.1 1.0 OAC A:J1O402 4.1 40.8 1.0 CAP A:J1O402 4.2 40.7 0.7 O3G A:ANP401 4.3 25.0 1.0 OAF A:J1O402 4.3 45.7 0.7 O1G A:ANP401 4.3 28.4 1.0 O1B A:ANP401 4.4 25.9 1.0 CE B:LYS195 4.4 34.2 1.0 O A:VAL181 4.4 26.2 1.0 CB A:ASP183 4.4 25.2 1.0 O2A A:ANP401 4.5 24.2 1.0 C8 A:ANP401 4.6 21.7 1.0 OG B:SER198 4.7 39.4 1.0 N7 A:ANP401 4.9 25.3 1.0 O A:HOH545 5.0 26.8 1.0

K.J.Mostert, N.Sharma, M.Van Der Zwaag, R.Staats, L.Koekemoer, R.Anand, O.C.M.Sibon, E.Strauss. The Coenzyme A Level Modulator Hopantenate (Hopan) Inhibits Phosphopantotenoylcysteine Synthetase Activity. Acs Chem.Biol. 2021.
ISSN: ESSN 1554-8937
PubMed: 34582681
DOI: 10.1021/ACSCHEMBIO.1C00535