Magnesium in PDB 8dzm: Crystal Structure of Human SAR1A in Complex with Ppgpp and Magnesium

The structure of Crystal Structure of Human SAR1A in Complex with Ppgpp and Magnesium, PDB code: 8dzm was solved by Q.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.42 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.125, 35.933, 76.118, 90, 101.52, 90
R / Rfree (%)	17 / 19.7

The binding sites of Magnesium atom in the Crystal Structure of Human SAR1A in Complex with Ppgpp and Magnesium (pdb code 8dzm). 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 SAR1A in Complex with Ppgpp and Magnesium, PDB code: 8dzm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human SAR1A in Complex with Ppgpp and Magnesium


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 SAR1A in Complex with Ppgpp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:16.1 occ:1.00 O2D A:G4P203 2.0 17.0 1.0 O A:HOH328 2.1 16.4 1.0 O2C A:G4P203 2.1 17.1 1.0 PD A:G4P203 3.2 18.2 1.0 PC A:G4P203 3.2 17.0 1.0 O3C A:G4P203 3.3 18.2 1.0 O1D A:G4P203 4.2 18.9 1.0 O A:HOH413 4.2 29.4 1.0 O2A A:G4P203 4.2 16.8 1.0 O3D A:G4P203 4.3 20.6 1.0 O3' A:G4P203 4.3 16.8 1.0 C3' A:G4P203 4.3 16.5 1.0 O A:HOH367 4.3 19.9 1.0 O1C A:G4P203 4.3 18.5 1.0 C5' A:G4P203 4.5 15.5 1.0 O A:HOH355 4.6 20.0 1.0 C4' A:G4P203 4.6 16.3 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human SAR1A in Complex with Ppgpp and Magnesium


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 SAR1A in Complex with Ppgpp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:17.9 occ:1.00 O A:HOH378 2.0 18.3 1.0 O1B A:G4P203 2.0 16.2 1.0 OG1 A:THR39 2.0 17.3 1.0 O A:HOH322 2.1 19.9 1.0 O A:HOH391 2.1 19.3 1.0 O A:HOH316 2.2 16.2 1.0 CB A:THR39 3.1 18.1 1.0 PB A:G4P203 3.3 14.6 1.0 O2B A:G4P203 3.5 15.9 1.0 N A:THR39 4.0 14.3 1.0 O2A A:G4P203 4.0 16.8 1.0 OD1 A:ASP75 4.1 21.3 1.0 CG2 A:THR39 4.1 19.3 1.0 CA A:THR39 4.1 14.5 1.0 O A:HOH320 4.1 22.3 1.0 O A:HOH443 4.2 49.8 1.0 OD2 A:ASP75 4.3 24.1 1.0 O A:HOH310 4.3 45.6 1.0 O3A A:G4P203 4.3 15.3 1.0 O A:HOH359 4.3 22.8 1.0 O3B A:G4P203 4.3 16.2 1.0 CG A:LYS38 4.4 18.5 1.0 PA A:G4P203 4.6 15.8 1.0 CG A:ASP75 4.6 19.8 1.0 O1A A:G4P203 4.7 17.1 1.0 O A:HOH355 4.8 20.0 1.0 O A:HOH338 4.9 65.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human SAR1A in Complex with Ppgpp and Magnesium


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 SAR1A in Complex with Ppgpp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:17.8 occ:1.00 O2B B:G4P203 2.0 14.9 1.0 O B:HOH333 2.0 18.2 1.0 OG1 B:THR39 2.1 20.6 1.0 O B:HOH350 2.1 20.6 1.0 O B:HOH386 2.1 19.9 1.0 O B:HOH321 2.1 19.0 1.0 CB B:THR39 3.2 20.1 1.0 PB B:G4P203 3.3 16.4 1.0 O1B B:G4P203 3.4 16.6 1.0 N B:THR39 4.0 13.8 1.0 O2A B:G4P203 4.0 15.8 1.0 OD1 B:ASP75 4.0 23.9 1.0 CG2 B:THR39 4.1 23.1 1.0 CA B:THR39 4.2 16.9 1.0 O B:HOH339 4.2 27.1 1.0 OD2 B:ASP75 4.2 26.2 1.0 O3B B:G4P203 4.3 16.5 1.0 O3A B:G4P203 4.3 13.8 1.0 CG B:LYS38 4.4 18.9 1.0 O B:HOH301 4.4 28.1 1.0 PA B:G4P203 4.6 15.6 1.0 CG B:ASP75 4.6 23.5 1.0 O1A B:G4P203 4.7 17.6 1.0 O B:HOH354 4.7 17.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human SAR1A in Complex with Ppgpp and Magnesium


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 SAR1A in Complex with Ppgpp and Magnesium within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:15.6 occ:1.00 O1D B:G4P203 2.0 15.2 1.0 O B:HOH328 2.1 15.1 1.0 O1C B:G4P203 2.1 14.8 1.0 PD B:G4P203 3.2 18.2 1.0 PC B:G4P203 3.3 17.1 1.0 O3C B:G4P203 3.3 17.5 1.0 O2D B:G4P203 4.1 20.3 1.0 O B:HOH402 4.2 28.5 1.0 O2A B:G4P203 4.3 15.8 1.0 C3' B:G4P203 4.3 15.2 1.0 O3' B:G4P203 4.3 17.4 1.0 O3D B:G4P203 4.3 20.6 1.0 O2C B:G4P203 4.3 19.2 1.0 O B:HOH358 4.3 20.6 1.0 C5' B:G4P203 4.5 19.2 1.0 O B:HOH354 4.6 17.5 1.0 C4' B:G4P203 4.7 17.4 1.0

Q.Huang, Q.Huang. N/A N/A.