Magnesium in PDB 8oum: Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp

The structure of Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp, PDB code: 8oum was solved by J.Menetrey, C.Jackson, J.B.Dacks, M.Elias, R.Vargova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.41 / 2.67
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	87.25, 54.88, 121.79, 90, 94.47, 90
R / Rfree (%)	23.6 / 26.7

The binding sites of Magnesium atom in the Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp (pdb code 8oum). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp, PDB code: 8oum:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:47.1 occ:1.00 O3G A:GTP201 2.0 60.3 1.0 O A:HOH301 2.0 41.0 1.0 OG1 A:THR46 2.1 60.6 1.0 OG1 A:THR29 2.1 58.2 1.0 O A:HOH302 2.2 60.1 1.0 O2B A:GTP201 2.2 59.4 1.0 CB A:THR46 3.1 59.8 1.0 PG A:GTP201 3.3 60.0 1.0 CB A:THR29 3.4 56.5 1.0 N A:THR46 3.4 59.6 1.0 PB A:GTP201 3.4 60.1 1.0 O3B A:GTP201 3.6 60.3 1.0 CA A:THR46 3.8 58.9 1.0 O1G A:GTP201 3.9 59.4 1.0 O A:LEU44 3.9 62.4 1.0 OD2 A:ASP65 4.1 58.4 1.0 CG2 A:THR29 4.2 56.5 1.0 O1A A:GTP201 4.2 59.1 1.0 CG2 A:THR46 4.3 60.2 1.0 N A:THR29 4.3 53.0 1.0 OD1 A:ASP65 4.4 58.2 1.0 CA A:THR29 4.4 54.5 1.0 O3A A:GTP201 4.4 59.5 1.0 O2G A:GTP201 4.4 59.9 1.0 C A:PRO45 4.5 60.7 1.0 O1B A:GTP201 4.5 60.6 1.0 O A:HOH320 4.7 48.0 1.0 CG A:ASP65 4.7 57.5 1.0 CA A:PRO45 4.7 61.3 1.0 PA A:GTP201 4.7 59.3 1.0 O2A A:GTP201 4.8 58.9 1.0 C A:LEU44 4.9 62.3 1.0

Magnesium binding site 2 out of 5 in the Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:46.5 occ:1.00 OG1 B:THR46 1.9 58.4 1.0 O B:HOH305 1.9 27.9 1.0 O3G B:GTP201 2.0 57.7 1.0 OG1 B:THR29 2.2 55.6 1.0 O2B B:GTP201 2.3 56.1 1.0 O B:HOH306 2.5 45.6 1.0 CB B:THR46 2.8 58.4 1.0 PG B:GTP201 3.3 57.2 1.0 N B:THR46 3.5 58.9 1.0 CB B:THR29 3.5 54.1 1.0 PB B:GTP201 3.6 56.5 1.0 CA B:THR46 3.7 59.0 1.0 O3B B:GTP201 3.7 56.9 1.0 O1G B:GTP201 3.8 57.3 1.0 OD2 B:ASP65 3.9 65.3 1.0 CG2 B:THR46 3.9 58.6 1.0 OD1 B:ASP65 4.1 63.1 1.0 O B:LEU44 4.1 61.2 1.0 N B:THR29 4.3 52.4 1.0 CG2 B:THR29 4.3 53.6 1.0 CG B:ASP65 4.4 62.7 1.0 CA B:THR29 4.5 52.1 1.0 O2G B:GTP201 4.5 56.3 1.0 O1B B:GTP201 4.6 56.4 1.0 O1A B:GTP201 4.6 55.5 1.0 C B:PRO45 4.6 59.0 1.0 O B:HOH321 4.6 27.2 1.0 O3A B:GTP201 4.6 56.4 1.0 O B:LEU66 4.8 61.2 1.0 CA B:PRO45 4.9 59.8 1.0 C B:THR46 4.9 60.2 1.0 CE B:LYS28 5.0 57.3 1.0

Magnesium binding site 3 out of 5 in the Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:52.0 occ:1.00 O3G C:GTP201 2.0 61.1 1.0 O C:HOH301 2.0 31.3 1.0 OG1 C:THR46 2.2 68.4 1.0 OG1 C:THR29 2.2 62.6 1.0 O2B C:GTP201 2.3 59.7 1.0 CB C:THR46 3.2 67.3 1.0 N C:THR46 3.3 68.4 1.0 CB C:THR29 3.3 61.1 1.0 PG C:GTP201 3.4 60.7 1.0 O C:LEU44 3.5 73.0 1.0 PB C:GTP201 3.5 60.3 1.0 O3B C:GTP201 3.6 60.6 1.0 CA C:THR46 3.8 67.2 1.0 O C:HOH307 4.0 43.5 1.0 O1A C:GTP201 4.0 60.5 1.0 O1G C:GTP201 4.1 60.5 1.0 CG2 C:THR29 4.1 60.2 1.0 C C:PRO45 4.3 69.5 1.0 OD2 C:ASP65 4.3 68.6 1.0 O3A C:GTP201 4.4 60.1 1.0 N C:THR29 4.4 58.5 1.0 O2G C:GTP201 4.4 60.5 1.0 CG2 C:THR46 4.4 66.8 1.0 CA C:PRO45 4.4 70.3 1.0 CA C:THR29 4.5 59.8 1.0 C C:LEU44 4.5 72.9 1.0 PA C:GTP201 4.6 60.5 1.0 O1B C:GTP201 4.7 60.4 1.0 O2A C:GTP201 4.7 60.1 1.0 OD1 C:ASP65 4.7 67.5 1.0 O C:HOH310 5.0 45.4 1.0 CG C:ASP65 5.0 66.5 1.0 O C:HOH311 5.0 38.0 1.0 N C:PRO45 5.0 71.2 1.0

Magnesium binding site 4 out of 5 in the Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg202 b:63.7 occ:1.00 O3G D:GTP201 1.9 59.4 1.0 O2B D:GTP201 1.9 58.7 1.0 O D:HOH301 1.9 75.0 1.0 O D:HOH305 2.1 64.0 1.0 OG1 D:THR29 2.2 58.7 1.0 OG1 D:THR46 2.4 66.8 1.0 PG D:GTP201 3.1 59.1 1.0 PB D:GTP201 3.2 58.5 1.0 CB D:THR46 3.3 66.2 1.0 CB D:THR29 3.3 57.8 1.0 O3B D:GTP201 3.4 58.7 1.0 N D:THR46 3.6 66.8 1.0 O1G D:GTP201 3.8 58.8 1.0 O D:LEU44 4.0 70.2 1.0 O1A D:GTP201 4.0 57.7 1.0 CA D:THR46 4.0 65.8 1.0 O3A D:GTP201 4.1 58.1 1.0 N D:THR29 4.2 56.6 1.0 OD2 D:ASP65 4.2 73.4 1.0 O1B D:GTP201 4.2 58.4 1.0 CG2 D:THR29 4.2 58.3 1.0 O2G D:GTP201 4.3 58.7 1.0 CA D:THR29 4.4 56.6 1.0 OD1 D:ASP65 4.4 70.9 1.0 CG2 D:THR46 4.4 66.2 1.0 PA D:GTP201 4.5 57.6 1.0 O2A D:GTP201 4.5 57.6 1.0 C D:PRO45 4.6 68.2 1.0 CA D:PRO45 4.7 69.2 1.0 CG D:ASP65 4.8 70.3 1.0 C D:LEU44 5.0 70.0 1.0 O D:HOH321 5.0 38.1 1.0

Magnesium binding site 5 out of 5 in the Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Arf Gtpase From the Asgard Gerdarchaea : GERDARFR1 Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg202 b:60.8 occ:1.00 O E:HOH302 1.9 46.5 1.0 OG1 E:THR29 1.9 59.8 1.0 O2B E:GTP201 1.9 72.9 1.0 O3G E:GTP201 2.1 72.5 1.0 O E:HOH303 2.2 46.0 1.0 OG1 E:THR46 2.3 69.3 1.0 CB E:THR29 3.2 58.5 1.0 CB E:THR46 3.2 69.2 1.0 PB E:GTP201 3.3 73.4 1.0 PG E:GTP201 3.3 72.3 1.0 O3B E:GTP201 3.5 72.8 1.0 N E:THR46 3.7 70.4 1.0 O1G E:GTP201 3.9 72.4 1.0 OD2 E:ASP65 4.0 60.1 1.0 N E:THR29 4.0 55.4 1.0 CA E:THR46 4.1 69.5 1.0 O E:LEU44 4.1 75.6 1.0 CG2 E:THR29 4.1 58.5 1.0 O1A E:GTP201 4.2 76.2 1.0 CA E:THR29 4.2 56.7 1.0 OD1 E:ASP65 4.2 57.6 1.0 O3A E:GTP201 4.2 74.7 1.0 O1B E:GTP201 4.3 73.3 1.0 CG2 E:THR46 4.4 68.9 1.0 CG E:ASP65 4.5 58.3 1.0 O2A E:GTP201 4.5 75.9 1.0 PA E:GTP201 4.6 76.0 1.0 O2G E:GTP201 4.6 71.7 1.0 C E:PRO45 4.8 71.4 1.0

J.Menetrey, J.Menetrey, C.Jackson, J.B.Dacks, M.Elias, R.Vargova. N/A N/A.