Magnesium in PDB 5lpn: Structure of Human RAB10 in Complex with the Bmerb Domain of Mical-1

The structure of Structure of Human RAB10 in Complex with the Bmerb Domain of Mical-1, PDB code: 5lpn was solved by A.Rai, A.Oprisko, J.Campos, Y.Fu, T.Friese, A.Itzen, R.S.Goody, M.P.Mueller, E.M.Gazdag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.390, 59.000, 198.180, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 28.7

The binding sites of Magnesium atom in the Structure of Human RAB10 in Complex with the Bmerb Domain of Mical-1 (pdb code 5lpn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Human RAB10 in Complex with the Bmerb Domain of Mical-1, PDB code: 5lpn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human RAB10 in Complex with the Bmerb Domain of Mical-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human RAB10 in Complex with the Bmerb Domain of Mical-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:62.0 occ:1.00 O3G A:GNP202 1.9 64.4 1.0 OG1 A:THR23 1.9 55.4 1.0 O A:HOH302 1.9 65.8 1.0 OG1 A:THR41 2.0 64.8 1.0 O A:HOH301 2.1 43.3 1.0 O2B A:GNP202 2.4 54.2 1.0 CB A:THR41 3.0 64.9 1.0 PG A:GNP202 3.2 59.3 1.0 CB A:THR23 3.3 45.3 1.0 PB A:GNP202 3.5 57.5 1.0 N3B A:GNP202 3.6 63.9 1.0 O2G A:GNP202 3.6 53.7 1.0 OD2 A:ASP64 3.6 55.1 1.0 N A:THR41 3.7 68.0 1.0 CA A:THR41 3.9 68.8 1.0 O1A A:GNP202 3.9 82.8 1.0 N A:THR23 4.0 42.5 1.0 O A:THR65 4.0 70.0 1.0 CG2 A:THR41 4.1 64.9 1.0 OD1 A:ASP64 4.1 78.2 1.0 CA A:THR23 4.2 46.7 1.0 CG A:ASP64 4.2 64.7 1.0 CG2 A:THR23 4.2 46.2 1.0 O1G A:GNP202 4.5 53.8 1.0 O1B A:GNP202 4.5 51.7 1.0 O3A A:GNP202 4.6 69.1 1.0 PA A:GNP202 4.7 66.7 1.0 O A:ILE39 4.7 89.7 1.0 C A:SER40 4.7 73.2 1.0 O2A A:GNP202 5.0 62.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Human RAB10 in Complex with the Bmerb Domain of Mical-1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human RAB10 in Complex with the Bmerb Domain of Mical-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg201 b:93.5 occ:1.00 O2G C:GNP202 1.9 91.8 1.0 OG1 C:THR23 2.0 78.8 1.0 OG1 C:THR41 2.0 85.8 1.0 O C:HOH302 2.0 88.2 1.0 O C:HOH301 2.4 86.5 1.0 O1B C:GNP202 2.4 95.2 1.0 CB C:THR41 3.0 85.0 1.0 CB C:THR23 3.1 77.0 1.0 PG C:GNP202 3.3 93.8 1.0 N C:THR41 3.4 88.7 1.0 PB C:GNP202 3.5 94.1 1.0 N3B C:GNP202 3.6 1.0 1.0 CA C:THR41 3.8 94.7 1.0 CG2 C:THR23 4.0 74.5 1.0 O2A C:GNP202 4.0 90.0 1.0 N C:THR23 4.0 60.8 1.0 O3G C:GNP202 4.1 0.8 1.0 O C:ILE39 4.2 0.6 1.0 CA C:THR23 4.2 64.0 1.0 CG2 C:THR41 4.2 82.9 1.0 O1G C:GNP202 4.3 85.3 1.0 O3A C:GNP202 4.3 90.1 1.0 O1A C:GNP202 4.3 97.0 1.0 PA C:GNP202 4.4 90.8 1.0 OD2 C:ASP64 4.5 82.5 1.0 C C:SER40 4.5 81.7 1.0 OD1 C:ASP64 4.7 91.7 1.0 O C:THR65 4.7 0.6 1.0 O2B C:GNP202 4.8 74.8 1.0 CA C:SER40 4.9 86.4 1.0 CG C:ASP64 4.9 88.2 1.0

A.Rai, A.Oprisko, J.Campos, Y.Fu, T.Friese, A.Itzen, R.S.Goody, E.M.Gazdag, M.P.Muller. Bmerb Domains Are Bivalent RAB8 Family Effectors Evolved By Gene Duplication. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27552051
DOI: 10.7554/ELIFE.18675