Magnesium in PDB 6stf: Human RAB8A Phosphorylated at SER111 in Complex with Gdp

The structure of Human RAB8A Phosphorylated at SER111 in Complex with Gdp, PDB code: 6stf was solved by S.Vieweg, K.Mulholland, B.Braeuning, N.Kachariya, Y.Lai, R.Toth, M.Sattler, M.Groll, A.Itzen, M.M.K.Muqit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.550, 75.180, 107.700, 90.00, 100.48, 90.00
R / Rfree (%)	23.3 / 26.2

The binding sites of Magnesium atom in the Human RAB8A Phosphorylated at SER111 in Complex with Gdp (pdb code 6stf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Human RAB8A Phosphorylated at SER111 in Complex with Gdp, PDB code: 6stf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Human RAB8A Phosphorylated at SER111 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human RAB8A Phosphorylated at SER111 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:44.5 occ:1.00 O A:HOH1003 1.9 33.4 1.0 O A:HOH1005 2.0 37.7 1.0 O A:HOH1008 2.0 46.8 1.0 O3B A:GDP901 2.0 39.0 1.0 O A:HOH1006 2.0 39.8 1.0 OG1 A:THR22 2.1 37.9 1.0 PB A:GDP901 3.1 38.9 1.0 O1B A:GDP901 3.3 40.2 1.0 CB A:THR22 3.3 37.9 1.0 O1A A:GDP901 4.0 39.7 1.0 OD2 A:ASP63 4.1 50.1 1.0 O2B A:GDP901 4.1 38.1 1.0 N A:THR22 4.2 36.9 1.0 O3A A:GDP901 4.2 39.0 1.0 OD1 A:ASP63 4.2 50.7 1.0 CG2 A:THR22 4.2 37.9 1.0 CA A:THR22 4.3 37.7 1.0 PA A:GDP901 4.4 39.2 1.0 O2A A:GDP901 4.5 39.0 1.0 CG A:ASP63 4.6 50.2 1.0 NZ A:LYS21 5.0 34.2 1.0

Magnesium binding site 2 out of 5 in the Human RAB8A Phosphorylated at SER111 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human RAB8A Phosphorylated at SER111 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:47.6 occ:1.00 O B:HOH1006 1.9 37.0 1.0 O B:HOH1002 1.9 39.1 1.0 O B:HOH1003 2.0 34.0 1.0 O3B B:GDP901 2.0 39.2 1.0 O B:HOH1008 2.1 28.4 1.0 OG1 B:THR22 2.2 36.3 1.0 PB B:GDP901 3.0 39.3 1.0 O1B B:GDP901 3.1 39.9 1.0 CB B:THR22 3.4 36.0 1.0 O1A B:GDP901 4.0 40.0 1.0 OD2 B:ASP63 4.0 50.7 1.0 O2B B:GDP901 4.1 38.8 1.0 OD1 B:ASP63 4.1 51.0 1.0 O3A B:GDP901 4.1 38.8 1.0 N B:THR22 4.1 35.0 1.0 PA B:GDP901 4.3 38.9 1.0 CG2 B:THR22 4.3 35.9 1.0 CA B:THR22 4.3 35.4 1.0 O2A B:GDP901 4.4 38.8 1.0 CG B:ASP63 4.5 51.0 1.0 NZ B:LYS21 4.9 35.3 1.0 CB B:ALA65 5.0 74.7 1.0

Magnesium binding site 3 out of 5 in the Human RAB8A Phosphorylated at SER111 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human RAB8A Phosphorylated at SER111 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg902 b:34.1 occ:1.00 O C:HOH1007 1.9 37.1 1.0 O3B C:GDP901 2.0 31.8 1.0 O C:HOH1002 2.0 25.1 1.0 O C:HOH1004 2.2 28.3 1.0 OG1 C:THR22 2.2 35.5 1.0 O C:HOH1001 2.2 28.5 1.0 PB C:GDP901 3.1 31.7 1.0 O2B C:GDP901 3.3 32.4 1.0 CB C:THR22 3.4 35.5 1.0 O2A C:GDP901 3.9 32.4 1.0 OD2 C:ASP63 4.1 48.5 1.0 OD1 C:ASP63 4.1 49.5 1.0 O1B C:GDP901 4.1 31.7 1.0 N C:THR22 4.2 35.9 1.0 O3A C:GDP901 4.2 31.6 1.0 CG2 C:THR22 4.3 35.2 1.0 CA C:THR22 4.3 35.8 1.0 PA C:GDP901 4.4 31.6 1.0 CG C:ASP63 4.5 48.5 1.0 O1A C:GDP901 4.6 31.8 1.0 O C:THR64 4.7 57.0 1.0 CA C:ALA65 4.8 60.2 1.0 NZ C:LYS21 5.0 39.2 1.0

Magnesium binding site 4 out of 5 in the Human RAB8A Phosphorylated at SER111 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human RAB8A Phosphorylated at SER111 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg902 b:48.8 occ:1.00 O D:HOH1001 1.9 30.7 1.0 O D:HOH1003 1.9 39.7 1.0 O D:HOH1006 1.9 37.1 1.0 O D:HOH1004 1.9 42.1 1.0 O3B D:GDP901 2.3 38.6 1.0 OG1 D:THR22 2.3 39.9 1.0 PB D:GDP901 3.4 38.9 1.0 O2B D:GDP901 3.5 40.1 1.0 CB D:THR22 3.5 39.1 1.0 O2A D:GDP901 3.8 39.5 1.0 OD2 D:ASP63 4.0 57.2 1.0 OD1 D:ASP63 4.3 57.2 1.0 CG2 D:THR22 4.4 38.9 1.0 O3A D:GDP901 4.4 39.0 1.0 N D:THR22 4.4 38.6 1.0 PA D:GDP901 4.5 39.0 1.0 O1B D:GDP901 4.5 38.0 1.0 CA D:THR22 4.6 38.7 1.0 CG D:ASP63 4.6 57.4 1.0 O1A D:GDP901 4.7 39.3 1.0

Magnesium binding site 5 out of 5 in the Human RAB8A Phosphorylated at SER111 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human RAB8A Phosphorylated at SER111 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg902 b:47.2 occ:1.00 O E:HOH1002 2.0 45.8 1.0 O2B E:GDP901 2.0 39.0 1.0 O E:HOH1006 2.0 33.4 1.0 O E:HOH1008 2.2 45.1 1.0 OG1 E:THR22 2.2 43.6 1.0 O E:HOH1003 2.4 29.9 1.0 PB E:GDP901 3.1 38.6 1.0 O3B E:GDP901 3.4 39.5 1.0 OD2 E:ASP63 3.5 54.7 1.0 CB E:THR22 3.6 42.9 1.0 OD1 E:ASP63 3.7 53.7 1.0 O1B E:GDP901 4.0 37.2 1.0 CG E:ASP63 4.0 53.5 1.0 N E:THR22 4.1 40.7 1.0 O2A E:GDP901 4.3 38.9 1.0 CA E:THR22 4.4 41.9 1.0 O3A E:GDP901 4.4 38.4 1.0 CG2 E:THR22 4.5 43.3 1.0 PA E:GDP901 4.7 38.4 1.0 NZ E:LYS21 4.7 38.8 1.0 CE E:LYS21 4.8 38.5 1.0 CB E:LYS21 4.8 37.9 1.0 O1A E:GDP901 4.9 38.3 1.0

S.Vieweg, K.Mulholland, B.Brauning, N.Kacharia, Y.C.Lai, R.Toth, P.K.Singh, I.Volpi, M.Sattler, M.Groll, A.Itzen, M.M.K.Muqit. PINK1-Dependent Phosphorylation of SERINE111 Within the SF3 Motif of Rab Gtpases Impairs Effector Interactions and LRRK2 Mediated Phosphorylation at THREONINE72. Biochem.J. 2020.
ISSN: ESSN 1470-8728
PubMed: 32227113
DOI: 10.1042/BCJ20190664