Magnesium in PDB 4uj3: Crystal Structure of Human RAB11-RABIN8-FIP3

The structure of Crystal Structure of Human RAB11-RABIN8-FIP3, PDB code: 4uj3 was solved by M.Vetter, E.Lorentzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.543 / 3.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.498, 165.374, 218.687, 90.00, 95.93, 90.00
R / Rfree (%)	19.79 / 25.04

The binding sites of Magnesium atom in the Crystal Structure of Human RAB11-RABIN8-FIP3 (pdb code 4uj3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Human RAB11-RABIN8-FIP3, PDB code: 4uj3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Human RAB11-RABIN8-FIP3


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 RAB11-RABIN8-FIP3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:62.0 occ:1.00 OG A:SER25 1.8 64.1 1.0 O3G A:GNP200 1.9 77.1 1.0 O2B A:GNP200 1.9 74.6 1.0 OG1 A:THR43 2.0 85.3 1.0 CB A:SER25 3.0 48.8 1.0 PG A:GNP200 3.0 75.3 1.0 PB A:GNP200 3.1 65.7 1.0 N3B A:GNP200 3.1 71.5 1.0 CB A:THR43 3.4 64.1 1.0 N A:SER25 3.8 54.0 1.0 O2A A:GNP200 3.8 65.5 1.0 O2G A:GNP200 3.8 76.3 1.0 OD2 A:ASP66 3.9 68.2 1.0 N A:THR43 3.9 89.3 1.0 CA A:SER25 3.9 49.8 1.0 O3A A:GNP200 4.1 57.2 1.0 O1B A:GNP200 4.2 61.0 1.0 OD1 A:ASP66 4.2 65.4 1.0 CA A:THR43 4.2 75.1 1.0 CG2 A:THR43 4.2 71.1 1.0 O1G A:GNP200 4.3 68.8 1.0 PA A:GNP200 4.3 61.8 1.0 O A:LYS41 4.5 91.4 1.0 CG A:ASP66 4.5 65.5 1.0 O1A A:GNP200 4.5 46.6 1.0 O A:THR67 4.7 58.2 1.0 C A:SER42 4.8 78.1 1.0 CA A:SER42 5.0 71.4 1.0 C A:LYS24 5.0 57.6 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Human RAB11-RABIN8-FIP3


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 RAB11-RABIN8-FIP3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:63.2 occ:1.00 OG D:SER25 1.9 59.8 1.0 O3G D:GNP200 2.0 65.0 1.0 OG1 D:THR43 2.1 69.3 1.0 O2B D:GNP200 2.2 69.8 1.0 PG D:GNP200 3.0 77.6 1.0 CB D:SER25 3.2 53.5 1.0 CB D:THR43 3.2 55.6 1.0 OD1 D:ASP66 3.2 54.8 1.0 PB D:GNP200 3.3 54.5 1.0 O2G D:GNP200 3.4 67.7 1.0 OD2 D:ASP66 3.4 67.6 1.0 N3B D:GNP200 3.6 63.7 1.0 N D:SER25 3.6 55.7 1.0 CG D:ASP66 3.7 61.6 1.0 CA D:SER25 3.8 58.1 1.0 O D:THR67 3.8 60.7 1.0 O1B D:GNP200 3.9 49.3 1.0 CG2 D:THR43 4.0 51.7 1.0 N D:THR43 4.3 74.2 1.0 O1G D:GNP200 4.4 66.3 1.0 CB D:LYS24 4.4 46.3 1.0 CA D:THR43 4.4 69.8 1.0 C D:THR67 4.6 70.0 1.0 O3A D:GNP200 4.6 55.1 1.0 CE D:LYS24 4.6 57.4 1.0 C D:LYS24 4.6 58.9 1.0 O2A D:GNP200 4.8 65.3 1.0 O1A D:GNP200 4.9 56.5 1.0 NZ D:LYS24 4.9 63.2 1.0 PA D:GNP200 4.9 62.2 1.0 CA D:LYS24 4.9 57.6 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Human RAB11-RABIN8-FIP3


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 RAB11-RABIN8-FIP3 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg201 b:50.8 occ:1.00 OG G:SER25 2.0 57.1 1.0 O2B G:GNP200 2.2 62.8 1.0 OG1 G:THR43 2.2 62.7 1.0 O3G G:GNP200 2.3 65.0 1.0 PG G:GNP200 3.2 72.2 1.0 CB G:THR43 3.3 56.1 1.0 O2G G:GNP200 3.3 64.0 1.0 PB G:GNP200 3.3 53.5 1.0 OD1 G:ASP66 3.3 50.9 1.0 CB G:SER25 3.4 56.0 1.0 OD2 G:ASP66 3.6 58.6 1.0 O G:THR67 3.6 53.5 1.0 N G:SER25 3.6 52.1 1.0 N3B G:GNP200 3.7 54.1 1.0 CG G:ASP66 3.9 56.7 1.0 O1B G:GNP200 3.9 47.1 1.0 CA G:SER25 3.9 52.4 1.0 CG2 G:THR43 4.0 54.2 1.0 CB G:LYS24 4.2 50.9 1.0 CE G:LYS24 4.3 46.1 1.0 O2A G:GNP200 4.3 53.7 1.0 C G:THR67 4.4 62.2 1.0 N G:THR43 4.5 63.4 1.0 CA G:THR43 4.5 64.4 1.0 O1G G:GNP200 4.6 84.2 1.0 O3A G:GNP200 4.6 35.7 1.0 C G:LYS24 4.6 53.3 1.0 NZ G:LYS24 4.8 49.9 1.0 N G:GLY69 4.9 70.5 1.0 CA G:LYS24 4.9 51.0 1.0 PA G:GNP200 4.9 57.3 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Human RAB11-RABIN8-FIP3


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 RAB11-RABIN8-FIP3 within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg201 b:70.3 occ:1.00 O3G J:GNP200 2.0 82.9 1.0 OG1 J:THR43 2.0 59.5 1.0 OG J:SER25 2.2 73.2 1.0 O2B J:GNP200 2.6 64.1 1.0 CB J:THR43 3.0 68.0 1.0 PG J:GNP200 3.1 85.0 1.0 OD1 J:ASP66 3.3 58.5 1.0 O2G J:GNP200 3.4 71.8 1.0 OD2 J:ASP66 3.5 51.1 1.0 CB J:SER25 3.5 58.0 1.0 O J:THR67 3.6 53.8 1.0 PB J:GNP200 3.6 64.3 1.0 CG2 J:THR43 3.7 58.3 1.0 N3B J:GNP200 3.8 78.9 1.0 CG J:ASP66 3.8 48.0 1.0 N J:SER25 3.9 58.0 1.0 CA J:SER25 4.1 52.1 1.0 C J:THR67 4.2 56.9 1.0 O1B J:GNP200 4.2 51.7 1.0 CA J:THR43 4.3 80.2 1.0 N J:THR43 4.3 68.4 1.0 CE J:LYS24 4.3 63.2 1.0 O1G J:GNP200 4.4 63.5 1.0 CB J:LYS24 4.4 46.1 1.0 CA J:ALA68 4.6 69.8 1.0 NZ J:LYS24 4.7 64.1 1.0 N J:ALA68 4.7 64.5 1.0 O2A J:GNP200 4.8 62.2 1.0 N J:THR67 4.9 61.9 1.0 C J:LYS24 4.9 61.3 1.0 O3A J:GNP200 4.9 54.0 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Human RAB11-RABIN8-FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human RAB11-RABIN8-FIP3 within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg201 b:58.6 occ:1.00 OG M:SER25 1.9 71.6 1.0 OG1 M:THR43 2.2 72.3 1.0 O3G M:GNP200 2.2 75.1 1.0 O2B M:GNP200 2.2 61.3 1.0 PG M:GNP200 3.0 84.3 1.0 O2G M:GNP200 3.1 65.8 1.0 OD1 M:ASP66 3.2 68.5 1.0 CB M:SER25 3.2 61.2 1.0 CB M:THR43 3.3 69.2 1.0 PB M:GNP200 3.3 62.0 1.0 OD2 M:ASP66 3.5 69.5 1.0 N3B M:GNP200 3.6 69.7 1.0 N M:SER25 3.6 67.6 1.0 O M:THR67 3.7 87.3 1.0 CG M:ASP66 3.7 73.8 1.0 CA M:SER25 3.8 54.0 1.0 O1B M:GNP200 3.9 58.8 1.0 CG2 M:THR43 4.1 57.4 1.0 CB M:LYS24 4.3 49.0 1.0 CE M:LYS24 4.3 72.1 1.0 N M:THR43 4.3 76.9 1.0 C M:THR67 4.4 75.8 1.0 CA M:THR43 4.4 78.7 1.0 O1G M:GNP200 4.4 69.1 1.0 O3A M:GNP200 4.6 56.2 1.0 C M:LYS24 4.6 65.3 1.0 NZ M:LYS24 4.6 63.6 1.0 O2A M:GNP200 4.7 68.6 1.0 N M:THR67 4.9 72.5 1.0 PA M:GNP200 4.9 67.1 1.0 N M:ALA68 5.0 86.3 1.0 CA M:LYS24 5.0 54.3 1.0 CA M:ALA68 5.0 87.1 1.0 O1A M:GNP200 5.0 59.0 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Human RAB11-RABIN8-FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human RAB11-RABIN8-FIP3 within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg201 b:76.7 occ:1.00 O3G P:GNP200 2.1 79.2 1.0 OG P:SER25 2.3 85.6 1.0 OG1 P:THR43 2.3 92.5 1.0 O2G P:GNP200 2.5 0.1 1.0 O2B P:GNP200 2.6 71.9 1.0 PG P:GNP200 2.7 92.0 1.0 CB P:THR43 3.2 99.2 1.0 OD1 P:ASP66 3.3 68.2 1.0 O P:THR67 3.5 93.6 1.0 OD2 P:ASP66 3.6 77.3 1.0 N3B P:GNP200 3.6 82.5 1.0 CB P:SER25 3.6 73.6 1.0 PB P:GNP200 3.7 81.2 1.0 CG P:ASP66 3.9 80.5 1.0 N P:SER25 3.9 84.8 1.0 O1G P:GNP200 4.0 86.8 1.0 C P:THR67 4.1 94.0 1.0 N P:THR43 4.1 0.5 1.0 CG2 P:THR43 4.2 1.0 1.0 CA P:SER25 4.2 76.0 1.0 CA P:THR43 4.3 0.4 1.0 O1B P:GNP200 4.5 71.6 1.0 O2A P:GNP200 4.5 85.8 1.0 CB P:LYS24 4.5 80.1 1.0 CE P:LYS24 4.6 83.4 1.0 CA P:ALA68 4.6 95.3 1.0 N P:ALA68 4.6 95.6 1.0 O3A P:GNP200 4.8 89.7 1.0 N P:THR67 4.9 90.0 1.0 N P:GLY69 4.9 0.1 1.0 C P:LYS24 4.9 79.9 1.0 CA P:THR67 4.9 87.9 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Human RAB11-RABIN8-FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Human RAB11-RABIN8-FIP3 within 5.0Å range: probe atom residue distance (Å) B Occ S:Mg201 b:61.5 occ:1.00 OG S:SER25 2.0 61.6 1.0 O3G S:GNP200 2.0 72.3 1.0 OG1 S:THR43 2.2 78.1 1.0 O2B S:GNP200 2.4 61.1 1.0 PG S:GNP200 2.9 81.7 1.0 OD1 S:ASP66 3.1 56.0 1.0 O2G S:GNP200 3.1 90.6 1.0 CB S:SER25 3.2 67.1 1.0 CB S:THR43 3.3 67.8 1.0 OD2 S:ASP66 3.4 69.9 1.0 PB S:GNP200 3.5 74.2 1.0 O S:THR67 3.6 64.9 1.0 N3B S:GNP200 3.6 80.7 1.0 NZ S:LYS24 3.6 80.5 1.0 N S:SER25 3.6 68.4 1.0 CG S:ASP66 3.7 69.6 1.0 CA S:SER25 3.9 69.6 1.0 CG2 S:THR43 4.0 79.2 1.0 O1B S:GNP200 4.3 63.0 1.0 O1G S:GNP200 4.3 76.7 1.0 C S:THR67 4.3 69.3 1.0 CB S:LYS24 4.4 60.5 1.0 O2A S:GNP200 4.4 85.4 1.0 N S:THR43 4.4 89.8 1.0 CA S:THR43 4.5 85.7 1.0 C S:LYS24 4.7 64.5 1.0 O3A S:GNP200 4.7 83.3 1.0 N S:THR67 4.9 58.1 1.0 CE S:LYS24 4.9 59.6 1.0 N S:ALA68 5.0 74.5 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Human RAB11-RABIN8-FIP3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Human RAB11-RABIN8-FIP3 within 5.0Å range: probe atom residue distance (Å) B Occ V:Mg201 b:68.9 occ:1.00 OG V:SER25 1.8 71.7 1.0 O3G V:GNP200 2.0 80.3 1.0 OG1 V:THR43 2.0 87.0 1.0 O2B V:GNP200 2.2 66.0 1.0 CB V:SER25 2.8 77.3 1.0 N3B V:GNP200 2.8 79.3 1.0 PG V:GNP200 3.0 93.7 1.0 PB V:GNP200 3.1 61.9 1.0 CB V:THR43 3.4 70.3 1.0 O2A V:GNP200 3.7 63.6 1.0 N V:SER25 3.9 67.5 1.0 N V:THR43 3.9 83.5 1.0 CA V:SER25 3.9 79.9 1.0 O1G V:GNP200 3.9 74.4 1.0 O3A V:GNP200 4.0 73.9 1.0 PA V:GNP200 4.1 67.9 1.0 O2G V:GNP200 4.1 76.1 1.0 OD1 V:ASP66 4.2 71.5 1.0 O1A V:GNP200 4.2 64.2 1.0 CA V:THR43 4.2 83.8 1.0 OD2 V:ASP66 4.3 80.0 1.0 CG2 V:THR43 4.3 69.6 1.0 O1B V:GNP200 4.3 54.6 1.0 O V:LYS41 4.7 82.7 1.0 CG V:ASP66 4.7 79.1 1.0 C V:SER42 4.8 87.0 1.0 O V:THR67 4.8 92.7 1.0 CA V:SER42 4.9 79.3 1.0

M.Vetter, R.Stehle, C.Basquin, E.Lorentzen. Structure of RAB11-FIP3-RABIN8 Reveals Simultaneous Binding of FIP3 and RABIN8 Effectors to RAB11. Nat.Struct.Mol.Biol. V. 22 695 2015.
ISSN: ISSN 1545-9993
PubMed: 26258637
DOI: 10.1038/NSMB.3065