Magnesium in PDB 4hlq: Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens

The structure of Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens, PDB code: 4hlq was solved by E.M.Gazdag, K.Gavriljuk, A.Itzen, C.Koetting, K.Gerwert, R.S.Goody, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.170, 118.640, 290.110, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 27.4

The structure of Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens also contains other interesting chemical elements:

Fluorine

(F)

15 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens (pdb code 4hlq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens, PDB code: 4hlq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:65.6 occ:1.00 OG1 B:THR40 1.9 54.8 1.0 OG B:SER22 1.9 55.7 1.0 O2B B:GDP202 2.0 53.3 1.0 F3 B:BEF203 2.1 64.8 1.0 CB B:THR40 2.9 55.7 1.0 PB B:GDP202 3.1 52.9 1.0 BE B:BEF203 3.2 64.5 1.0 CB B:SER22 3.3 56.4 1.0 O B:THR64 3.6 54.1 1.0 N B:SER22 3.6 55.4 1.0 O3B B:GDP202 3.6 51.8 1.0 CG2 B:THR40 3.7 55.8 1.0 O1B B:GDP202 3.7 53.8 1.0 OD1 B:ASP63 3.7 56.5 1.0 OD2 B:ASP63 3.9 59.5 1.0 CA B:SER22 3.9 56.1 1.0 NZ B:LYS21 4.0 54.2 1.0 CG B:ASP63 4.1 57.1 1.0 CA B:THR40 4.2 56.8 1.0 F2 B:BEF203 4.2 64.2 1.0 N B:THR40 4.2 57.5 1.0 F1 B:BEF203 4.2 64.5 1.0 O2A B:GDP202 4.3 54.8 1.0 CE B:LYS21 4.3 54.4 1.0 O3A B:GDP202 4.3 53.9 1.0 CB B:LYS21 4.5 54.6 1.0 PA B:GDP202 4.7 55.0 1.0 C B:LYS21 4.7 55.6 1.0 C B:THR64 4.8 54.5 1.0 O1A B:GDP202 4.9 54.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg201 b:55.6 occ:1.00 OG D:SER22 2.0 63.0 1.0 OG1 D:THR40 2.0 62.5 1.0 F1 D:BEF203 2.2 76.1 1.0 BE D:BEF203 2.9 76.1 1.0 CB D:SER22 2.9 63.5 1.0 F3 D:BEF203 3.0 75.8 1.0 O3A D:GDP202 3.0 66.3 1.0 O3B D:GDP202 3.2 68.0 1.0 N D:THR40 3.2 64.6 1.0 CB D:THR40 3.2 63.3 1.0 PB D:GDP202 3.5 67.5 1.0 O1B D:GDP202 3.6 67.8 1.0 CA D:THR40 3.8 64.2 1.0 NH1 C:ARG105 3.9 69.1 1.0 O D:ILE38 3.9 67.0 1.0 C D:SER39 4.2 65.6 1.0 PA D:GDP202 4.3 65.8 1.0 CA D:SER22 4.3 63.5 1.0 CA D:SER39 4.3 66.2 1.0 O2A D:GDP202 4.4 66.3 1.0 F2 D:BEF203 4.4 75.8 1.0 CG2 D:THR40 4.4 63.5 1.0 OD2 D:ASP63 4.5 65.9 1.0 N D:SER22 4.5 63.1 1.0 O1A D:GDP202 4.7 65.9 1.0 CZ C:ARG105 4.8 67.9 1.0 NZ D:LYS21 4.9 64.5 1.0 O2B D:GDP202 4.9 67.7 1.0 C D:ILE38 4.9 67.8 1.0 O D:THR64 4.9 64.4 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg201 b:61.8 occ:1.00 O3B F:GDP202 1.7 64.2 1.0 OG F:SER22 1.9 59.6 1.0 OG1 F:THR40 2.2 62.0 1.0 F2 F:BEF203 2.3 71.0 1.0 BE F:BEF203 2.9 70.9 1.0 PB F:GDP202 3.0 64.1 1.0 F3 F:BEF203 3.0 71.4 1.0 CB F:SER22 3.2 59.7 1.0 CB F:THR40 3.3 62.6 1.0 O2B F:GDP202 3.3 64.3 1.0 O3A F:GDP202 3.7 63.7 1.0 OD2 F:ASP63 3.8 63.9 1.0 N F:SER22 3.9 58.9 1.0 OD1 F:ASP63 3.9 62.8 1.0 N F:THR40 4.1 63.0 1.0 O2A F:GDP202 4.1 63.6 1.0 O1B F:GDP202 4.1 64.2 1.0 CA F:SER22 4.1 59.6 1.0 O F:THR64 4.2 62.0 1.0 PA F:GDP202 4.3 63.3 1.0 CG F:ASP63 4.3 63.2 1.0 CG2 F:THR40 4.3 63.3 1.0 CA F:THR40 4.3 63.5 1.0 NH1 E:ARG105 4.4 61.5 1.0 F1 F:BEF203 4.4 70.4 1.0 O1A F:GDP202 4.4 62.8 1.0 CB F:LYS21 4.8 58.3 1.0 NZ F:LYS21 4.8 59.1 1.0 O F:ILE38 5.0 63.6 1.0 C F:LYS21 5.0 58.6 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg201 b:61.3 occ:1.00 OG1 H:THR40 2.3 94.7 1.0 O3B H:GDP202 2.4 80.8 1.0 OG H:SER22 2.5 97.7 1.0 O2B H:GDP202 2.6 80.3 1.0 F1 H:BEF203 2.7 0.7 1.0 PB H:GDP202 2.8 80.5 1.0 BE H:BEF203 2.8 0.4 1.0 O3A H:GDP202 3.0 79.1 1.0 O1A H:GDP202 3.1 77.8 1.0 CB H:SER22 3.2 98.9 1.0 CB H:THR40 3.4 94.6 1.0 N H:THR40 3.5 94.9 1.0 F2 H:BEF203 3.5 0.6 1.0 PA H:GDP202 3.7 78.0 1.0 NH1 G:ARG105 3.8 90.6 1.0 O H:ILE38 3.9 98.7 1.0 CA H:THR40 4.1 95.4 1.0 F3 H:BEF203 4.1 0.9 1.0 N H:SER22 4.2 96.5 1.0 O1B H:GDP202 4.2 80.2 1.0 CA H:SER22 4.3 98.7 1.0 C H:SER39 4.5 96.5 1.0 O2A H:GDP202 4.5 78.3 1.0 CA H:SER39 4.6 96.2 1.0 CG2 H:THR40 4.6 96.2 1.0 O H:THR64 4.8 94.6 1.0 OD2 H:ASP63 4.9 99.5 1.0 O5' H:GDP202 4.9 76.3 1.0 C H:ILE38 5.0 99.7 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Human RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens


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 RAB1B Bound to Gdp and BEF3 in Complex with the Gap Domain of TBC1D20 From Homo Sapiens within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg201 b:61.5 occ:1.00 OG1 J:THR40 1.7 76.6 1.0 OG J:SER22 2.0 75.8 1.0 O3B J:GDP202 2.2 86.0 1.0 F2 J:BEF203 2.7 95.4 1.0 PB J:GDP202 3.1 85.3 1.0 CB J:THR40 3.1 76.6 1.0 CB J:SER22 3.2 77.4 1.0 O3A J:GDP202 3.3 86.3 1.0 O1B J:GDP202 3.3 85.2 1.0 BE J:BEF203 3.5 96.0 1.0 CG2 J:THR40 3.6 77.6 1.0 OD2 J:ASP63 3.8 80.2 1.0 N J:THR40 4.0 78.1 1.0 F3 J:BEF203 4.1 96.2 1.0 N J:SER22 4.1 76.6 1.0 O2A J:GDP202 4.1 86.9 1.0 CA J:THR40 4.1 77.1 1.0 OD1 J:ASP63 4.1 78.5 1.0 CA J:SER22 4.2 77.6 1.0 O J:THR64 4.3 76.1 1.0 PA J:GDP202 4.3 87.4 1.0 CG J:ASP63 4.4 78.7 1.0 O2B J:GDP202 4.4 84.8 1.0 NH1 I:ARG105 4.5 82.2 1.0 O J:ILE38 4.7 83.2 1.0 F1 J:BEF203 4.9 96.6 1.0

K.Gavriljuk, E.M.Gazdag, A.Itzen, C.Kotting, R.S.Goody, K.Gerwert. Catalytic Mechanism of A Mammalian Rab-Rabgap Complex in Atomic Detail. Proc.Natl.Acad.Sci.Usa V. 109 21348 2012.
ISSN: ISSN 0027-8424
PubMed: 23236136
DOI: 10.1073/PNAS.1214431110