Magnesium in PDB 1vg8: Gppnhp-Bound RAB7

The structure of Gppnhp-Bound RAB7, PDB code: 1vg8 was solved by A.Rak, O.Pylypenko, A.Niculae, K.Pyatkov, R.S.Goody, K.Alexandrov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.56 / 1.70
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.058, 57.071, 74.310, 71.73, 71.69, 77.65
R / Rfree (%)	19.8 / 22.4

The binding sites of Magnesium atom in the Gppnhp-Bound RAB7 (pdb code 1vg8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Gppnhp-Bound RAB7, PDB code: 1vg8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Gppnhp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gppnhp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:16.2 occ:1.00 O2B A:GNP1400 2.0 13.9 1.0 O2G A:GNP1400 2.0 17.3 1.0 OG1 A:THR1040 2.1 17.3 1.0 OG1 A:THR1022 2.1 15.1 1.0 O A:HOH5314 2.1 19.6 1.0 O A:HOH5002 2.2 14.2 1.0 CB A:THR1040 3.1 18.5 1.0 CB A:THR1022 3.2 16.4 1.0 PG A:GNP1400 3.2 18.1 1.0 PB A:GNP1400 3.3 15.1 1.0 N3B A:GNP1400 3.5 15.1 1.0 N A:THR1022 3.9 14.6 1.0 O3G A:GNP1400 3.9 17.5 1.0 N A:THR1040 3.9 20.8 1.0 OD1 A:ASP1063 4.0 17.4 1.0 O2A A:GNP1400 4.0 16.8 1.0 CA A:THR1022 4.1 15.5 1.0 CA A:THR1040 4.1 20.0 1.0 OD2 A:ASP1063 4.1 17.3 1.0 CG2 A:THR1022 4.2 17.3 1.0 CG2 A:THR1040 4.2 17.9 1.0 O1B A:GNP1400 4.3 14.9 1.0 O3A A:GNP1400 4.3 16.3 1.0 O A:HOH5087 4.3 23.1 1.0 O1G A:GNP1400 4.4 20.7 1.0 CG A:ASP1063 4.4 17.8 1.0 O A:LYS1038 4.5 23.8 1.0 O A:THR1064 4.5 19.2 1.0 PA A:GNP1400 4.6 17.9 1.0 O1A A:GNP1400 4.8 15.4 1.0 CB A:LYS1021 4.8 12.8 1.0 C A:ALA1039 4.9 21.7 1.0 CE A:LYS1021 5.0 17.1 1.0 C A:LYS1021 5.0 15.9 1.0 NZ A:LYS1021 5.0 16.5 1.0

Magnesium binding site 2 out of 4 in the Gppnhp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Gppnhp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2401 b:15.9 occ:1.00 O2G B:GNP2400 2.0 14.3 1.0 OG1 B:THR2022 2.0 13.3 1.0 O B:HOH5006 2.1 14.4 1.0 O2B B:GNP2400 2.1 13.2 1.0 OG1 B:THR2040 2.1 16.1 1.0 O B:HOH5315 2.1 17.9 1.0 CB B:THR2040 3.1 18.0 1.0 CB B:THR2022 3.1 17.9 1.0 PG B:GNP2400 3.2 18.7 1.0 PB B:GNP2400 3.3 14.9 1.0 N3B B:GNP2400 3.5 14.9 1.0 N B:THR2040 3.8 19.4 1.0 N B:THR2022 3.9 14.5 1.0 O3G B:GNP2400 3.9 17.2 1.0 OD2 B:ASP2063 4.0 21.4 1.0 CA B:THR2040 4.0 19.9 1.0 CA B:THR2022 4.1 15.5 1.0 O2A B:GNP2400 4.1 19.4 1.0 OD1 B:ASP2063 4.1 17.9 1.0 CG2 B:THR2040 4.2 18.3 1.0 CG2 B:THR2022 4.2 18.3 1.0 O B:HOH5063 4.3 24.4 1.0 O3A B:GNP2400 4.3 15.7 1.0 O1B B:GNP2400 4.3 15.1 1.0 CG B:ASP2063 4.4 21.5 1.0 O1G B:GNP2400 4.5 18.7 1.0 O B:THR2064 4.5 17.5 1.0 PA B:GNP2400 4.6 16.4 1.0 O B:LYS2038 4.6 23.2 1.0 O1A B:GNP2400 4.8 16.4 1.0 C B:ALA2039 4.8 22.2 1.0 CB B:LYS2021 4.9 15.0 1.0 C B:LYS2021 5.0 16.0 1.0

Magnesium binding site 3 out of 4 in the Gppnhp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Gppnhp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3401 b:16.5 occ:1.00 O2G C:GNP3400 2.0 14.7 1.0 O2B C:GNP3400 2.0 13.4 1.0 OG1 C:THR3022 2.1 13.3 1.0 O C:HOH5001 2.1 14.6 1.0 O C:HOH5009 2.2 17.2 1.0 OG1 C:THR3040 2.2 15.5 1.0 CB C:THR3040 3.1 17.8 1.0 CB C:THR3022 3.1 18.5 1.0 PG C:GNP3400 3.2 19.2 1.0 PB C:GNP3400 3.3 15.4 1.0 N3B C:GNP3400 3.5 15.6 1.0 N C:THR3040 3.9 19.6 1.0 N C:THR3022 3.9 15.2 1.0 O3G C:GNP3400 3.9 17.5 1.0 OD2 C:ASP3063 4.0 19.5 1.0 CA C:THR3040 4.1 19.4 1.0 OD1 C:ASP3063 4.1 18.8 1.0 O2A C:GNP3400 4.1 18.8 1.0 CA C:THR3022 4.1 16.2 1.0 CG2 C:THR3022 4.2 16.4 1.0 CG2 C:THR3040 4.2 18.8 1.0 O3A C:GNP3400 4.3 15.7 1.0 O1B C:GNP3400 4.3 14.6 1.0 O C:HOH5072 4.3 28.0 1.0 CG C:ASP3063 4.4 20.1 1.0 O1G C:GNP3400 4.4 19.7 1.0 O C:THR3064 4.5 16.9 1.0 PA C:GNP3400 4.5 16.1 1.0 O C:LYS3038 4.5 22.8 1.0 O1A C:GNP3400 4.7 16.2 1.0 CB C:LYS3021 4.8 15.0 1.0 C C:ALA3039 4.9 21.6 1.0 NZ C:LYS3021 5.0 14.5 1.0 C C:LYS3021 5.0 17.6 1.0

Magnesium binding site 4 out of 4 in the Gppnhp-Bound RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Gppnhp-Bound RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg4401 b:15.7 occ:1.00 O2B D:GNP4400 2.0 13.9 1.0 O2G D:GNP4400 2.0 16.8 1.0 OG1 D:THR4022 2.0 16.0 1.0 OG1 D:THR4040 2.1 16.2 1.0 O D:HOH5316 2.1 13.8 1.0 O D:HOH5003 2.1 18.7 1.0 CB D:THR4040 3.1 19.2 1.0 PG D:GNP4400 3.2 18.5 1.0 CB D:THR4022 3.2 17.8 1.0 PB D:GNP4400 3.3 14.6 1.0 N3B D:GNP4400 3.5 14.8 1.0 O3G D:GNP4400 3.8 17.6 1.0 N D:THR4040 3.9 20.2 1.0 N D:THR4022 3.9 14.1 1.0 OD1 D:ASP4063 4.0 19.1 1.0 CA D:THR4040 4.1 19.7 1.0 O2A D:GNP4400 4.1 17.9 1.0 CA D:THR4022 4.1 15.9 1.0 OD2 D:ASP4063 4.1 17.6 1.0 CG2 D:THR4022 4.2 17.0 1.0 CG2 D:THR4040 4.2 21.0 1.0 O1B D:GNP4400 4.3 14.2 1.0 O3A D:GNP4400 4.3 15.7 1.0 O1G D:GNP4400 4.4 22.3 1.0 O D:HOH5059 4.4 25.4 1.0 CG D:ASP4063 4.5 18.8 1.0 O D:THR4064 4.5 19.3 1.0 O D:LYS4038 4.6 23.2 1.0 PA D:GNP4400 4.6 17.7 1.0 O1A D:GNP4400 4.8 15.5 1.0 C D:ALA4039 4.9 21.7 1.0 CB D:LYS4021 4.9 14.2 1.0 NZ D:LYS4021 5.0 16.6 1.0 CE D:LYS4021 5.0 16.6 1.0

A.Rak, O.Pylypenko, A.Niculae, K.Pyatkov, R.S.Goody, K.Alexandrov. Structure of the RAB7:Rep-1 Complex: Insights Into the Mechanism of Rab Prenylation and Choroideremia Disease Cell(Cambridge,Mass.) V. 117 749 2004.
ISSN: ISSN 0092-8674
PubMed: 15186776
DOI: 10.1016/J.CELL.2004.05.017