Magnesium in PDB 3law: Structure of Gtp-Bound L129F Mutant RAB7

The structure of Structure of Gtp-Bound L129F Mutant RAB7, PDB code: 3law was solved by B.A.Mccray, E.Skordalakes, J.P.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 2.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	35.554, 89.335, 89.378, 71.24, 85.97, 85.91
R / Rfree (%)	22 / 27.3

The binding sites of Magnesium atom in the Structure of Gtp-Bound L129F Mutant RAB7 (pdb code 3law). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Gtp-Bound L129F Mutant RAB7, PDB code: 3law:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of Gtp-Bound L129F Mutant RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Gtp-Bound L129F Mutant RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1401 b:32.7 occ:1.00 O2G A:GNP1400 2.2 26.6 1.0 OG1 A:THR22 2.3 10.6 1.0 OG1 A:THR40 2.5 43.4 1.0 O2B A:GNP1400 2.5 24.6 1.0 OD2 A:ASP63 2.8 32.6 1.0 O A:THR64 3.0 39.9 1.0 PG A:GNP1400 3.1 30.8 1.0 O3G A:GNP1400 3.1 28.5 1.0 CB A:THR40 3.3 43.1 1.0 OD1 A:ASP63 3.5 35.3 1.0 PB A:GNP1400 3.6 25.7 1.0 CG A:ASP63 3.6 33.8 1.0 CB A:THR22 3.6 10.3 1.0 N A:THR22 3.7 9.0 1.0 N3B A:GNP1400 3.8 28.4 1.0 CE A:LYS21 4.0 10.1 1.0 CG2 A:THR40 4.1 42.2 1.0 CB A:LYS21 4.1 8.3 1.0 CA A:THR22 4.1 10.5 1.0 C A:THR64 4.2 39.6 1.0 O1B A:GNP1400 4.2 26.2 1.0 O1G A:GNP1400 4.5 28.2 1.0 NZ A:LYS21 4.5 11.3 1.0 C A:LYS21 4.5 8.5 1.0 CA A:THR40 4.5 43.2 1.0 CG2 A:THR22 4.6 8.7 1.0 N A:THR40 4.7 44.0 1.0 N A:THR64 4.8 36.6 1.0 CA A:LYS21 4.8 8.3 1.0 O3A A:GNP1400 4.9 25.6 1.0 CA A:ALA65 5.0 43.2 1.0

Magnesium binding site 2 out of 5 in the Structure of Gtp-Bound L129F Mutant RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Gtp-Bound L129F Mutant RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1401 b:23.5 occ:1.00 O2G B:GNP1400 1.9 27.6 1.0 OG1 B:THR22 1.9 21.2 1.0 O2B B:GNP1400 2.3 23.3 1.0 OG1 B:THR40 2.4 48.4 1.0 PG B:GNP1400 3.0 31.1 1.0 OD2 B:ASP63 3.2 38.7 1.0 OD1 B:ASP63 3.3 37.7 1.0 CB B:THR22 3.3 21.0 1.0 PB B:GNP1400 3.4 24.3 1.0 O3G B:GNP1400 3.4 30.1 1.0 CB B:THR40 3.5 48.3 1.0 O B:THR64 3.6 39.2 1.0 N3B B:GNP1400 3.6 27.8 1.0 CG B:ASP63 3.6 37.0 1.0 N B:THR22 3.8 19.5 1.0 CA B:THR22 4.0 21.0 1.0 O1B B:GNP1400 4.2 26.8 1.0 CG2 B:THR22 4.2 21.2 1.0 CG2 B:THR40 4.3 47.8 1.0 O1G B:GNP1400 4.3 28.8 1.0 CB B:LYS21 4.5 17.1 1.0 O2A B:GNP1400 4.5 26.2 1.0 N B:THR40 4.5 48.4 1.0 CA B:THR40 4.6 48.4 1.0 O3A B:GNP1400 4.6 25.5 1.0 NZ B:LYS21 4.7 10.1 1.0 CE B:LYS21 4.8 12.6 1.0 C B:THR64 4.8 39.0 1.0 C B:LYS21 4.8 18.5 1.0 PA B:GNP1400 4.9 25.3 1.0 O1A B:GNP1400 5.0 25.5 1.0

Magnesium binding site 3 out of 5 in the Structure of Gtp-Bound L129F Mutant RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Gtp-Bound L129F Mutant RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1401 b:19.6 occ:1.00 O2G C:GNP1400 2.0 30.6 1.0 OG1 C:THR22 2.0 18.1 1.0 OG1 C:THR40 2.1 56.8 1.0 O2B C:GNP1400 2.2 21.8 1.0 PG C:GNP1400 3.1 31.5 1.0 CB C:THR22 3.3 17.4 1.0 OD1 C:ASP63 3.4 33.1 1.0 PB C:GNP1400 3.4 24.0 1.0 CB C:THR40 3.4 56.4 1.0 N3B C:GNP1400 3.6 28.2 1.0 O3G C:GNP1400 3.7 30.7 1.0 O C:THR64 3.9 36.8 1.0 N C:THR22 3.9 17.1 1.0 OD2 C:ASP63 3.9 37.4 1.0 N C:THR40 4.0 55.7 1.0 CG C:ASP63 4.1 34.3 1.0 CA C:THR22 4.1 18.0 1.0 O2A C:GNP1400 4.2 26.4 1.0 CA C:THR40 4.2 56.1 1.0 O1B C:GNP1400 4.3 22.1 1.0 CG2 C:THR22 4.3 16.9 1.0 CG2 C:THR40 4.4 55.9 1.0 O1G C:GNP1400 4.4 32.2 1.0 O3A C:GNP1400 4.6 26.3 1.0 CB C:LYS21 4.7 16.1 1.0 O C:LYS38 4.7 54.4 1.0 PA C:GNP1400 4.8 26.1 1.0 O1A C:GNP1400 4.9 26.0 1.0 C C:LYS21 4.9 16.5 1.0 C C:ALA39 5.0 55.4 1.0

Magnesium binding site 4 out of 5 in the Structure of Gtp-Bound L129F Mutant RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Gtp-Bound L129F Mutant RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1401 b:37.3 occ:1.00 O2G D:GNP1400 1.9 35.5 1.0 OG1 D:THR22 2.3 18.6 1.0 OG1 D:THR40 2.5 55.8 1.0 O2B D:GNP1400 2.5 26.3 1.0 PG D:GNP1400 3.0 36.2 1.0 OD2 D:ASP63 3.2 36.6 1.0 O D:THR64 3.2 40.9 1.0 O3G D:GNP1400 3.3 32.7 1.0 CB D:THR40 3.4 55.9 1.0 OD1 D:ASP63 3.4 34.9 1.0 PB D:GNP1400 3.6 25.6 1.0 CG D:ASP63 3.6 35.2 1.0 CB D:THR22 3.7 18.9 1.0 N3B D:GNP1400 3.7 30.8 1.0 N D:THR22 4.0 17.8 1.0 NZ D:LYS21 4.2 13.6 1.0 CG2 D:THR40 4.3 56.0 1.0 O1G D:GNP1400 4.3 34.3 1.0 CA D:THR22 4.3 18.7 1.0 O1B D:GNP1400 4.3 26.6 1.0 C D:THR64 4.3 40.6 1.0 CE D:LYS21 4.3 11.9 1.0 CB D:LYS21 4.3 15.1 1.0 N D:THR40 4.5 55.6 1.0 CA D:THR40 4.5 55.7 1.0 CG2 D:THR22 4.6 18.9 1.0 O2A D:GNP1400 4.8 25.4 1.0 CA D:ALA65 4.9 43.4 1.0 N D:GLY66 4.9 46.0 1.0 O3A D:GNP1400 4.9 26.5 1.0 C D:LYS21 4.9 16.9 1.0 N D:ALA65 5.0 42.1 1.0

Magnesium binding site 5 out of 5 in the Structure of Gtp-Bound L129F Mutant RAB7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Gtp-Bound L129F Mutant RAB7 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1401 b:32.3 occ:1.00 O2G E:GNP1400 2.0 32.0 1.0 O2B E:GNP1400 2.1 22.6 1.0 OG1 E:THR40 2.3 51.3 1.0 OG1 E:THR22 2.5 24.2 1.0 PG E:GNP1400 2.9 33.9 1.0 O3G E:GNP1400 3.1 32.2 1.0 PB E:GNP1400 3.2 22.8 1.0 OD1 E:ASP63 3.4 35.2 1.0 N3B E:GNP1400 3.5 29.0 1.0 CB E:THR40 3.5 51.4 1.0 O E:THR64 3.6 40.4 1.0 OD2 E:ASP63 3.6 33.1 1.0 N E:THR22 3.7 22.9 1.0 CB E:THR22 3.7 23.0 1.0 CG E:ASP63 3.9 34.7 1.0 O1B E:GNP1400 4.0 21.0 1.0 CE E:LYS21 4.0 23.6 1.0 CB E:LYS21 4.1 22.2 1.0 O2A E:GNP1400 4.1 24.6 1.0 CA E:THR22 4.2 23.4 1.0 O1G E:GNP1400 4.2 31.4 1.0 CG2 E:THR40 4.3 50.7 1.0 O3A E:GNP1400 4.5 22.1 1.0 C E:LYS21 4.6 22.2 1.0 C E:THR64 4.6 39.9 1.0 N E:THR40 4.6 51.5 1.0 NZ E:LYS21 4.6 25.5 1.0 CA E:THR40 4.7 51.4 1.0 PA E:GNP1400 4.7 22.9 1.0 CA E:LYS21 4.8 22.2 1.0 O1A E:GNP1400 4.9 20.6 1.0 CG2 E:THR22 4.9 21.9 1.0 CA E:ALA65 5.0 43.1 1.0 N E:LYS21 5.0 22.4 1.0

B.A.Mccray, E.Skordalakes, J.P.Taylor. Disease Mutations in RAB7 Result in Unregulated Nucleotide Exchange and Inappropriate Activation. Hum.Mol.Genet. V. 19 1033 2010.
ISSN: ISSN 0964-6906
PubMed: 20028791
DOI: 10.1093/HMG/DDP567