Magnesium in PDB 1t91: Crystal Structure of Human Small Gtpase RAB7(Gtp)

The structure of Crystal Structure of Human Small Gtpase RAB7(Gtp), PDB code: 1t91 was solved by H.Song, W.Hong, M.Wu, T.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.695, 56.777, 74.510, 71.51, 71.72, 77.75
R / Rfree (%)	24.3 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of Human Small Gtpase RAB7(Gtp) (pdb code 1t91). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Small Gtpase RAB7(Gtp), PDB code: 1t91:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Small Gtpase RAB7(Gtp)


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 Small Gtpase RAB7(Gtp) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1301 b:25.5 occ:1.00 OG1 A:THR40 2.0 6.7 1.0 O1G A:GTP1401 2.0 25.1 1.0 O2B A:GTP1401 2.1 24.0 1.0 OG1 A:THR22 2.2 8.9 1.0 O A:HOH1406 2.3 20.8 1.0 CB A:THR40 2.9 10.5 1.0 PG A:GTP1401 3.2 22.2 1.0 PB A:GTP1401 3.2 19.3 1.0 CB A:THR22 3.3 10.0 1.0 O3B A:GTP1401 3.5 25.6 1.0 N A:THR40 3.6 9.7 1.0 CA A:THR40 3.8 9.6 1.0 O2G A:GTP1401 3.9 21.0 1.0 CG2 A:THR40 4.1 11.2 1.0 N A:THR22 4.1 9.0 1.0 OD2 A:ASP63 4.1 8.1 1.0 O2A A:GTP1401 4.1 24.5 1.0 OD1 A:ASP63 4.2 7.0 1.0 O3A A:GTP1401 4.3 24.0 1.0 O1B A:GTP1401 4.3 20.3 1.0 CA A:THR22 4.3 9.1 1.0 O3G A:GTP1401 4.4 30.2 1.0 CG2 A:THR22 4.4 9.2 1.0 O A:HOH1407 4.4 27.1 1.0 O A:THR64 4.4 9.9 1.0 O A:LYS38 4.4 7.3 1.0 CG A:ASP63 4.6 7.9 1.0 C A:ALA39 4.6 8.6 1.0 PA A:GTP1401 4.6 24.4 1.0 O1A A:GTP1401 4.8 18.7 1.0 CA A:ALA39 5.0 9.2 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Small Gtpase RAB7(Gtp)


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 Small Gtpase RAB7(Gtp) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1302 b:27.0 occ:1.00 OG1 B:THR40 1.9 21.8 1.0 O1G B:GTP1402 2.0 22.3 1.0 O2B B:GTP1402 2.1 18.6 1.0 OG1 B:THR22 2.1 22.9 1.0 O B:HOH1430 2.3 19.3 1.0 CB B:THR40 2.9 24.4 1.0 PG B:GTP1402 3.2 24.4 1.0 PB B:GTP1402 3.2 22.7 1.0 CB B:THR22 3.3 23.1 1.0 O3B B:GTP1402 3.5 23.9 1.0 N B:THR40 3.6 27.2 1.0 CA B:THR40 3.8 26.2 1.0 O2G B:GTP1402 3.9 26.6 1.0 OD2 B:ASP63 4.1 21.1 1.0 CG2 B:THR40 4.1 26.3 1.0 N B:THR22 4.1 21.2 1.0 O2A B:GTP1402 4.1 30.2 1.0 OD1 B:ASP63 4.2 20.4 1.0 CA B:THR22 4.3 22.2 1.0 CG2 B:THR22 4.3 24.3 1.0 O3A B:GTP1402 4.3 23.8 1.0 O1B B:GTP1402 4.3 22.4 1.0 O3G B:GTP1402 4.4 28.8 1.0 O B:THR64 4.5 20.3 1.0 O B:LYS38 4.5 26.7 1.0 CG B:ASP63 4.5 19.1 1.0 PA B:GTP1402 4.6 25.4 1.0 C B:ALA39 4.6 28.0 1.0 O1A B:GTP1402 4.8 18.6 1.0 CA B:ALA39 5.0 28.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Small Gtpase RAB7(Gtp)


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 Small Gtpase RAB7(Gtp) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1303 b:27.9 occ:1.00 OG1 C:THR40 2.0 21.7 1.0 O1G C:GTP1403 2.0 21.6 1.0 O2B C:GTP1403 2.1 20.1 1.0 OG1 C:THR22 2.2 20.3 1.0 O C:HOH1434 2.2 18.4 1.0 CB C:THR40 2.9 24.9 1.0 PG C:GTP1403 3.2 24.9 1.0 PB C:GTP1403 3.2 22.1 1.0 CB C:THR22 3.3 22.0 1.0 O3B C:GTP1403 3.5 23.4 1.0 N C:THR40 3.6 26.3 1.0 CA C:THR40 3.8 26.2 1.0 O2G C:GTP1403 3.9 23.6 1.0 O C:HOH1456 4.1 27.1 1.0 OD2 C:ASP63 4.1 21.5 1.0 N C:THR22 4.1 20.0 1.0 CG2 C:THR40 4.1 24.8 1.0 O2A C:GTP1403 4.1 25.8 1.0 OD1 C:ASP63 4.2 19.6 1.0 CA C:THR22 4.3 21.5 1.0 O3A C:GTP1403 4.3 24.6 1.0 O1B C:GTP1403 4.3 22.7 1.0 CG2 C:THR22 4.3 21.3 1.0 O3G C:GTP1403 4.4 27.5 1.0 O C:THR64 4.4 19.4 1.0 O C:LYS38 4.5 25.6 1.0 CG C:ASP63 4.5 20.8 1.0 PA C:GTP1403 4.6 24.5 1.0 C C:ALA39 4.6 27.2 1.0 O1A C:GTP1403 4.8 18.4 1.0 CA C:ALA39 5.0 27.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Small Gtpase RAB7(Gtp)


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 Small Gtpase RAB7(Gtp) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1304 b:25.4 occ:1.00 OG1 D:THR40 1.9 21.5 1.0 O1G D:GTP1404 2.0 21.4 1.0 O2B D:GTP1404 2.1 20.8 1.0 OG1 D:THR22 2.2 22.7 1.0 O D:HOH1482 2.4 18.8 1.0 CB D:THR40 2.9 22.9 1.0 PG D:GTP1404 3.2 23.1 1.0 PB D:GTP1404 3.2 19.9 1.0 CB D:THR22 3.3 20.6 1.0 O3B D:GTP1404 3.5 24.7 1.0 N D:THR40 3.6 24.2 1.0 CA D:THR40 3.8 23.7 1.0 O2G D:GTP1404 3.9 22.9 1.0 CG2 D:THR40 4.1 26.5 1.0 OD2 D:ASP63 4.1 16.2 1.0 N D:THR22 4.1 19.8 1.0 O2A D:GTP1404 4.1 26.0 1.0 OD1 D:ASP63 4.2 15.4 1.0 O D:HOH1407 4.3 22.0 1.0 O3A D:GTP1404 4.3 22.3 1.0 O1B D:GTP1404 4.3 19.4 1.0 CA D:THR22 4.3 20.5 1.0 O3G D:GTP1404 4.4 27.7 1.0 CG2 D:THR22 4.4 22.8 1.0 O D:LYS38 4.4 22.5 1.0 O D:THR64 4.4 21.8 1.0 CG D:ASP63 4.6 20.3 1.0 C D:ALA39 4.6 24.3 1.0 PA D:GTP1404 4.6 23.8 1.0 O1A D:GTP1404 4.8 22.9 1.0 CA D:ALA39 5.0 24.4 1.0

M.Wu, T.Wang, E.Loh, W.Hong, H.Song. Structural Basis For Recruitment of Rilp By Small Gtpase RAB7. Embo J. V. 24 1491 2005.
ISSN: ISSN 0261-4189
PubMed: 15933719
DOI: 10.1038/SJ.EMBOJ.7600643