Magnesium in PDB 3a58: Crystal Structure of SEC3P - RHO1P Complex From Saccharomyces Cerevisiae

The structure of Crystal Structure of SEC3P - RHO1P Complex From Saccharomyces Cerevisiae, PDB code: 3a58 was solved by M.Yamashita, Y.Sato, A.Yamagata, H.Mimura, A.Yoshikawa, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.85 / 2.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	116.000, 116.054, 247.675, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 26.5

The binding sites of Magnesium atom in the Crystal Structure of SEC3P - RHO1P Complex From Saccharomyces Cerevisiae (pdb code 3a58). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of SEC3P - RHO1P Complex From Saccharomyces Cerevisiae, PDB code: 3a58:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of SEC3P - RHO1P Complex From Saccharomyces Cerevisiae


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 SEC3P - RHO1P Complex From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:47.0 occ:1.00 OG1 B:THR24 1.9 54.8 1.0 O B:HOH195 1.9 51.2 1.0 O B:HOH194 2.2 46.6 1.0 O2B B:GNP301 2.2 53.0 1.0 O2G B:GNP301 2.3 50.3 1.0 OG1 B:THR42 2.6 53.7 1.0 CB B:THR24 2.9 56.1 1.0 N3B B:GNP301 2.9 56.3 1.0 PB B:GNP301 3.2 53.7 1.0 PG B:GNP301 3.2 54.5 1.0 CB B:THR42 3.3 51.2 1.0 O2A B:GNP301 3.5 57.7 1.0 N B:THR24 3.7 56.3 1.0 CA B:THR24 3.9 55.4 1.0 CG2 B:THR24 3.9 51.4 1.0 N B:THR42 4.0 51.1 1.0 O3A B:GNP301 4.0 54.8 1.0 PA B:GNP301 4.1 55.9 1.0 O1A B:GNP301 4.1 49.8 1.0 OD2 B:ASP64 4.2 58.5 1.0 O3G B:GNP301 4.2 54.5 1.0 CA B:THR42 4.3 51.3 1.0 O1B B:GNP301 4.4 53.6 1.0 O1G B:GNP301 4.4 54.1 1.0 O B:VAL40 4.4 51.4 1.0 OD1 B:ASP64 4.4 58.3 1.0 CG2 B:THR42 4.5 48.9 1.0 CG B:ASP64 4.7 58.4 1.0 C B:PRO41 4.8 51.1 1.0 O B:THR65 4.8 61.2 1.0 C B:LYS23 4.9 56.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of SEC3P - RHO1P Complex From Saccharomyces Cerevisiae


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 SEC3P - RHO1P Complex From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:39.0 occ:1.00 O D:HOH213 2.0 35.6 1.0 OG1 D:THR24 2.0 39.7 1.0 OG1 D:THR42 2.0 46.0 1.0 O D:HOH189 2.1 30.9 1.0 O2G D:GNP301 2.1 33.3 1.0 O2B D:GNP301 2.2 27.1 1.0 CB D:THR42 3.0 44.0 1.0 CB D:THR24 3.1 40.9 1.0 PG D:GNP301 3.3 36.9 1.0 PB D:GNP301 3.4 35.0 1.0 N3B D:GNP301 3.5 33.5 1.0 OD2 D:ASP64 3.8 44.6 1.0 N D:THR24 3.8 37.7 1.0 N D:THR42 4.0 41.4 1.0 CA D:THR24 4.0 39.5 1.0 CG2 D:THR42 4.0 40.6 1.0 CA D:THR42 4.1 41.9 1.0 OD1 D:ASP64 4.1 40.9 1.0 O1G D:GNP301 4.1 37.4 1.0 CG2 D:THR24 4.2 39.4 1.0 O2A D:GNP301 4.2 42.1 1.0 O D:THR65 4.2 39.0 1.0 CG D:ASP64 4.3 39.6 1.0 O3A D:GNP301 4.4 36.8 1.0 O1B D:GNP301 4.5 35.5 1.0 O3G D:GNP301 4.5 39.1 1.0 O1A D:GNP301 4.6 36.9 1.0 PA D:GNP301 4.6 38.4 1.0 O D:VAL40 4.8 40.8 1.0 CB D:LYS23 4.8 33.1 1.0 C D:LYS23 4.8 39.4 1.0 C D:PRO41 4.9 40.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of SEC3P - RHO1P Complex From Saccharomyces Cerevisiae


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 SEC3P - RHO1P Complex From Saccharomyces Cerevisiae within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:57.4 occ:1.00 OG1 F:THR24 2.0 58.4 1.0 O F:HOH195 2.0 46.6 1.0 O2G F:GNP301 2.2 64.5 1.0 O F:HOH189 2.4 58.5 1.0 O2B F:GNP301 2.4 62.1 1.0 OG1 F:THR42 2.5 77.5 1.0 CB F:THR42 2.6 78.9 1.0 CB F:THR24 3.3 59.1 1.0 PG F:GNP301 3.4 63.8 1.0 PB F:GNP301 3.6 62.8 1.0 N3B F:GNP301 3.6 63.2 1.0 CG2 F:THR42 3.6 77.3 1.0 N F:THR42 3.7 78.5 1.0 CA F:THR42 3.8 79.0 1.0 OD1 F:ASP64 4.0 65.8 1.0 OD2 F:ASP64 4.0 69.8 1.0 N F:THR24 4.1 60.9 1.0 O F:THR65 4.1 72.6 1.0 O1G F:GNP301 4.2 59.6 1.0 CA F:THR24 4.2 59.9 1.0 CG2 F:THR24 4.2 56.5 1.0 CG F:ASP64 4.3 70.6 1.0 O1B F:GNP301 4.4 58.7 1.0 O2A F:GNP301 4.5 68.4 1.0 O3G F:GNP301 4.6 64.5 1.0 O F:VAL40 4.6 76.0 1.0 C F:PRO41 4.7 77.7 1.0 O3A F:GNP301 4.7 61.9 1.0 C F:THR42 4.9 79.7 1.0 PA F:GNP301 5.0 64.5 1.0 O1A F:GNP301 5.0 65.8 1.0 CB F:LYS23 5.0 60.0 1.0

M.Yamashita, K.Kurokawa, Y.Sato, A.Yamagata, H.Mimura, A.Yoshikawa, K.Sato, A.Nakano, S.Fukai. Structural Basis For the Rho- and Phosphoinositide-Dependent Localization of the Exocyst Subunit SEC3 Nat.Struct.Mol.Biol. V. 17 180 2010.
ISSN: ISSN 1545-9993
PubMed: 20062059
DOI: 10.1038/NSMB.1722