Magnesium in PDB 3eih: Crystal Structure of S.Cerevisiae VPS4 in the Presence of Atpgammas

The structure of Crystal Structure of S.Cerevisiae VPS4 in the Presence of Atpgammas, PDB code: 3eih was solved by M.D.Gonciarz, F.G.Whitby, D.M.Eckert, C.Kieffer, A.Heroux, W.I.Sundquist, C.P.Hill, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.00 / 3.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.956, 119.804, 156.831, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 30.5

The binding sites of Magnesium atom in the Crystal Structure of S.Cerevisiae VPS4 in the Presence of Atpgammas (pdb code 3eih). 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 S.Cerevisiae VPS4 in the Presence of Atpgammas, PDB code: 3eih:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of S.Cerevisiae VPS4 in the Presence of Atpgammas


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 S.Cerevisiae VPS4 in the Presence of Atpgammas within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:51.9 occ:1.00 OG A:SER180 2.1 57.8 1.0 O2B A:AGS501 2.2 74.9 1.0 O2G A:AGS501 2.4 82.2 1.0 OD1 A:ASP232 2.9 73.0 1.0 O2A A:AGS501 3.4 72.0 1.0 CB A:SER180 3.5 56.2 1.0 PG A:AGS501 3.5 81.9 1.0 PB A:AGS501 3.6 74.9 1.0 CG A:ASP232 3.8 69.2 1.0 S1G A:AGS501 3.9 82.2 1.0 OD2 A:ASP232 3.9 72.3 1.0 O3B A:AGS501 4.1 77.7 1.0 N A:SER180 4.2 55.7 1.0 O3A A:AGS501 4.3 74.5 1.0 CA A:SER180 4.3 56.0 1.0 PA A:AGS501 4.5 71.9 1.0 O1B A:AGS501 4.8 73.9 1.0 O3G A:AGS501 4.9 82.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of S.Cerevisiae VPS4 in the Presence of Atpgammas


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 S.Cerevisiae VPS4 in the Presence of Atpgammas within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:59.8 occ:1.00 O2G B:AGS501 1.9 0.3 1.0 OG B:SER180 2.5 69.9 1.0 O2B B:AGS501 2.8 0.5 1.0 OD1 B:ASP232 3.1 95.3 1.0 PG B:AGS501 3.2 0.3 1.0 O2A B:AGS501 3.6 0.7 1.0 PB B:AGS501 3.8 0.5 1.0 S1G B:AGS501 3.8 0.6 1.0 O3A B:AGS501 3.8 0.3 1.0 CB B:SER180 3.9 69.8 1.0 O3B B:AGS501 4.0 0.8 1.0 CG B:ASP232 4.1 94.8 1.0 PA B:AGS501 4.4 0.3 1.0 O3G B:AGS501 4.4 0.1 1.0 N B:SER180 4.4 69.8 1.0 OD2 B:ASP232 4.5 93.9 1.0 CA B:SER180 4.7 69.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of S.Cerevisiae VPS4 in the Presence of Atpgammas


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 S.Cerevisiae VPS4 in the Presence of Atpgammas within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:0.8 occ:1.00 OG C:SER180 2.1 0.4 1.0 O2 C:EDO501 2.8 55.0 1.0 OD2 C:ASP232 3.0 0.3 1.0 CB C:SER180 3.3 0.6 1.0 OD1 C:ASP232 3.3 0.9 1.0 C1 C:EDO501 3.4 58.7 1.0 C2 C:EDO501 3.4 56.5 1.0 CG C:ASP232 3.6 0.6 1.0 O1 C:EDO501 3.6 61.1 1.0 N C:SER180 3.6 0.3 1.0 CA C:SER180 3.6 0.6 1.0 NE2 C:GLN233 4.2 0.7 1.0 C C:LYS179 4.3 0.7 1.0 CB C:LYS179 4.6 0.1 1.0 O C:LYS179 4.9 0.8 1.0 CD C:GLN233 5.0 0.9 1.0 CA C:LYS179 5.0 0.3 1.0 CB C:ALA275 5.0 93.6 1.0

M.D.Gonciarz, F.G.Whitby, D.M.Eckert, C.Kieffer, A.Heroux, W.I.Sundquist, C.P.Hill. Biochemical and Structural Studies of Yeast VPS4 Oligomerization. J.Mol.Biol. V. 384 878 2008.
ISSN: ISSN 0022-2836
PubMed: 18929572
DOI: 10.1016/J.JMB.2008.09.066