Magnesium in PDB 3vr3: Crystal Structure of Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3]

All present enzymatic activity of Crystal Structure of Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3]:
3.6.3.15;

The structure of Crystal Structure of Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3], PDB code: 3vr3 was solved by S.Arai, S.Saijo, K.Suzuki, K.Mizutani, Y.Kakinuma, Y.Ishizuka-Katsura, N.Ohsawa, T.Terada, M.Shirouzu, S.Yokoyama, S.Iwata, I.Yamato, T.Murata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.99 / 3.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.110, 124.130, 245.330, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.9

The binding sites of Magnesium atom in the Crystal Structure of Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3] (pdb code 3vr3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3], PDB code: 3vr3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3]


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 Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3] within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:62.3 occ:1.00 OG1 B:THR239 2.1 0.7 1.0 O2G B:ANP601 2.1 73.0 1.0 O1B B:ANP601 2.4 71.2 1.0 N3B B:ANP601 3.0 72.0 1.0 OE2 B:GLU265 3.0 92.9 1.0 PG B:ANP601 3.1 73.2 1.0 CB B:THR239 3.1 0.0 1.0 NH1 B:ARG262 3.3 91.4 1.0 PB B:ANP601 3.3 71.7 1.0 OE1 B:GLU261 3.6 88.5 1.0 O1A B:ANP601 3.9 71.5 1.0 O1G B:ANP601 4.0 72.6 1.0 N B:THR239 4.0 0.0 1.0 NH1 E:ARG350 4.1 0.7 1.0 CD B:GLU265 4.1 92.6 1.0 CG2 B:THR239 4.1 0.9 1.0 CA B:THR239 4.2 0.8 1.0 O3G B:ANP601 4.2 72.0 1.0 O3A B:ANP601 4.3 71.8 1.0 CZ B:ARG262 4.3 92.0 1.0 O2A B:ANP601 4.3 71.8 1.0 PA B:ANP601 4.3 71.6 1.0 OD1 B:ASP329 4.5 88.3 1.0 O2B B:ANP601 4.5 71.7 1.0 OE1 B:GLU265 4.6 91.7 1.0 CD B:GLU261 4.8 87.2 1.0 NH2 B:ARG262 4.8 91.9 1.0 OD2 B:ASP329 4.9 86.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3]


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 Amp-Pnp Bound A3B3 Complex From Enterococcus Hirae V-Atpase [BA3B3] within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:46.6 occ:1.00 O2G C:ANP601 1.8 55.3 1.0 OG1 C:THR239 1.9 52.7 1.0 O1B C:ANP601 2.2 53.2 1.0 PG C:ANP601 3.1 54.6 1.0 CB C:THR239 3.2 53.2 1.0 PB C:ANP601 3.4 53.5 1.0 N3B C:ANP601 3.4 53.9 1.0 NH1 C:ARG262 3.5 65.0 1.0 OE2 C:GLU265 3.6 65.9 1.0 OE1 C:GLU261 3.7 65.2 1.0 N C:THR239 4.0 51.5 1.0 O1G C:ANP601 4.0 53.8 1.0 OD2 C:ASP329 4.0 61.3 1.0 CA C:THR239 4.1 52.4 1.0 CG2 C:THR239 4.1 54.2 1.0 O3G C:ANP601 4.2 54.8 1.0 O1A C:ANP601 4.3 54.6 1.0 O2B C:ANP601 4.4 53.4 1.0 OD1 C:ASP329 4.5 57.6 1.0 CD C:GLU265 4.5 64.8 1.0 CD C:GLU261 4.5 62.9 1.0 O3A C:ANP601 4.5 54.1 1.0 O2A C:ANP601 4.6 53.4 1.0 OE1 C:GLU265 4.7 63.7 1.0 CG C:ASP329 4.7 57.9 1.0 CZ C:ARG262 4.7 65.2 1.0 PA C:ANP601 4.7 54.4 1.0 NH1 F:ARG350 4.8 75.2 1.0 CG C:GLU261 4.9 60.6 1.0 CB C:LYS238 5.0 48.5 1.0

S.Arai, S.Saijo, K.Suzuki, K.Mizutani, Y.Kakinuma, Y.Ishizuka-Katsura, N.Ohsawa, T.Terada, M.Shirouzu, S.Yokoyama, S.Iwata, I.Yamato, T.Murata. Rotation Mechanism of Enterococcus Hirae V(1)-Atpase Based on Asymmetric Crystal Structures Nature V. 493 703 2013.
ISSN: ISSN 0028-0836
PubMed: 23334411
DOI: 10.1038/NATURE11778