Magnesium in PDB 3vr6: Crystal Structure of Amp-Pnp Bound Enterococcus Hirae V1-Atpase [BV1]

All present enzymatic activity of Crystal Structure of Amp-Pnp Bound Enterococcus Hirae V1-Atpase [BV1]:
3.6.3.15;

The structure of Crystal Structure of Amp-Pnp Bound Enterococcus Hirae V1-Atpase [BV1], PDB code: 3vr6 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)	48.58 / 2.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	126.149, 127.416, 225.252, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 24.6

The binding sites of Magnesium atom in the Crystal Structure of Amp-Pnp Bound Enterococcus Hirae V1-Atpase [BV1] (pdb code 3vr6). 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 Enterococcus Hirae V1-Atpase [BV1], PDB code: 3vr6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Amp-Pnp Bound Enterococcus Hirae V1-Atpase [BV1]


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 Enterococcus Hirae V1-Atpase [BV1] within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:24.9 occ:1.00 O2G B:ANP601 1.8 15.0 1.0 OG1 B:THR239 1.9 24.7 1.0 O B:HOH729 2.0 11.8 1.0 O B:HOH730 2.0 15.5 1.0 O B:HOH728 2.1 12.9 1.0 O1B B:ANP601 2.2 16.9 1.0 PG B:ANP601 3.2 16.3 1.0 CB B:THR239 3.2 24.9 1.0 PB B:ANP601 3.3 15.0 1.0 N3B B:ANP601 3.4 12.7 1.0 NH1 B:ARG262 3.5 16.1 1.0 O1G B:ANP601 4.0 13.0 1.0 O B:HOH702 4.0 33.8 1.0 OE2 B:GLU265 4.0 31.6 1.0 CG2 B:THR239 4.0 24.8 1.0 N B:THR239 4.1 25.4 1.0 CA B:THR239 4.1 25.3 1.0 OE1 B:GLU261 4.2 35.6 1.0 OE1 B:GLU265 4.2 32.7 1.0 OD2 B:ASP329 4.3 31.6 1.0 O3G B:ANP601 4.3 15.8 1.0 O2A B:ANP601 4.3 22.7 1.0 O1A B:ANP601 4.3 26.8 1.0 O3A B:ANP601 4.3 19.3 1.0 O2B B:ANP601 4.4 12.2 1.0 CD B:GLU265 4.4 30.3 1.0 PA B:ANP601 4.5 22.6 1.0 OD1 B:ASP329 4.5 31.9 1.0 NH1 E:ARG350 4.6 26.4 1.0 CZ B:ARG262 4.7 21.6 1.0 O B:HOH798 4.8 31.0 1.0 CD B:GLU261 4.8 34.6 1.0 CG B:ASP329 4.8 29.4 1.0 CE B:LYS238 4.9 28.6 1.0 NZ B:LYS238 5.0 30.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Amp-Pnp Bound Enterococcus Hirae V1-Atpase [BV1]


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 Enterococcus Hirae V1-Atpase [BV1] within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:27.3 occ:1.00 O2G C:ANP601 1.9 16.6 1.0 OG1 C:THR239 1.9 28.7 1.0 O1B C:ANP601 2.1 13.6 1.0 O C:HOH741 2.2 22.7 1.0 O C:HOH725 2.2 20.2 1.0 O C:HOH726 2.4 16.2 1.0 CB C:THR239 3.0 29.7 1.0 PG C:ANP601 3.2 17.2 1.0 PB C:ANP601 3.3 13.1 1.0 N3B C:ANP601 3.6 13.4 1.0 NH1 C:ARG262 3.7 30.0 1.0 OE1 C:GLU261 3.8 48.0 1.0 N C:THR239 3.8 28.3 1.0 O1G C:ANP601 3.9 17.6 1.0 CA C:THR239 3.9 28.8 1.0 O1A C:ANP601 4.0 20.1 1.0 O C:HOH727 4.0 22.4 1.0 CG2 C:THR239 4.1 30.9 1.0 OE2 C:GLU265 4.1 34.7 1.0 O2A C:ANP601 4.3 16.4 1.0 OD1 C:ASP329 4.3 31.7 1.0 O3A C:ANP601 4.3 18.5 1.0 PA C:ANP601 4.4 19.8 1.0 NH1 F:ARG350 4.4 33.7 1.0 O3G C:ANP601 4.4 18.6 1.0 O2B C:ANP601 4.5 17.6 1.0 OE1 C:GLU265 4.5 35.4 1.0 OD2 C:ASP329 4.5 30.9 1.0 CD C:GLU261 4.6 45.6 1.0 CD C:GLU265 4.6 35.4 1.0 CG C:ASP329 4.9 29.5 1.0 C C:LYS238 4.9 28.5 1.0 CE C:LYS238 5.0 27.8 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