Magnesium in PDB 5ze9: Crystal Structure of Amp-Pnp Bound Mutant A3B3 Complex From Enterococcus Hirae V-Atpase

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

The structure of Crystal Structure of Amp-Pnp Bound Mutant A3B3 Complex From Enterococcus Hirae V-Atpase, PDB code: 5ze9 was solved by S.Maruyama, K.Suzuki, H.Sasaki, K.Mizutani, Y.Saito, F.L.Imai, Y.Ishizuka-Katsura, M.Shirouzu, Y.Ichiro, T.Murata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.87 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.830, 151.370, 235.490, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.6

The binding sites of Magnesium atom in the Crystal Structure of Amp-Pnp Bound Mutant A3B3 Complex From Enterococcus Hirae V-Atpase (pdb code 5ze9). 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 Amp-Pnp Bound Mutant A3B3 Complex From Enterococcus Hirae V-Atpase, PDB code: 5ze9:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Amp-Pnp Bound Mutant A3B3 Complex From Enterococcus Hirae V-Atpase


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 Mutant A3B3 Complex From Enterococcus Hirae V-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:24.3 occ:1.00 O2G A:ANP601 2.0 26.5 1.0 O2B A:ANP601 2.0 21.7 1.0 O A:HOH765 2.1 21.1 1.0 O A:HOH704 2.1 23.9 1.0 OG1 A:THR239 2.1 30.4 1.0 O A:HOH783 2.2 25.9 1.0 PG A:ANP601 3.1 27.9 1.0 CB A:THR239 3.2 31.5 1.0 PB A:ANP601 3.2 26.2 1.0 N3B A:ANP601 3.4 28.0 1.0 NH1 A:ARG262 3.8 25.8 1.0 O3G A:ANP601 3.9 26.4 1.0 OE2 A:GLU265 3.9 34.4 1.0 N A:THR239 4.0 25.0 1.0 O A:HOH766 4.0 22.7 1.0 O1A A:ANP601 4.2 20.8 1.0 OE1 A:GLU261 4.2 40.1 1.0 CA A:THR239 4.2 32.7 1.0 OD2 A:ASP329 4.2 33.1 1.0 O1B A:ANP601 4.2 26.1 1.0 CG2 A:THR239 4.3 25.9 1.0 O1G A:ANP601 4.3 29.0 1.0 OD1 A:ASP329 4.3 37.5 1.0 O3A A:ANP601 4.3 28.0 1.0 OE1 A:GLU265 4.4 35.0 1.0 CD A:GLU265 4.5 34.5 1.0 PA A:ANP601 4.6 27.5 1.0 NH1 D:ARG350 4.7 32.1 1.0 O2A A:ANP601 4.7 30.5 1.0 CG A:ASP329 4.7 33.6 1.0 CD A:GLU261 4.9 38.3 1.0 O D:HOH617 5.0 34.9 1.0 CB A:LYS238 5.0 24.2 1.0 CZ A:ARG262 5.0 29.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Amp-Pnp Bound Mutant A3B3 Complex From Enterococcus Hirae V-Atpase


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 Mutant A3B3 Complex From Enterococcus Hirae V-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:24.1 occ:1.00 O2G B:ANP601 1.9 22.0 0.6 OG1 B:THR239 2.0 24.2 1.0 O B:HOH795 2.0 16.4 1.0 O B:HOH746 2.1 21.9 1.0 O2B B:ANP601 2.1 18.9 1.0 O B:HOH731 2.2 17.6 1.0 CB B:THR239 3.1 23.6 1.0 PG B:ANP601 3.1 39.8 0.6 PB B:ANP601 3.3 19.3 1.0 O1G B:ANP601 3.5 49.5 0.6 N3B B:ANP601 3.7 23.1 1.0 N B:THR239 3.9 21.5 1.0 NH1 B:ARG262 4.0 21.5 1.0 OD2 B:ASP329 4.0 27.8 1.0 CA B:THR239 4.1 20.4 1.0 OD1 B:ASP329 4.1 25.0 1.0 OE1 B:GLU261 4.1 28.4 1.0 OE2 B:GLU265 4.1 28.4 1.0 CG2 B:THR239 4.1 21.5 1.0 O2A B:ANP601 4.3 23.0 1.0 O B:HOH704 4.3 30.0 1.0 O3A B:ANP601 4.4 22.6 1.0 OE1 B:GLU265 4.4 28.5 1.0 O1B B:ANP601 4.4 18.7 1.0 O3G B:ANP601 4.4 51.2 0.6 CG B:ASP329 4.5 27.0 1.0 PA B:ANP601 4.6 22.2 1.0 CD B:GLU265 4.6 28.2 1.0 NH1 E:ARG350 4.6 28.6 1.0 O B:HOH733 4.6 25.2 1.0 O1A B:ANP601 4.6 18.6 1.0 CD B:GLU261 4.7 30.0 1.0 CE B:LYS238 4.9 23.5 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Amp-Pnp Bound Mutant A3B3 Complex From Enterococcus Hirae V-Atpase


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 Amp-Pnp Bound Mutant A3B3 Complex From Enterococcus Hirae V-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg602 b:21.7 occ:1.00 O C:HOH764 2.0 15.4 1.0 O1B C:ANP601 2.1 20.9 1.0 O C:HOH737 2.1 18.1 1.0 O1G C:ANP601 2.1 21.5 1.0 OG1 C:THR239 2.1 21.8 1.0 O C:HOH750 2.2 20.9 1.0 CB C:THR239 3.1 19.5 1.0 PG C:ANP601 3.2 27.8 0.2 PB C:ANP601 3.3 23.5 1.0 O2G C:ANP601 3.7 28.9 0.2 N3B C:ANP601 3.7 22.8 1.0 N C:THR239 3.9 19.4 1.0 OD2 C:ASP329 4.0 26.4 1.0 NH1 C:ARG262 4.0 21.7 1.0 CA C:THR239 4.1 22.4 1.0 O2A C:ANP601 4.1 22.7 1.0 OE2 C:GLU265 4.1 30.6 1.0 O C:HOH702 4.1 26.9 1.0 CG2 C:THR239 4.1 18.0 1.0 OD1 C:ASP329 4.2 26.2 1.0 OE1 C:GLU261 4.2 32.2 1.0 O C:HOH708 4.3 21.4 1.0 O3A C:ANP601 4.3 17.9 1.0 O2B C:ANP601 4.4 20.1 1.0 OE1 C:GLU265 4.4 21.8 1.0 PA C:ANP601 4.5 21.4 1.0 O1A C:ANP601 4.5 19.6 1.0 CG C:ASP329 4.5 27.3 1.0 O3G C:ANP601 4.6 30.6 0.2 CD C:GLU265 4.6 26.6 1.0 NH1 F:ARG350 4.8 22.8 1.0 CD C:GLU261 4.8 30.6 1.0 CB C:LYS238 4.9 25.2 1.0

S.Maruyama, K.Suzuki, M.Imamura, H.Sasaki, H.Matsunami, K.Mizutani, Y.Saito, F.L.Imai, Y.Ishizuka-Katsura, T.Kimura-Someya, M.Shirouzu, T.Uchihashi, T.Ando, I.Yamato, T.Murata. Metastable Asymmetrical Structure of A Shaftless V1MOTOR. Sci Adv V. 5 U8149 2019.
ISSN: ESSN 2375-2548
PubMed: 30729160
DOI: 10.1126/SCIADV.AAU8149