Magnesium in PDB 7dqe: Crystal Structure of the Adp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase

All present enzymatic activity of Crystal Structure of the Adp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase:
7.2.2.1;

The structure of Crystal Structure of the Adp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase, PDB code: 7dqe was solved by S.Maruyama, K.Nakamoto, K.Suzuki, K.Mizutani, F.L.Imai, Y.Ishizuka-Katsura, M.Shirouzu, T.Murata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.63 / 2.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	120.03, 121.09, 231.47, 90, 90, 90
R / Rfree (%)	22.6 / 25.3

The binding sites of Magnesium atom in the Crystal Structure of the Adp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase (pdb code 7dqe). 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 the Adp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase, PDB code: 7dqe:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Adp-Bound Mutant A(S23C)3B(N64C)3 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 the Adp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:21.2 occ:1.00 OG1 A:THR239 2.2 26.1 1.0 O A:HOH701 2.3 26.4 1.0 O1B A:ADP602 2.3 21.1 1.0 O A:HOH702 2.6 29.0 1.0 O4 A:SO4603 2.6 36.6 1.0 O2 A:SO4603 2.9 36.2 1.0 O A:HOH704 3.2 50.5 1.0 S A:SO4603 3.3 36.0 1.0 PB A:ADP602 3.4 20.9 1.0 CB A:THR239 3.5 26.1 1.0 O3B A:ADP602 3.5 21.2 1.0 O1A A:ADP602 3.6 28.7 1.0 N A:THR239 4.0 25.9 1.0 OD1 A:ASP329 4.1 25.4 1.0 CA A:THR239 4.3 25.8 1.0 OD2 A:ASP329 4.3 24.5 1.0 O1 A:SO4603 4.3 36.0 1.0 O3A A:ADP602 4.3 30.9 1.0 PA A:ADP602 4.3 27.7 1.0 NH2 A:ARG333 4.3 19.9 1.0 O3 A:SO4603 4.3 36.2 1.0 NH1 D:ARG350 4.4 28.5 1.0 CG2 A:THR239 4.5 26.0 1.0 OE1 A:GLU265 4.5 26.7 1.0 O2A A:ADP602 4.5 26.8 1.0 OE2 A:GLU265 4.5 28.3 1.0 NH1 A:ARG262 4.6 22.7 1.0 O2B A:ADP602 4.6 20.7 1.0 CB A:LYS238 4.6 26.4 1.0 CG A:ASP329 4.7 24.5 1.0 CD A:GLU265 4.9 27.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Adp-Bound Mutant A(S23C)3B(N64C)3 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 the Adp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:26.3 occ:1.00 OG1 B:THR239 2.0 26.6 1.0 O B:HOH710 2.1 38.1 1.0 O B:HOH701 2.1 32.9 1.0 O3B B:ADP602 2.7 27.4 1.0 CB B:THR239 3.2 26.9 1.0 NH1 B:ARG262 3.2 21.7 1.0 O1B B:ADP602 3.3 25.9 1.0 OE2 B:GLU265 3.4 25.7 1.0 O1A B:ADP602 3.4 19.0 1.0 PB B:ADP602 3.5 26.9 1.0 NH1 E:ARG350 3.9 34.5 1.0 O B:HOH708 3.9 24.2 1.0 OE1 B:GLU265 4.0 25.8 1.0 CG2 B:THR239 4.0 27.1 1.0 OE1 B:GLU261 4.1 23.1 1.0 CD B:GLU265 4.1 25.5 1.0 PA B:ADP602 4.2 18.1 1.0 O3A B:ADP602 4.2 16.9 1.0 N B:THR239 4.3 26.1 1.0 CA B:THR239 4.3 26.5 1.0 CZ B:ARG262 4.5 21.1 1.0 OD1 B:ASP329 4.5 29.1 1.0 O2A B:ADP602 4.6 17.2 1.0 CD B:GLU261 4.7 22.8 1.0 OD2 B:ASP329 4.8 28.6 1.0 CZ E:ARG350 4.8 33.5 1.0 O2B B:ADP602 4.9 27.4 1.0 NZ B:LYS238 4.9 31.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Adp-Bound Mutant A(S23C)3B(N64C)3 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 the Adp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:36.5 occ:1.00 O C:HOH705 2.1 22.2 1.0 OG1 C:THR239 2.2 24.9 1.0 O C:HOH701 2.4 24.1 1.0 O1B C:ADP602 2.5 19.1 1.0 O C:HOH709 2.7 35.4 1.0 CB C:THR239 3.6 24.3 1.0 PB C:ADP602 3.6 19.9 1.0 O3B C:ADP602 3.6 19.9 1.0 NH1 C:ARG262 3.8 22.2 1.0 O F:HOH522 3.9 28.3 1.0 OE1 C:GLU261 3.9 23.1 1.0 OE2 C:GLU265 3.9 23.6 1.0 O2A C:ADP602 4.1 25.9 1.0 OD1 C:ASP329 4.2 26.1 1.0 OD2 C:ASP329 4.2 26.5 1.0 OE1 C:GLU265 4.3 21.9 1.0 N C:THR239 4.3 23.1 1.0 CG2 C:THR239 4.4 23.9 1.0 CA C:THR239 4.4 23.2 1.0 CD C:GLU261 4.4 23.8 1.0 O3A C:ADP602 4.5 30.4 1.0 CD C:GLU265 4.5 23.0 1.0 CG C:ASP329 4.6 26.0 1.0 PA C:ADP602 4.7 25.0 1.0 O2B C:ADP602 4.8 19.9 1.0 NH1 F:ARG350 4.8 23.3 1.0 O1A C:ADP602 4.8 24.3 1.0 CG C:GLU261 4.8 22.9 1.0 NZ C:LYS238 4.9 25.3 1.0

M.Imamura, S.Maruyama, K.Nakamoto, F.Kawai, T.Akiyama, K.Mizutani, K.Suzuki, M.Shirouzu, R.Iino, T.Uchihashi, T.Ando, T.Murata. The Combination of High-Speed Afm and X-Ray Crystallography Reveals Rotary Catalytic Mechanism of Shaftless V1-Atpase To Be Published.