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

Enzymatic activity of Crystal Structure of the Amp-Pnp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase

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

Protein crystallography data

The structure of Crystal Structure of the Amp-Pnp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase, PDB code: 7dqd was solved by S.Maruyama, 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) 49.37 / 3.38
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 117.57, 123.38, 230.28, 90, 90.07, 90
R / Rfree (%) 26.1 / 28.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Amp-Pnp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase (pdb code 7dqd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Amp-Pnp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase, PDB code: 7dqd:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7dqd

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Amp-Pnp-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 Amp-Pnp-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:Mg602

b:8.9
occ:1.00
 O2G B:ANP601 2.0 25.8 1.0
OG1 B:THR239 2.0 48.2 1.0
N3B B:ANP601 2.5 20.8 1.0
PG B:ANP601 2.7 34.4 1.0
O1B B:ANP601 2.8 24.8 1.0
CB B:THR239 2.8 49.5 1.0
O1A B:ANP601 3.0 45.4 1.0
PB B:ANP601 3.2 24.9 1.0
O3G B:ANP601 3.5 28.1 1.0
O2A B:ANP601 3.6 45.7 1.0
PA B:ANP601 3.6 45.6 1.0
CG2 B:THR239 3.8 50.1 1.0
OE2 B:GLU265 3.8 61.8 1.0
NH1 B:ARG262 3.8 60.9 1.0
O3A B:ANP601 3.9 43.9 1.0
NH2 E:ARG350 3.9 66.6 1.0
N B:THR239 3.9 48.3 1.0
CA B:THR239 3.9 48.4 1.0
O1G B:ANP601 4.0 34.1 1.0
OD1 B:ASP329 4.2 47.2 1.0
CD B:GLU265 4.3 61.1 1.0
OE1 B:GLU265 4.3 59.8 1.0
OE1 B:GLU261 4.5 56.0 1.0
O2B B:ANP601 4.5 24.5 1.0
CZ B:ARG262 4.9 61.7 1.0

Magnesium binding site 2 out of 4 in 7dqd

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Magnesium binding site 2 out of 4 in the Crystal Structure of the Amp-Pnp-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 Amp-Pnp-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:Mg602

b:49.8
occ:1.00
 O2G C:ANP601 2.1 71.9 1.0
OE1 C:GLU265 2.5 55.2 1.0
OG1 C:THR239 2.5 51.3 1.0
OE2 C:GLU261 2.9 64.1 1.0
OE2 C:GLU265 3.1 53.5 1.0
CD C:GLU265 3.1 55.4 1.0
CB C:THR239 3.4 53.5 1.0
CG2 C:THR239 3.4 55.3 1.0
PG C:ANP601 3.5 113.1 1.0
O1B C:ANP601 3.8 35.5 1.0
NH1 C:ARG262 4.0 57.0 1.0
O3G C:ANP601 4.1 99.5 1.0
CD C:GLU261 4.1 62.1 1.0
OD2 C:ASP329 4.1 52.8 1.0
O1G C:ANP601 4.2 112.9 1.0
CG C:GLU265 4.5 58.8 1.0
OD1 C:ASP329 4.7 50.2 1.0
CG C:ASP329 4.7 51.5 1.0
N3B C:ANP601 4.7 32.5 1.0
CA C:THR239 4.8 52.5 1.0
OE1 C:GLU261 4.8 61.2 1.0
PB C:ANP601 4.9 35.7 1.0
O1A C:ANP601 4.9 51.7 1.0

Magnesium binding site 3 out of 4 in 7dqd

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Amp-Pnp-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 Amp-Pnp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg602

b:26.1
occ:1.00
 O1G J:ANP601 1.8 71.5 1.0
OG1 J:THR239 1.8 76.3 1.0
O1B J:ANP601 2.0 29.7 1.0
NZ J:LYS238 2.6 78.2 1.0
PG J:ANP601 3.1 71.7 1.0
OE1 J:GLU261 3.1 77.8 1.0
CB J:THR239 3.3 76.3 1.0
PB J:ANP601 3.3 29.6 1.0
N3B J:ANP601 3.6 49.2 1.0
OD2 J:ASP329 3.6 81.0 1.0
OE2 J:GLU265 3.7 72.5 1.0
OD1 J:ASP329 3.8 80.0 1.0
O3G J:ANP601 3.9 58.9 1.0
N J:THR239 4.0 76.5 1.0
CE J:LYS238 4.0 78.5 1.0
O1A J:ANP601 4.0 46.3 1.0
CD J:GLU261 4.1 75.5 1.0
CG2 J:THR239 4.1 75.8 1.0
CG J:ASP329 4.1 80.0 1.0
CA J:THR239 4.1 76.2 1.0
O2B J:ANP601 4.2 32.3 1.0
O2G J:ANP601 4.3 29.4 1.0
O3A J:ANP601 4.4 39.7 1.0
OE2 J:GLU261 4.4 74.7 1.0
PA J:ANP601 4.6 47.1 1.0
O2A J:ANP601 4.6 48.1 1.0
CD J:GLU265 4.8 72.7 1.0
NH1 J:ARG262 4.8 73.0 1.0

Magnesium binding site 4 out of 4 in 7dqd

Go back to Magnesium Binding Sites List in 7dqd
Magnesium binding site 4 out of 4 in the Crystal Structure of the Amp-Pnp-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 4 of Crystal Structure of the Amp-Pnp-Bound Mutant A(S23C)3B(N64C)3 Complex From Enterococcus Hirae V-Atpase within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg602

b:27.6
occ:1.00
 OE2 K:GLU261 1.9 57.5 1.0
O2G K:ANP601 2.0 29.6 1.0
OG1 K:THR239 2.3 52.1 1.0
O1G K:ANP601 2.5 85.6 1.0
PG K:ANP601 2.7 85.7 1.0
CD K:GLU261 3.1 56.5 1.0
NH1 K:ARG262 3.3 40.7 1.0
O1B K:ANP601 3.3 35.0 1.0
OE1 K:GLU265 3.4 40.2 1.0
OD2 K:ASP329 3.5 54.9 1.0
O3G K:ANP601 3.6 69.9 1.0
CB K:THR239 3.7 46.3 1.0
OE1 K:GLU261 3.9 56.3 1.0
OD1 K:ASP329 4.0 56.0 1.0
N3B K:ANP601 4.1 41.6 1.0
CG K:ASP329 4.2 53.9 1.0
CG K:GLU261 4.2 55.6 1.0
CG2 K:THR239 4.2 51.1 1.0
PB K:ANP601 4.3 35.2 1.0
NZ K:LYS238 4.5 55.0 1.0
CD K:GLU265 4.5 42.4 1.0
CZ K:ARG262 4.5 41.0 1.0
CA K:THR239 4.7 43.0 1.0
CE K:LYS238 4.7 51.4 1.0
N K:THR239 4.7 44.0 1.0
O1A K:ANP601 4.8 62.5 1.0
OE2 K:GLU265 4.8 42.5 1.0

Reference:

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 Catalysis To Be Published.
Page generated: Wed Oct 2 15:59:05 2024

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