Magnesium in PDB 2hld: Crystal Structure of Yeast Mitochondrial F1-Atpase

All present enzymatic activity of Crystal Structure of Yeast Mitochondrial F1-Atpase:
3.6.3.14;

The structure of Crystal Structure of Yeast Mitochondrial F1-Atpase, PDB code: 2hld was solved by V.Kabaleeswaran, N.Puri, J.E.Walker, A.G.Leslie, D.M.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	111.524, 294.132, 190.432, 90.00, 101.67, 90.00
R / Rfree (%)	20.7 / 24.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Yeast Mitochondrial F1-Atpase (pdb code 2hld). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Crystal Structure of Yeast Mitochondrial F1-Atpase, PDB code: 2hld:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-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 Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg700 b:34.8 occ:1.00 O2G A:ANP600 2.2 18.5 1.0 O2B A:ANP600 2.3 27.9 1.0 OG1 A:THR178 2.4 70.9 1.0 CB A:THR178 3.2 53.9 1.0 PG A:ANP600 3.2 21.6 1.0 PB A:ANP600 3.3 27.5 1.0 N3B A:ANP600 3.4 24.9 1.0 O2A A:ANP600 3.6 30.0 1.0 O3G A:ANP600 3.7 14.0 1.0 CG2 A:THR178 4.0 50.5 1.0 OD2 A:ASP271 4.2 61.7 1.0 O3A A:ANP600 4.2 35.9 1.0 N A:THR178 4.3 63.5 1.0 PA A:ANP600 4.3 34.8 1.0 CA A:THR178 4.3 60.6 1.0 O1G A:ANP600 4.5 23.0 1.0 O1A A:ANP600 4.5 36.6 1.0 O1B A:ANP600 4.6 31.0 1.0 OD1 A:ASP271 4.9 74.7 1.0

Magnesium binding site 2 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-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 Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg700 b:43.9 occ:1.00 OG1 B:THR178 2.0 77.5 1.0 O2G B:ANP600 2.1 34.8 1.0 O2B B:ANP600 2.2 37.2 1.0 CB B:THR178 3.1 63.6 1.0 PG B:ANP600 3.4 34.7 1.0 PB B:ANP600 3.4 38.9 1.0 N3B B:ANP600 3.7 29.1 1.0 OD2 B:ASP271 3.9 65.7 1.0 N B:THR178 4.0 66.5 1.0 CG2 B:THR178 4.0 56.0 1.0 OD1 B:ASP271 4.0 79.7 1.0 O2A B:ANP600 4.1 36.6 1.0 CA B:THR178 4.2 64.1 1.0 O3G B:ANP600 4.3 36.9 1.0 CG B:ASP271 4.5 75.3 1.0 O3A B:ANP600 4.5 41.7 1.0 O1G B:ANP600 4.5 36.3 1.0 O1B B:ANP600 4.6 37.9 1.0 PA B:ANP600 4.6 40.6 1.0 O1A B:ANP600 4.8 37.0 1.0

Magnesium binding site 3 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-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 Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg700 b:43.7 occ:1.00 O2B C:ANP600 2.0 28.7 1.0 OG1 C:THR178 2.2 75.2 1.0 O2G C:ANP600 2.2 25.2 1.0 PB C:ANP600 3.4 38.4 1.0 PG C:ANP600 3.4 31.2 1.0 CB C:THR178 3.4 61.4 1.0 N3B C:ANP600 3.7 25.4 1.0 OD1 C:ASP271 3.9 69.8 1.0 OD2 C:ASP271 4.0 72.4 1.0 N C:THR178 4.0 64.8 1.0 O3G C:ANP600 4.3 38.6 1.0 CG2 C:THR178 4.3 62.5 1.0 CA C:THR178 4.3 64.1 1.0 O1B C:ANP600 4.4 35.8 1.0 O2A C:ANP600 4.4 36.3 1.0 CG C:ASP271 4.4 72.6 1.0 O1G C:ANP600 4.5 37.2 1.0 O3A C:ANP600 4.5 37.5 1.0 PA C:ANP600 4.8 37.5 1.0 O1A C:ANP600 4.8 36.7 1.0

Magnesium binding site 4 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-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 Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg700 b:46.6 occ:1.00 OG1 D:THR164 2.0 71.6 1.0 O2G D:ANP600 2.0 54.1 1.0 O2B D:ANP600 2.5 45.1 1.0 CB D:THR164 3.0 65.2 1.0 PG D:ANP600 3.3 44.6 1.0 OE2 D:GLU193 3.5 71.2 1.0 PB D:ANP600 3.5 44.5 1.0 N3B D:ANP600 3.6 51.7 1.0 OE1 D:GLU189 3.7 92.1 1.0 CG2 D:THR164 3.7 57.1 1.0 O2A D:ANP600 3.8 62.0 1.0 NH1 D:ARG190 3.8 72.0 1.0 OE1 D:GLU193 3.9 64.3 1.0 CD D:GLU193 4.0 64.3 1.0 O3G D:ANP600 4.2 51.7 1.0 CA D:THR164 4.2 65.2 1.0 N D:THR164 4.2 64.5 1.0 O1G D:ANP600 4.4 56.7 1.0 OD2 D:ASP256 4.4 70.5 1.0 O3A D:ANP600 4.5 37.5 1.0 PA D:ANP600 4.5 46.3 1.0 CD D:GLU189 4.6 84.0 1.0 NH1 C:ARG375 4.6 68.3 1.0 O1A D:ANP600 4.7 44.0 1.0 O1B D:ANP600 4.7 53.0 1.0 OD1 D:ASP256 4.8 72.2 1.0 CZ D:ARG190 5.0 67.6 1.0

Magnesium binding site 5 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg700 b:44.3 occ:1.00 O2G F:ANP600 2.0 58.4 1.0 OG1 F:THR164 2.0 73.5 1.0 O2B F:ANP600 2.4 48.8 1.0 CB F:THR164 3.2 63.6 1.0 OE1 F:GLU189 3.3 94.6 1.0 PG F:ANP600 3.3 49.1 1.0 PB F:ANP600 3.6 40.6 1.0 N3B F:ANP600 3.7 38.7 1.0 NH1 F:ARG190 3.9 63.4 1.0 O F:HOH810 3.9 32.3 1.0 O3G F:ANP600 4.0 48.4 1.0 CG2 F:THR164 4.1 69.5 1.0 N F:THR164 4.1 61.9 1.0 OE1 F:GLU193 4.1 83.2 1.0 CD F:GLU189 4.2 94.8 1.0 OD2 F:ASP256 4.2 72.6 1.0 CA F:THR164 4.2 64.2 1.0 O2A F:ANP600 4.2 42.4 1.0 OE2 F:GLU193 4.3 79.2 1.0 OD1 F:ASP256 4.4 80.2 1.0 O1G F:ANP600 4.5 52.2 1.0 O1B F:ANP600 4.6 45.5 1.0 CD F:GLU193 4.6 79.7 1.0 O3A F:ANP600 4.6 45.8 1.0 OE2 F:GLU189 4.7 90.6 1.0 CE F:LYS163 4.8 63.4 1.0 PA F:ANP600 4.8 43.0 1.0 CG F:ASP256 4.8 77.7 1.0 CB F:LYS163 4.9 61.7 1.0 NH1 B:ARG375 4.9 59.0 1.0 NZ F:LYS163 4.9 49.4 1.0 O1A F:ANP600 5.0 41.0 1.0

Magnesium binding site 6 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg700 b:31.0 occ:1.00 O2B J:ANP600 2.0 43.1 1.0 OG1 J:THR178 2.1 72.3 1.0 O2G J:ANP600 2.4 34.8 1.0 CB J:THR178 3.2 61.7 1.0 PB J:ANP600 3.5 35.4 1.0 PG J:ANP600 3.7 35.3 1.0 OD2 J:ASP271 3.7 62.4 1.0 OD1 J:ASP271 3.9 76.9 1.0 N3B J:ANP600 3.9 23.4 1.0 N J:THR178 4.1 61.2 1.0 CG2 J:THR178 4.1 57.6 1.0 CA J:THR178 4.2 62.7 1.0 CG J:ASP271 4.3 71.6 1.0 O1B J:ANP600 4.4 37.0 1.0 O1G J:ANP600 4.6 35.6 1.0 O3A J:ANP600 4.6 36.4 1.0 O3G J:ANP600 4.6 32.4 1.0 O2A J:ANP600 4.6 26.6 1.0

Magnesium binding site 7 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg700 b:52.0 occ:1.00 O2G K:ANP600 1.9 57.8 1.0 O2B K:ANP600 2.0 49.9 1.0 OG1 K:THR178 2.2 70.8 1.0 O2A K:ANP600 3.0 51.9 1.0 CB K:THR178 3.2 67.9 1.0 PG K:ANP600 3.2 54.4 1.0 PB K:ANP600 3.3 50.5 1.0 N3B K:ANP600 3.5 53.0 1.0 N K:THR178 4.0 68.1 1.0 O3G K:ANP600 4.0 50.9 1.0 CG2 K:THR178 4.2 59.8 1.0 PA K:ANP600 4.2 54.1 1.0 CA K:THR178 4.2 67.9 1.0 O3A K:ANP600 4.2 54.6 1.0 OD2 K:ASP271 4.3 60.8 1.0 O1G K:ANP600 4.4 60.1 1.0 OD1 K:ASP271 4.5 69.4 1.0 O1B K:ANP600 4.5 54.0 1.0 CG K:ASP271 4.8 73.8 1.0

Magnesium binding site 8 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg700 b:49.0 occ:1.00 OG1 L:THR178 1.9 72.4 1.0 O2G L:ANP600 2.1 25.7 1.0 O2B L:ANP600 2.5 24.5 1.0 CB L:THR178 3.2 53.8 1.0 PG L:ANP600 3.6 26.5 1.0 OD2 L:ASP271 3.6 68.8 1.0 PB L:ANP600 3.7 30.3 1.0 OD1 L:ASP271 3.9 80.7 1.0 CG2 L:THR178 3.9 52.8 1.0 N L:THR178 4.0 60.8 1.0 N3B L:ANP600 4.1 17.1 1.0 CA L:THR178 4.2 58.1 1.0 CG L:ASP271 4.2 66.7 1.0 O L:HOH812 4.3 42.6 1.0 O3G L:ANP600 4.4 31.9 1.0 O1G L:ANP600 4.7 33.3 1.0 O1B L:ANP600 4.7 31.2 1.0 O2A L:ANP600 4.8 23.6 1.0 O3A L:ANP600 4.8 32.2 1.0 O L:HOH802 5.0 24.9 1.0

Magnesium binding site 9 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg700 b:52.4 occ:1.00 OG1 M:THR164 1.9 71.1 1.0 O2G M:ANP600 2.0 65.0 1.0 O2B M:ANP600 2.3 37.3 1.0 OE1 M:GLU189 3.3 97.6 1.0 PG M:ANP600 3.3 53.1 1.0 CB M:THR164 3.3 57.0 1.0 PB M:ANP600 3.7 45.1 1.0 OD2 M:ASP256 3.7 75.3 1.0 O1G M:ANP600 3.7 60.6 1.0 OD1 M:ASP256 3.7 78.9 1.0 CD M:GLU189 3.9 96.4 1.0 N M:THR164 3.9 56.7 1.0 N3B M:ANP600 4.0 31.4 1.0 CA M:THR164 4.1 54.8 1.0 CG2 M:THR164 4.1 49.4 1.0 CG M:ASP256 4.2 75.4 1.0 NH1 M:ARG190 4.2 64.5 1.0 CE M:LYS163 4.3 57.7 1.0 O3G M:ANP600 4.4 52.8 1.0 OE2 M:GLU193 4.4 69.6 1.0 OE1 M:GLU193 4.5 66.8 1.0 OE2 M:GLU189 4.5 92.9 1.0 CB M:LYS163 4.6 58.2 1.0 O1B M:ANP600 4.6 44.9 1.0 CG M:GLU189 4.6 76.3 1.0 O2A M:ANP600 4.7 42.7 1.0 CD M:GLU193 4.8 62.1 1.0 O3A M:ANP600 4.8 45.2 1.0 NZ M:LYS163 5.0 62.3 1.0 C M:LYS163 5.0 59.5 1.0

Magnesium binding site 10 out of 15 in the Crystal Structure of Yeast Mitochondrial F1-Atpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Yeast Mitochondrial F1-Atpase within 5.0Å range: probe atom residue distance (Å) B Occ O:Mg700 b:48.1 occ:1.00 O2G O:ANP600 2.0 74.7 1.0 OG1 O:THR164 2.1 80.6 1.0 O2B O:ANP600 2.2 57.9 1.0 PG O:ANP600 3.2 65.1 1.0 PB O:ANP600 3.2 54.3 1.0 N3B O:ANP600 3.2 59.5 1.0 OE1 O:GLU189 3.4 90.5 1.0 CB O:THR164 3.4 70.4 1.0 O3G O:ANP600 3.9 59.9 1.0 N O:THR164 4.1 65.9 1.0 CD O:GLU189 4.1 91.4 1.0 NH1 O:ARG190 4.1 64.0 1.0 O1B O:ANP600 4.1 69.2 1.0 O2A O:ANP600 4.2 61.7 1.0 OD1 O:ASP256 4.3 79.9 1.0 CE O:LYS163 4.3 61.6 1.0 OD2 O:ASP256 4.3 66.7 1.0 CG2 O:THR164 4.3 65.5 1.0 CA O:THR164 4.3 69.1 1.0 OE1 O:GLU193 4.4 69.4 1.0 O1G O:ANP600 4.4 68.0 1.0 OE2 O:GLU189 4.4 97.3 1.0 O3A O:ANP600 4.5 65.5 1.0 NZ O:LYS163 4.6 53.9 1.0 OE2 O:GLU193 4.7 68.3 1.0 CG O:ASP256 4.8 71.7 1.0 CB O:LYS163 4.8 64.5 1.0 PA O:ANP600 4.9 60.3 1.0 CD O:GLU193 4.9 68.0 1.0 NH1 K:ARG375 5.0 59.7 1.0

V.Kabaleeswaran, N.Puri, J.E.Walker, A.G.Leslie, D.M.Mueller. Novel Features of the Rotary Catalytic Mechanism Revealed in the Structure of Yeast F(1) Atpase. Embo J. V. 25 5433 2006.
ISSN: ISSN 0261-4189
PubMed: 17082766
DOI: 10.1038/SJ.EMBOJ.7601410