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Magnesium in PDB 3zia: The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1

Enzymatic activity of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1

All present enzymatic activity of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1:
3.6.3.14;

Protein crystallography data

The structure of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1, PDB code: 3zia was solved by G.C.Robinson, J.V.Bason, M.G.Montgomery, I.M.Fearnley, D.M.Mueller, A.G.W.Leslie, J.E.Walker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 181.81 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 118.224, 187.846, 181.812, 90.00, 89.96, 90.00
R / Rfree (%) 22.4 / 26.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 (pdb code 3zia). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1, PDB code: 3zia:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3zia

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Magnesium binding site 1 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:51.0
occ:1.00
 O A:HOH2005 2.0 45.1 1.0
O A:HOH2007 2.0 45.2 1.0
O A:HOH2006 2.1 42.1 1.0
OG1 A:THR178 2.2 54.9 1.0
O2G A:ATP600 2.2 45.8 0.8
O2B A:ATP600 2.2 52.1 1.0
CB A:THR178 3.2 55.8 1.0
PG A:ATP600 3.3 52.0 0.8
PB A:ATP600 3.3 50.9 1.0
O3B A:ATP600 3.5 50.8 1.0
N A:THR178 3.9 55.1 1.0
OD2 A:ASP271 4.0 58.0 1.0
O1G A:ATP600 4.0 50.8 0.8
OD1 A:ASP271 4.0 58.8 1.0
CA A:THR178 4.1 55.6 1.0
CG2 A:THR178 4.3 55.3 1.0
O A:HOH2009 4.4 47.8 1.0
O2A A:ATP600 4.4 45.7 1.0
O1B A:ATP600 4.4 50.9 1.0
O3A A:ATP600 4.4 53.2 1.0
CG A:ASP271 4.4 53.4 1.0
O3G A:ATP600 4.6 56.3 0.8
O1A A:ATP600 4.7 53.7 1.0
PA A:ATP600 4.7 50.8 1.0
CB A:LYS177 5.0 54.7 1.0

Magnesium binding site 2 out of 10 in 3zia

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Magnesium binding site 2 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:40.9
occ:1.00
 O B:HOH2045 2.0 40.4 1.0
O B:HOH2090 2.1 34.0 1.0
O B:HOH2046 2.1 45.7 1.0
OG1 B:THR178 2.2 34.2 1.0
O1B B:ADP600 2.2 39.6 1.0
O B:HOH2047 2.3 39.5 1.0
CB B:THR178 3.2 36.1 1.0
PB B:ADP600 3.4 42.6 1.0
O3B B:ADP600 3.5 33.8 1.0
OD1 B:ASP271 4.0 37.0 1.0
N B:THR178 4.0 36.7 1.0
CA B:THR178 4.2 35.8 1.0
O1A B:ADP600 4.2 29.3 1.0
OD2 B:ASP271 4.2 38.3 1.0
CG2 B:THR178 4.3 31.9 1.0
O2B B:ADP600 4.5 41.4 1.0
O3A B:ADP600 4.5 43.9 1.0
CG B:ASP271 4.5 35.3 1.0
PA B:ADP600 4.7 38.4 1.0
O B:HOH2044 4.8 32.1 1.0
O2A B:ADP600 4.8 33.9 1.0

Magnesium binding site 3 out of 10 in 3zia

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Magnesium binding site 3 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:27.9
occ:1.00
 O C:HOH2045 2.0 29.8 1.0
O C:HOH2046 2.0 30.8 1.0
O C:HOH2093 2.1 28.7 1.0
O C:HOH2044 2.1 31.2 1.0
OG1 C:THR178 2.2 33.8 1.0
O1B C:ADP600 2.2 29.8 1.0
CB C:THR178 3.1 33.9 1.0
PB C:ADP600 3.4 33.7 1.0
O3B C:ADP600 3.5 40.0 1.0
N C:THR178 3.9 35.4 1.0
OD2 C:ASP271 3.9 27.3 1.0
OD1 C:ASP271 4.0 23.3 1.0
CA C:THR178 4.1 34.7 1.0
O1A C:ADP600 4.1 28.1 1.0
CG2 C:THR178 4.2 33.7 1.0
CG C:ASP271 4.4 28.3 1.0
O2B C:ADP600 4.4 31.0 1.0
O C:HOH2062 4.5 29.7 1.0
O3A C:ADP600 4.6 35.5 1.0
PA C:ADP600 4.7 39.0 1.0
O2A C:ADP600 5.0 36.2 1.0
C C:LYS177 5.0 36.3 1.0

Magnesium binding site 4 out of 10 in 3zia

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Magnesium binding site 4 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:35.6
occ:1.00
 O C:HOH2090 2.0 30.4 1.0
O D:HOH2019 2.1 39.3 1.0
O D:HOH2021 2.1 36.0 1.0
O D:HOH2018 2.2 38.3 1.0
O1B D:ADP600 2.2 39.2 1.0
OG1 D:THR164 2.2 45.5 1.0
CB D:THR164 3.1 45.1 1.0
PB D:ADP600 3.5 38.9 1.0
O3B D:ADP600 3.6 41.6 1.0
O D:HOH2020 3.9 42.7 1.0
N D:THR164 4.0 44.8 1.0
OD2 D:ASP256 4.1 39.2 1.0
CG2 D:THR164 4.1 45.1 1.0
CA D:THR164 4.1 45.4 1.0
OE2 D:GLU193 4.1 39.8 1.0
NH1 D:ARG190 4.1 31.4 1.0
OE1 D:GLU193 4.1 39.3 1.0
O1A D:ADP600 4.1 40.2 1.0
OE1 D:GLU189 4.2 45.1 1.0
OD1 D:ASP256 4.4 40.6 1.0
O2B D:ADP600 4.5 33.9 1.0
CD D:GLU193 4.5 36.9 1.0
O3A D:ADP600 4.5 35.0 1.0
PA D:ADP600 4.6 42.1 1.0
CD D:GLU189 4.6 42.7 1.0
NH1 C:ARG375 4.6 48.4 1.0
O2A D:ADP600 4.7 46.7 1.0
CG D:ASP256 4.7 42.8 1.0
CE D:LYS163 4.8 39.4 1.0
O D:HOH2017 4.8 34.5 1.0
CB D:LYS163 4.8 43.8 1.0
C D:LYS163 5.0 44.5 1.0
O D:HOH2022 5.0 38.3 1.0

Magnesium binding site 5 out of 10 in 3zia

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Magnesium binding site 5 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:24.7
occ:1.00
 O F:HOH2043 2.0 23.7 1.0
O F:HOH2044 2.1 26.7 1.0
OG1 F:THR164 2.2 26.3 1.0
O1B F:ADP600 2.2 30.5 1.0
O F:HOH2047 2.2 25.1 1.0
O F:HOH2045 2.2 26.5 1.0
CB F:THR164 3.1 29.6 1.0
PB F:ADP600 3.4 26.7 1.0
O3B F:ADP600 3.6 27.3 1.0
OE1 F:GLU189 3.9 29.2 1.0
NH1 F:ARG190 4.0 32.1 1.0
N F:THR164 4.0 29.1 1.0
OE2 F:GLU193 4.1 36.6 1.0
O1A F:ADP600 4.1 28.4 1.0
OD2 F:ASP256 4.1 25.9 1.0
CA F:THR164 4.1 29.0 1.0
O F:HOH2048 4.2 28.8 1.0
CG2 F:THR164 4.2 27.9 1.0
OD1 F:ASP256 4.3 29.8 1.0
O3A F:ADP600 4.4 30.2 1.0
O2B F:ADP600 4.4 27.4 1.0
OE1 F:GLU193 4.5 35.2 1.0
O B:HOH2085 4.5 38.3 1.0
CD F:GLU189 4.6 32.2 1.0
O F:HOH2042 4.6 29.9 1.0
PA F:ADP600 4.6 30.1 1.0
CG F:ASP256 4.7 24.2 1.0
CD F:GLU193 4.7 35.0 1.0
O2A F:ADP600 4.7 31.4 1.0
O B:HOH2084 4.8 37.8 1.0
CB F:LYS163 4.9 28.6 1.0

Magnesium binding site 6 out of 10 in 3zia

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Magnesium binding site 6 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg601

b:45.3
occ:1.00
 O K:HOH2014 2.1 43.5 1.0
O K:HOH2015 2.1 43.1 1.0
O K:HOH2013 2.1 40.4 1.0
O2G K:ATP600 2.2 38.7 0.8
OG1 K:THR178 2.2 47.0 1.0
O2B K:ATP600 2.2 45.0 1.0
CB K:THR178 3.2 49.5 1.0
PG K:ATP600 3.3 48.7 0.8
PB K:ATP600 3.3 45.9 1.0
O3B K:ATP600 3.5 45.9 1.0
N K:THR178 3.9 49.5 1.0
OD2 K:ASP271 4.0 48.6 1.0
O1G K:ATP600 4.0 49.5 0.8
OD1 K:ASP271 4.1 49.4 1.0
CA K:THR178 4.1 49.3 1.0
CG2 K:THR178 4.3 49.0 1.0
O2A K:ATP600 4.4 54.6 1.0
O1B K:ATP600 4.4 49.6 1.0
O3A K:ATP600 4.4 54.9 1.0
CG K:ASP271 4.4 45.8 1.0
O3G K:ATP600 4.5 50.7 0.8
O1A K:ATP600 4.7 51.2 1.0
PA K:ATP600 4.7 52.9 1.0
O K:HOH2012 4.9 38.5 1.0
CB K:LYS177 5.0 49.7 1.0

Magnesium binding site 7 out of 10 in 3zia

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Magnesium binding site 7 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:24.8
occ:1.00
 O L:HOH2077 2.0 24.7 1.0
O L:HOH2156 2.1 27.2 1.0
O L:HOH2075 2.1 23.2 1.0
O1B L:ADP600 2.2 27.6 1.0
OG1 L:THR178 2.2 22.7 1.0
O L:HOH2076 2.2 32.1 1.0
CB L:THR178 3.2 22.2 1.0
PB L:ADP600 3.4 25.1 1.0
O3B L:ADP600 3.5 30.5 1.0
N L:THR178 4.0 21.9 1.0
O L:HOH2085 4.0 25.0 1.0
OD1 L:ASP271 4.0 18.7 1.0
CA L:THR178 4.2 21.9 1.0
OD2 L:ASP271 4.2 21.0 1.0
O1A L:ADP600 4.2 25.4 1.0
CG2 L:THR178 4.3 16.5 1.0
O2B L:ADP600 4.4 18.4 1.0
O3A L:ADP600 4.5 30.5 1.0
CG L:ASP271 4.5 22.8 1.0
PA L:ADP600 4.6 31.4 1.0
O L:HOH2074 4.7 16.6 1.0
O2A L:ADP600 4.8 33.4 1.0

Magnesium binding site 8 out of 10 in 3zia

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Magnesium binding site 8 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg601

b:34.1
occ:1.00
 O M:HOH2032 2.0 38.4 1.0
O M:HOH2033 2.1 35.3 1.0
O M:HOH2031 2.1 33.6 1.0
O M:HOH2076 2.1 35.2 1.0
OG1 M:THR178 2.2 39.4 1.0
O1B M:ADP600 2.2 36.4 1.0
CB M:THR178 3.1 42.1 1.0
PB M:ADP600 3.4 42.1 1.0
O3B M:ADP600 3.5 49.1 1.0
N M:THR178 3.9 42.5 1.0
OD2 M:ASP271 3.9 29.2 1.0
OD1 M:ASP271 4.0 33.2 1.0
CA M:THR178 4.1 42.4 1.0
O1A M:ADP600 4.1 43.2 1.0
CG2 M:THR178 4.2 41.6 1.0
O2B M:ADP600 4.4 37.0 1.0
CG M:ASP271 4.4 33.9 1.0
O3A M:ADP600 4.5 46.8 1.0
PA M:ADP600 4.7 51.5 1.0
O2A M:ADP600 5.0 57.6 1.0

Magnesium binding site 9 out of 10 in 3zia

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Magnesium binding site 9 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg601

b:40.7
occ:1.00
 O M:HOH2070 2.0 39.8 1.0
O N:HOH2016 2.0 42.5 1.0
O N:HOH2019 2.1 46.1 1.0
OG1 N:THR164 2.2 49.0 1.0
O1B N:ADP600 2.2 39.3 1.0
O N:HOH2017 2.2 43.0 1.0
CB N:THR164 3.0 49.1 1.0
PB N:ADP600 3.5 41.5 1.0
O3B N:ADP600 3.7 45.0 1.0
O N:HOH2018 4.0 41.8 1.0
N N:THR164 4.0 48.6 1.0
OD2 N:ASP256 4.1 50.5 1.0
CG2 N:THR164 4.1 49.7 1.0
CA N:THR164 4.1 49.3 1.0
OE2 N:GLU193 4.1 50.0 1.0
OE1 N:GLU193 4.1 48.4 1.0
O1A N:ADP600 4.1 41.5 1.0
NH1 N:ARG190 4.2 32.4 1.0
OE1 N:GLU189 4.2 55.6 1.0
OD1 N:ASP256 4.4 54.2 1.0
O2B N:ADP600 4.5 37.3 1.0
CD N:GLU193 4.5 50.6 1.0
O3A N:ADP600 4.5 46.5 1.0
NH1 M:ARG375 4.6 60.1 1.0
PA N:ADP600 4.6 43.7 1.0
CD N:GLU189 4.6 53.7 1.0
O N:HOH2015 4.7 48.4 1.0
O2A N:ADP600 4.7 46.2 1.0
CG N:ASP256 4.7 50.1 1.0
CE N:LYS163 4.8 41.9 1.0
CB N:LYS163 4.8 48.0 1.0
C N:LYS163 4.9 48.5 1.0

Magnesium binding site 10 out of 10 in 3zia

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Magnesium binding site 10 out of 10 in the The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg601

b:25.2
occ:1.00
 O P:HOH2033 2.0 22.3 1.0
O P:HOH2032 2.1 26.3 1.0
OG1 P:THR164 2.2 26.9 1.0
O P:HOH2035 2.2 26.6 1.0
O1B P:ADP600 2.2 24.2 1.0
O P:HOH2034 2.2 24.4 1.0
CB P:THR164 3.1 30.3 1.0
PB P:ADP600 3.4 26.8 1.0
O3B P:ADP600 3.6 32.7 1.0
OE1 P:GLU189 3.9 30.4 1.0
NH1 P:ARG190 3.9 24.2 1.0
N P:THR164 4.0 29.2 1.0
OE2 P:GLU193 4.1 35.3 1.0
OD2 P:ASP256 4.1 29.8 1.0
O1A P:ADP600 4.1 28.5 1.0
CA P:THR164 4.1 30.0 1.0
CG2 P:THR164 4.2 31.0 1.0
O P:HOH2036 4.2 29.1 1.0
OD1 P:ASP256 4.3 29.5 1.0
OE1 P:GLU193 4.4 37.0 1.0
O2B P:ADP600 4.5 29.1 1.0
O3A P:ADP600 4.5 23.3 1.0
O L:HOH2140 4.5 27.0 1.0
CD P:GLU189 4.6 26.5 1.0
PA P:ADP600 4.6 25.4 1.0
CD P:GLU193 4.6 31.7 1.0
O2A P:ADP600 4.7 22.1 1.0
CG P:ASP256 4.7 28.0 1.0
O P:HOH2031 4.7 22.9 1.0
CB P:LYS163 4.9 26.6 1.0

Reference:

G.C.Robinson, J.V.Bason, M.G.Montgomery, I.M.Fearnley, D.M.Mueller, A.G.W.Leslie, J.E.Walker. The Structure of F1-Atpase From Saccharomyces Cerevisiae Inhibited By Its Regulatory Protein IF1. Open Biol. V. 3 164 2013.
ISSN: ESSN 2046-2441
PubMed: 23407639
DOI: 10.1098/RSOB.120164
Page generated: Mon Dec 14 09:03:42 2020

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