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Magnesium in PDB 5fl7: Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase

Enzymatic activity of Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase

All present enzymatic activity of Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase:
3.6.1.34; 3.6.3.14;

Protein crystallography data

The structure of Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase, PDB code: 5fl7 was solved by K.Parey, M.Bublitz, T.Meier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.366 / 3.50
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 169.500, 182.200, 193.000, 90.00, 90.00, 90.00
R / Rfree (%) 27.39 / 30.54

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase (pdb code 5fl7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase, PDB code: 5fl7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 5fl7

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Magnesium binding site 1 out of 5 in the Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:0.5
occ:1.00
 O A:HOH2002 2.0 0.7 1.0
OG1 A:THR202 2.0 0.8 1.0
O1G A:ATP600 2.1 0.9 1.0
O A:HOH2001 2.1 0.8 1.0
O A:HOH2003 2.1 0.5 1.0
O2B A:ATP600 2.1 0.7 1.0
CB A:THR202 2.9 0.2 1.0
PB A:ATP600 3.4 1.0 1.0
PG A:ATP600 3.4 0.5 1.0
O3B A:ATP600 3.7 0.0 1.0
CG2 A:THR202 3.8 0.8 1.0
OD2 A:ASP295 3.8 0.8 1.0
CA A:THR202 4.1 0.1 1.0
N A:THR202 4.2 0.6 1.0
OD1 A:ASP295 4.2 0.5 1.0
O3G A:ATP600 4.2 0.0 1.0
O1B A:ATP600 4.3 0.3 1.0
O2A A:ATP600 4.4 0.9 1.0
CG A:ASP295 4.5 0.6 1.0
O2G A:ATP600 4.5 0.1 1.0
O3A A:ATP600 4.5 0.2 1.0
NE2 A:GLN234 4.6 1.0 1.0
PA A:ATP600 4.8 0.3 1.0
O1A A:ATP600 4.8 0.8 1.0
CD A:GLN234 5.0 0.5 1.0

Magnesium binding site 2 out of 5 in 5fl7

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Magnesium binding site 2 out of 5 in the Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:0.3
occ:1.00
 O2G B:ATP600 2.0 0.8 1.0
O2B B:ATP600 2.0 0.5 1.0
OG1 B:THR202 2.1 0.4 1.0
O B:HOH2001 2.1 0.2 1.0
O B:HOH2003 2.1 0.1 1.0
O B:HOH2002 2.1 0.3 1.0
PB B:ATP600 3.0 0.4 1.0
CB B:THR202 3.1 0.6 1.0
O3B B:ATP600 3.1 0.4 1.0
PG B:ATP600 3.1 0.8 1.0
O2A B:ATP600 3.8 0.4 1.0
O3G B:ATP600 3.9 0.7 1.0
OD1 B:ASP295 3.9 0.7 1.0
O1B B:ATP600 4.0 0.5 1.0
CG2 B:THR202 4.0 0.3 1.0
N B:THR202 4.1 0.8 1.0
OE1 B:GLN234 4.1 0.1 1.0
CA B:THR202 4.2 0.8 1.0
O3A B:ATP600 4.3 0.1 1.0
O1G B:ATP600 4.3 0.4 1.0
PA B:ATP600 4.5 0.1 1.0
OD2 B:ASP295 4.5 0.8 1.0
CG B:ASP295 4.7 0.2 1.0
O1A B:ATP600 4.9 0.7 1.0

Magnesium binding site 3 out of 5 in 5fl7

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Magnesium binding site 3 out of 5 in the Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:0.2
occ:1.00
 O2B C:ATP600 2.0 0.0 1.0
OG1 C:THR202 2.0 0.7 1.0
O1G C:ATP600 2.0 0.4 1.0
O C:HOH2003 2.0 0.5 1.0
O C:HOH2001 2.1 0.3 1.0
O C:HOH2002 2.1 0.8 1.0
CB C:THR202 3.1 0.9 1.0
PG C:ATP600 3.3 0.1 1.0
PB C:ATP600 3.4 0.8 1.0
O3B C:ATP600 3.7 0.3 1.0
O3G C:ATP600 3.7 0.1 1.0
CG2 C:THR202 4.1 0.1 1.0
OD2 C:ASP295 4.1 0.3 1.0
N C:THR202 4.1 0.8 1.0
OD1 C:ASP295 4.1 0.7 1.0
CA C:THR202 4.2 0.1 1.0
O1B C:ATP600 4.3 0.9 1.0
O3A C:ATP600 4.3 0.5 1.0
NE2 C:GLN234 4.5 0.8 1.0
O2G C:ATP600 4.5 0.2 1.0
CG C:ASP295 4.6 0.8 1.0
O2A C:ATP600 4.7 0.4 1.0
O1A C:ATP600 4.8 0.6 1.0
PA C:ATP600 4.8 0.1 1.0
NZ C:LYS201 4.9 0.1 1.0

Magnesium binding site 4 out of 5 in 5fl7

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Magnesium binding site 4 out of 5 in the Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:0.7
occ:1.00
 O D:HOH2002 2.0 0.1 1.0
O1B D:ADP600 2.0 0.1 1.0
O D:HOH2004 2.1 0.1 1.0
OG1 D:THR195 2.1 0.1 1.0
O D:HOH2003 2.1 0.5 1.0
O D:HOH2001 2.1 0.6 1.0
CB D:THR195 3.2 0.7 1.0
PB D:ADP600 3.2 0.7 1.0
NH1 D:ARG221 3.4 0.5 1.0
O3B D:ADP600 3.6 0.1 1.0
N D:THR195 4.0 0.7 1.0
OE1 D:GLU224 4.0 0.8 1.0
OE2 D:GLU224 4.1 0.8 1.0
OE1 D:GLU220 4.1 0.6 1.0
O2B D:ADP600 4.1 1.0 1.0
O2A D:ADP600 4.1 0.8 1.0
CA D:THR195 4.2 0.3 1.0
CG2 D:THR195 4.2 0.5 1.0
O3A D:ADP600 4.4 0.4 1.0
CD D:GLU224 4.5 0.8 1.0
CZ D:ARG221 4.5 0.6 1.0
PA D:ADP600 4.6 0.4 1.0
O1A D:ADP600 4.8 0.5 1.0
NH2 D:ARG221 4.9 0.4 1.0
OD2 D:ASP287 4.9 0.3 1.0

Magnesium binding site 5 out of 5 in 5fl7

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Magnesium binding site 5 out of 5 in the Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the F1C10 Complex From Yarrowia Lipolytica Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:0.2
occ:1.00
 O F:HOH2004 2.0 0.8 1.0
O F:HOH2003 2.1 0.7 1.0
O F:HOH2001 2.1 0.9 1.0
O F:HOH2002 2.1 0.2 1.0
OG1 F:THR195 2.1 0.4 1.0
O2B F:ADP600 2.1 0.0 1.0
PB F:ADP600 2.9 0.9 1.0
O1B F:ADP600 3.3 0.1 1.0
CB F:THR195 3.4 0.6 1.0
O3B F:ADP600 3.5 0.7 1.0
OE1 F:GLU220 3.5 0.5 1.0
N F:THR195 4.0 1.0 1.0
NH1 F:ARG221 4.1 0.9 1.0
CA F:THR195 4.3 0.7 1.0
CG2 F:THR195 4.4 0.2 1.0
O3A F:ADP600 4.4 0.1 1.0
CD F:GLU220 4.4 0.3 1.0
OD1 F:ASP287 4.4 0.8 1.0
OE1 F:GLU224 4.5 0.7 1.0
NZ F:LYS194 4.6 0.4 1.0
OE2 F:GLU224 4.6 0.1 1.0
O2A F:ADP600 4.8 0.5 1.0
OD2 F:ASP287 4.8 0.8 1.0
CE F:LYS194 4.9 0.8 1.0
OE2 F:GLU220 5.0 0.2 1.0
PA F:ADP600 5.0 1.0 1.0
CB F:LYS194 5.0 0.9 1.0

Reference:

A.Hahn, K.Parey, M.Bublitz, D.J.Mills, V.Zickermann, J.Vonck, W.Kuhlbrandt, T.Meier. Structure of A Complete Atp Synthase Dimer Reveals the Molecular Basis of Inner Mitochondrial Membrane Morphology. Mol.Cell V. 63 445 2016.
ISSN: ISSN 1097-2765
PubMed: 27373333
DOI: 10.1016/J.MOLCEL.2016.05.037
Page generated: Sun Sep 29 04:19:39 2024

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