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Magnesium in PDB 6q45: F1-Atpase From Fusobacterium Nucleatum

Protein crystallography data

The structure of F1-Atpase From Fusobacterium Nucleatum, PDB code: 6q45 was solved by J.Petri, Y.Nakatani, M.G.Montgomery, S.A.Ferguson, D.Aragao, A.G.W.Leslie, A.Heikal, J.E.Walker, G.M.Cook, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.34 / 3.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 111.940, 200.209, 201.725, 90.00, 102.20, 90.00
R / Rfree (%) 23.7 / 28

Magnesium Binding Sites:

The binding sites of Magnesium atom in the F1-Atpase From Fusobacterium Nucleatum (pdb code 6q45). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the F1-Atpase From Fusobacterium Nucleatum, PDB code: 6q45:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6q45

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Magnesium binding site 1 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:56.6
occ:1.00
 O A:HOH702 2.2 58.2 1.0
O A:HOH701 2.2 57.4 1.0
O1B A:ATP600 2.2 56.6 1.0
O1G A:ATP600 2.2 58.4 1.0
OG1 A:THR176 2.2 59.0 1.0
O A:HOH703 2.2 58.5 1.0
CB A:THR176 3.2 61.5 1.0
PB A:ATP600 3.3 57.3 1.0
PG A:ATP600 3.4 60.1 1.0
O3B A:ATP600 3.4 59.3 1.0
OD2 A:ASP261 3.9 69.9 1.0
N A:THR176 4.1 61.3 1.0
OD1 A:ASP261 4.1 74.9 1.0
CG2 A:THR176 4.1 61.2 1.0
O3G A:ATP600 4.2 60.7 1.0
CA A:THR176 4.2 61.9 1.0
O2A A:ATP600 4.3 60.0 1.0
O2B A:ATP600 4.4 58.0 1.0
O3A A:ATP600 4.4 58.9 1.0
CG A:ASP261 4.4 72.9 1.0
O2G A:ATP600 4.5 60.1 1.0
PA A:ATP600 4.6 59.7 1.0
O1A A:ATP600 4.7 59.7 1.0

Magnesium binding site 2 out of 10 in 6q45

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Magnesium binding site 2 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:82.3
occ:1.00
 O1G B:ATP600 2.2 84.2 1.0
O B:HOH702 2.2 83.4 1.0
O B:HOH701 2.2 83.0 1.0
OG1 B:THR176 2.2 80.8 1.0
O B:HOH703 2.2 82.2 1.0
O1B B:ATP600 2.2 79.3 1.0
CB B:THR176 3.1 79.9 1.0
PB B:ATP600 3.4 77.9 1.0
PG B:ATP600 3.4 86.4 1.0
O3B B:ATP600 3.5 82.7 1.0
O1A B:ATP600 3.9 82.3 1.0
O3G B:ATP600 4.0 86.2 1.0
OD1 B:ASP261 4.1 76.1 1.0
OD2 B:ASP261 4.1 77.7 1.0
CG2 B:THR176 4.1 80.6 1.0
N B:THR176 4.1 78.6 1.0
CA B:THR176 4.2 79.3 1.0
O2B B:ATP600 4.4 79.1 1.0
OE1 B:GLN200 4.5 64.9 1.0
O3A B:ATP600 4.5 79.1 1.0
CG B:ASP261 4.5 77.2 1.0
PA B:ATP600 4.6 81.2 1.0
O2G B:ATP600 4.6 86.2 1.0
O2A B:ATP600 4.7 80.5 1.0

Magnesium binding site 3 out of 10 in 6q45

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Magnesium binding site 3 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:67.0
occ:1.00
 OG1 C:THR176 2.2 67.4 1.0
O C:HOH703 2.2 67.5 1.0
O1G C:ATP600 2.2 70.7 1.0
O C:HOH702 2.2 67.5 1.0
O C:HOH701 2.2 69.1 1.0
O1B C:ATP600 2.2 67.3 1.0
CB C:THR176 3.2 66.2 1.0
PB C:ATP600 3.3 67.8 1.0
O3B C:ATP600 3.3 71.4 1.0
PG C:ATP600 3.4 75.2 1.0
OD2 C:ASP261 4.0 61.5 1.0
N C:THR176 4.0 65.7 1.0
OD1 C:ASP261 4.1 60.2 1.0
CG2 C:THR176 4.2 66.1 1.0
CA C:THR176 4.2 65.7 1.0
O2B C:ATP600 4.3 68.7 1.0
O2G C:ATP600 4.4 74.7 1.0
O3G C:ATP600 4.4 76.0 1.0
O1A C:ATP600 4.4 70.2 1.0
CG C:ASP261 4.5 61.6 1.0
O3A C:ATP600 4.5 69.0 1.0
O2A C:ATP600 4.7 72.3 1.0
PA C:ATP600 4.7 70.8 1.0
CB C:LYS175 4.9 64.2 1.0

Magnesium binding site 4 out of 10 in 6q45

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Magnesium binding site 4 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:66.5
occ:1.00
 O D:HOH702 2.2 65.8 1.0
O D:HOH701 2.2 66.3 1.0
O D:HOH703 2.2 69.8 1.0
OG1 D:THR156 2.2 68.5 1.0
O1B D:ADP600 2.2 70.1 1.0
O D:HOH704 2.2 69.2 1.0
CB D:THR156 3.1 68.8 1.0
PB D:ADP600 3.3 74.8 1.0
NH1 D:ARG182 3.4 70.9 1.0
O2B D:ADP600 3.5 77.6 1.0
CG2 D:THR156 4.0 68.4 1.0
O1A D:ADP600 4.0 75.0 1.0
OE1 D:GLU185 4.2 69.4 1.0
CA D:THR156 4.2 69.3 1.0
OE2 D:GLU185 4.3 71.4 1.0
N D:THR156 4.3 69.8 1.0
OD2 D:ASP243 4.3 60.6 1.0
NZ D:LYS155 4.3 76.6 1.0
OE1 D:GLU181 4.4 78.9 1.0
CD D:GLU181 4.4 78.4 1.0
O3A D:ADP600 4.4 74.0 1.0
O3B D:ADP600 4.4 75.9 1.0
OE2 D:GLU181 4.4 79.9 1.0
OD1 D:ASP243 4.5 60.2 1.0
PA D:ADP600 4.5 74.2 1.0
CZ D:ARG182 4.6 68.8 1.0
CD D:GLU185 4.7 70.8 1.0
O2A D:ADP600 4.7 74.0 1.0
CG D:LYS155 4.8 73.8 1.0
NH2 D:ARG182 4.8 68.8 1.0
CG D:ASP243 4.8 60.5 1.0
CE D:LYS155 4.9 76.2 1.0
CG D:GLU181 5.0 75.8 1.0

Magnesium binding site 5 out of 10 in 6q45

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Magnesium binding site 5 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:70.5
occ:1.00
 O F:HOH701 2.2 71.3 1.0
O F:HOH703 2.2 72.4 1.0
OG1 F:THR156 2.2 70.7 1.0
O2B F:ADP600 2.2 75.1 1.0
O F:HOH702 2.2 71.1 1.0
O F:HOH704 2.2 70.8 1.0
CB F:THR156 3.0 71.5 1.0
PB F:ADP600 3.4 81.5 1.0
O1B F:ADP600 3.6 81.0 1.0
NH1 F:ARG182 3.6 75.0 1.0
CG2 F:THR156 3.9 70.9 1.0
OE2 F:GLU185 3.9 73.8 1.0
OE1 F:GLU181 3.9 87.9 1.0
O1A F:ADP600 4.0 88.7 1.0
OD2 F:ASP243 4.1 89.6 1.0
CA F:THR156 4.2 72.7 1.0
N F:THR156 4.3 74.7 1.0
OD1 F:ASP243 4.4 85.7 1.0
O3A F:ADP600 4.4 83.2 1.0
OE1 F:GLU185 4.4 78.0 1.0
O2A F:ADP600 4.4 87.8 1.0
PA F:ADP600 4.5 86.6 1.0
O3B F:ADP600 4.5 82.1 1.0
CD F:GLU181 4.5 87.3 1.0
NZ F:LYS155 4.5 84.8 1.0
CD F:GLU185 4.6 76.8 1.0
CG F:ASP243 4.7 86.8 1.0
CZ F:ARG182 4.7 74.3 1.0
CG F:LYS155 4.8 77.1 1.0
CE F:LYS155 4.9 82.8 1.0

Magnesium binding site 6 out of 10 in 6q45

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Magnesium binding site 6 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg601

b:0.1
occ:1.00
 O I:HOH702 2.2 100.0 1.0
O2B I:ATP600 2.2 0.8 1.0
O I:HOH703 2.2 0.7 1.0
O I:HOH701 2.2 100.0 1.0
O2G I:ATP600 2.2 0.4 1.0
OG1 I:THR176 2.2 0.8 1.0
CB I:THR176 3.2 0.5 1.0
PB I:ATP600 3.3 0.2 1.0
PG I:ATP600 3.4 0.2 1.0
O3B I:ATP600 3.4 0.7 1.0
OD2 I:ASP261 3.8 0.5 1.0
OD1 I:ASP261 4.0 0.9 1.0
O2A I:ATP600 4.1 99.8 1.0
N I:THR176 4.1 0.4 1.0
CG2 I:THR176 4.2 0.9 1.0
CA I:THR176 4.2 0.5 1.0
O1B I:ATP600 4.3 0.0 1.0
CG I:ASP261 4.3 0.0 1.0
O1G I:ATP600 4.4 0.2 1.0
O3G I:ATP600 4.4 0.3 1.0
O3A I:ATP600 4.4 0.7 1.0
PA I:ATP600 4.6 98.8 1.0
O1A I:ATP600 4.8 0.8 1.0
CB I:LYS175 5.0 0.5 1.0

Magnesium binding site 7 out of 10 in 6q45

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Magnesium binding site 7 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg601

b:0.4
occ:1.00
 O1G J:ATP600 2.2 0.9 1.0
OG1 J:THR176 2.2 0.8 1.0
O J:HOH703 2.2 0.7 1.0
O J:HOH701 2.2 0.2 1.0
O1B J:ATP600 2.2 0.2 1.0
O J:HOH702 2.2 0.1 1.0
CB J:THR176 3.1 1.0 1.0
PG J:ATP600 3.2 0.2 1.0
PB J:ATP600 3.4 0.6 1.0
O3G J:ATP600 3.4 0.1 1.0
O3B J:ATP600 3.5 0.1 1.0
O1A J:ATP600 3.9 0.3 1.0
CG2 J:THR176 4.0 0.2 1.0
OD2 J:ASP261 4.1 0.4 1.0
OD1 J:ASP261 4.2 0.5 1.0
N J:THR176 4.2 0.9 1.0
CA J:THR176 4.2 0.5 1.0
O2A J:ATP600 4.3 0.8 1.0
PA J:ATP600 4.3 0.8 1.0
O3A J:ATP600 4.4 0.9 1.0
OE1 J:GLN200 4.4 0.6 1.0
O2B J:ATP600 4.5 0.1 1.0
O2G J:ATP600 4.6 0.8 1.0
CG J:ASP261 4.6 1.0 1.0

Magnesium binding site 8 out of 10 in 6q45

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Magnesium binding site 8 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg601

b:68.9
occ:1.00
 O2B K:ATP600 2.2 68.5 1.0
O K:HOH701 2.2 69.6 1.0
O K:HOH703 2.2 69.7 1.0
O K:HOH702 2.2 68.3 1.0
O2G K:ATP600 2.2 70.0 1.0
OG1 K:THR176 2.2 70.3 1.0
CB K:THR176 3.1 73.8 1.0
PB K:ATP600 3.3 69.9 1.0
PG K:ATP600 3.4 69.3 1.0
O3B K:ATP600 3.5 69.5 1.0
O1A K:ATP600 3.9 68.5 1.0
OD2 K:ASP261 4.0 77.5 1.0
CG2 K:THR176 4.0 74.6 1.0
O3G K:ATP600 4.0 68.6 1.0
OD1 K:ASP261 4.1 77.3 1.0
N K:THR176 4.2 76.3 1.0
CA K:THR176 4.2 74.3 1.0
O1B K:ATP600 4.4 71.8 1.0
O3A K:ATP600 4.5 69.1 1.0
CG K:ASP261 4.5 76.7 1.0
PA K:ATP600 4.6 69.1 1.0
O1G K:ATP600 4.6 69.3 1.0
O2A K:ATP600 4.7 70.2 1.0

Magnesium binding site 9 out of 10 in 6q45

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Magnesium binding site 9 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:76.4
occ:1.00
 O L:HOH704 2.2 77.9 1.0
OG1 L:THR156 2.2 79.8 1.0
O2B L:ADP600 2.2 74.2 1.0
O L:HOH701 2.2 75.9 1.0
O L:HOH702 2.2 76.7 1.0
O L:HOH703 2.2 75.5 1.0
CB L:THR156 3.1 85.9 1.0
PB L:ADP600 3.3 71.8 1.0
O3B L:ADP600 3.4 73.9 1.0
NH1 L:ARG182 3.5 91.1 1.0
CG2 L:THR156 4.1 85.9 1.0
O2A L:ADP600 4.1 78.2 1.0
NZ L:LYS155 4.2 90.9 1.0
CA L:THR156 4.2 88.6 1.0
N L:THR156 4.3 89.8 1.0
OE1 L:GLU185 4.3 93.0 1.0
OD2 L:ASP243 4.3 86.7 1.0
CD L:GLU181 4.4 89.2 1.0
O3A L:ADP600 4.4 74.7 1.0
OE1 L:GLU181 4.4 89.7 1.0
OE2 L:GLU181 4.4 89.2 1.0
O1B L:ADP600 4.4 72.9 1.0
OD1 L:ASP243 4.4 90.7 1.0
OE2 L:GLU185 4.4 90.2 1.0
PA L:ADP600 4.6 76.6 1.0
CZ L:ARG182 4.6 90.2 1.0
CG L:LYS155 4.7 88.4 1.0
O1A L:ADP600 4.7 76.9 1.0
CE L:LYS155 4.8 90.3 1.0
CG L:ASP243 4.8 89.9 1.0
CD L:GLU185 4.8 91.9 1.0
NH2 L:ARG182 4.8 90.3 1.0
CG L:GLU181 5.0 88.7 1.0

Magnesium binding site 10 out of 10 in 6q45

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Magnesium binding site 10 out of 10 in the F1-Atpase From Fusobacterium Nucleatum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of F1-Atpase From Fusobacterium Nucleatum within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg601

b:75.5
occ:1.00
 OG1 N:THR156 2.2 78.9 1.0
O2B N:ADP600 2.2 76.8 1.0
O N:HOH702 2.2 76.0 1.0
O N:HOH704 2.2 77.2 1.0
O N:HOH701 2.2 75.8 1.0
O N:HOH703 2.2 77.8 1.0
CB N:THR156 3.0 82.4 1.0
PB N:ADP600 3.3 80.0 1.0
O1B N:ADP600 3.4 79.7 1.0
NH1 N:ARG182 3.6 0.9 1.0
CG2 N:THR156 3.9 82.4 1.0
OE2 N:GLU185 3.9 0.2 1.0
O1A N:ADP600 4.0 88.3 1.0
OE1 N:GLU181 4.0 0.7 1.0
CA N:THR156 4.2 83.7 1.0
OD2 N:ASP243 4.2 93.5 1.0
N N:THR156 4.2 85.8 1.0
O2A N:ADP600 4.3 85.5 1.0
O3A N:ADP600 4.3 82.9 1.0
O3B N:ADP600 4.4 79.8 1.0
PA N:ADP600 4.4 86.2 1.0
OD1 N:ASP243 4.5 93.9 1.0
NZ N:LYS155 4.5 94.6 1.0
OE1 N:GLU185 4.5 0.1 1.0
CD N:GLU181 4.6 0.1 1.0
CD N:GLU185 4.6 0.2 1.0
CZ N:ARG182 4.7 0.3 1.0
CG N:LYS155 4.7 89.8 1.0
CG N:ASP243 4.8 93.6 1.0
CE N:LYS155 4.9 93.9 1.0

Reference:

J.Petri, Y.Nakatani, M.G.Montgomery, S.A.Ferguson, D.Aragao, A.G.W.Leslie, A.Heikal, J.E.Walker, G.M.Cook. Structure of F1-Atpase From the Obligate Anaerobe Fusobacterium Nucleatum. Open Biology V. 9 90066 2019.
ISSN: ESSN 2046-2441
PubMed: 31238823
DOI: 10.1098/RSOB.190066
Page generated: Tue Oct 1 15:23:14 2024

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