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Magnesium in PDB 5ik2: Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)

Enzymatic activity of Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)

All present enzymatic activity of Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant):
3.6.3.14;

Protein crystallography data

The structure of Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant), PDB code: 5ik2 was solved by S.A.Ferguson, G.M.Cook, M.G.Montgomery, 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) 201.40 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 148.240, 131.290, 212.010, 90.00, 108.20, 90.00
R / Rfree (%) 21.3 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant) (pdb code 5ik2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant), PDB code: 5ik2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5ik2

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Magnesium binding site 1 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:31.4
occ:1.00
 O A:HOH701 2.2 31.4 1.0
O1B A:ADP600 2.2 31.6 1.0
O A:HOH703 2.2 31.1 1.0
OG1 A:THR176 2.2 32.2 1.0
O A:HOH702 2.2 31.3 1.0
O A:HOH704 2.2 31.1 1.0
CB A:THR176 3.4 32.7 1.0
PB A:ADP600 3.5 31.6 1.0
O3B A:ADP600 3.9 31.7 1.0
O2A A:ADP600 3.9 32.6 1.0
OD1 A:ASP261 4.0 29.0 1.0
OD2 A:ASP261 4.0 28.5 1.0
O A:HOH844 4.2 24.5 1.0
N A:THR176 4.3 32.7 1.0
CG2 A:THR176 4.3 32.7 1.0
CA A:THR176 4.4 32.9 1.0
CG A:ASP261 4.5 28.7 1.0
O2B A:ADP600 4.5 31.3 1.0
O3A A:ADP600 4.5 32.1 1.0
PA A:ADP600 4.8 32.0 1.0
CE2 A:PHE318 5.0 30.9 1.0

Magnesium binding site 2 out of 10 in 5ik2

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Magnesium binding site 2 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:23.0
occ:1.00
 O B:HOH701 2.2 23.2 1.0
O2B B:ADP600 2.2 23.8 1.0
O B:HOH702 2.2 23.1 1.0
O B:HOH703 2.2 23.5 1.0
OG1 B:THR176 2.2 23.6 1.0
O B:HOH704 2.2 23.1 1.0
CB B:THR176 3.3 24.1 1.0
PB B:ADP600 3.4 24.2 1.0
O1B B:ADP600 3.7 24.0 1.0
OD2 B:ASP261 4.0 23.4 1.0
O1A B:ADP600 4.1 24.4 1.0
OD1 B:ASP261 4.2 23.3 1.0
N B:THR176 4.2 24.2 1.0
CG2 B:THR176 4.2 23.9 1.0
OE1 B:GLN200 4.3 25.6 1.0
CA B:THR176 4.3 24.3 1.0
O3B B:ADP600 4.4 23.8 1.0
O3A B:ADP600 4.5 24.2 1.0
CG B:ASP261 4.5 23.2 1.0
PA B:ADP600 4.6 24.2 1.0
O B:HOH832 4.7 22.9 1.0
O2A B:ADP600 4.7 24.2 1.0
O B:HOH894 4.8 22.7 1.0
O B:HOH844 4.9 25.1 1.0
O B:HOH862 4.9 23.3 1.0

Magnesium binding site 3 out of 10 in 5ik2

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Magnesium binding site 3 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:24.1
occ:1.00
 OG1 C:THR176 2.2 24.3 1.0
O2B C:ADP600 2.2 23.8 1.0
CB C:THR176 3.3 24.7 1.0
PB C:ADP600 3.4 23.4 1.0
O3B C:ADP600 3.7 23.8 1.0
OD2 C:ASP261 4.0 21.6 1.0
OD1 C:ASP261 4.1 22.0 1.0
O2A C:ADP600 4.1 23.1 1.0
O C:HOH841 4.1 20.2 1.0
N C:THR176 4.2 24.8 1.0
CA C:THR176 4.3 24.8 1.0
CG2 C:THR176 4.3 24.7 1.0
O1B C:ADP600 4.4 23.3 1.0
O C:HOH819 4.4 21.4 1.0
CG C:ASP261 4.5 22.1 1.0
O3A C:ADP600 4.5 23.3 1.0
PA C:ADP600 4.6 23.0 1.0
O C:HOH859 4.7 15.8 1.0
O1A C:ADP600 4.8 23.0 1.0
CE2 C:PHE318 4.9 23.5 1.0

Magnesium binding site 4 out of 10 in 5ik2

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Magnesium binding site 4 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:30.2
occ:1.00
 O1B D:ADP600 2.2 29.5 1.0
OG1 D:THR158 2.2 30.9 1.0
CB D:THR158 3.4 31.8 1.0
PB D:ADP600 3.4 29.1 1.0
O3B D:ADP600 3.7 29.2 1.0
NH1 D:ARG184 3.7 33.5 1.0
OE1 D:GLU183 4.1 35.0 1.0
N D:THR158 4.1 31.5 1.0
O2A D:ADP600 4.2 29.1 1.0
O D:HOH839 4.2 26.1 1.0
OD1 D:ASP245 4.2 29.9 1.0
OE1 D:GLU187 4.3 37.6 1.0
CA D:THR158 4.3 31.9 1.0
OE2 D:GLU187 4.3 38.5 1.0
OD2 D:ASP245 4.3 29.8 1.0
O3A D:ADP600 4.4 29.3 1.0
NH1 C:ARG365 4.4 31.7 1.0
CG2 D:THR158 4.4 31.8 1.0
O2B D:ADP600 4.5 29.0 1.0
PA D:ADP600 4.6 29.1 1.0
O1A D:ADP600 4.6 29.1 1.0
CD D:GLU183 4.7 34.5 1.0
CD D:GLU187 4.7 38.2 1.0
CG D:ASP245 4.7 30.0 1.0
O D:HOH823 4.8 30.4 1.0
O D:HOH819 4.8 22.4 1.0
CE D:LYS157 4.9 30.1 1.0
CB D:LYS157 4.9 30.4 1.0
CZ D:ARG184 4.9 33.4 1.0

Magnesium binding site 5 out of 10 in 5ik2

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Magnesium binding site 5 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:22.7
occ:1.00
 OG1 F:THR158 2.2 23.2 1.0
O2B F:ADP600 2.2 22.7 1.0
CB F:THR158 3.4 23.8 1.0
PB F:ADP600 3.4 22.7 1.0
O3B F:ADP600 3.7 22.9 1.0
NH1 F:ARG184 3.9 25.5 1.0
OE1 F:GLU183 3.9 24.8 1.0
O2A F:ADP600 4.0 23.7 1.0
N F:THR158 4.2 24.1 1.0
OD2 F:ASP245 4.2 24.7 1.0
O F:HOH874 4.2 15.8 1.0
CG2 F:THR158 4.3 23.8 1.0
CA F:THR158 4.3 24.1 1.0
OD1 F:ASP245 4.4 24.3 1.0
OE2 F:GLU187 4.4 31.2 1.0
OE1 F:GLU187 4.4 31.4 1.0
O3A F:ADP600 4.4 23.2 1.0
O1B F:ADP600 4.5 22.6 1.0
PA F:ADP600 4.5 23.6 1.0
O1A F:ADP600 4.6 23.3 1.0
O F:HOH804 4.6 18.8 1.0
CD F:GLU183 4.6 24.8 1.0
O F:HOH837 4.7 16.1 1.0
CG F:ASP245 4.7 24.7 1.0
CD F:GLU187 4.8 31.5 1.0
O F:HOH823 4.8 22.4 1.0
CE F:LYS157 5.0 23.0 1.0
CB F:LYS157 5.0 23.3 1.0

Magnesium binding site 6 out of 10 in 5ik2

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Magnesium binding site 6 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:23.9
occ:1.00
 OG1 I:THR176 2.2 24.4 1.0
O I:HOH704 2.2 23.9 1.0
O1B I:ADP600 2.2 24.4 1.0
CB I:THR176 3.3 24.8 1.0
PB I:ADP600 3.4 24.8 1.0
O3B I:ADP600 3.7 24.8 1.0
OD1 I:ASP261 4.1 20.3 1.0
OD2 I:ASP261 4.1 20.3 1.0
O1A I:ADP600 4.1 25.9 1.0
N I:THR176 4.2 25.4 1.0
CA I:THR176 4.3 25.1 1.0
CG2 I:THR176 4.3 24.8 1.0
O2B I:ADP600 4.4 24.9 1.0
O3A I:ADP600 4.5 25.3 1.0
CG I:ASP261 4.5 20.6 1.0
O I:HOH864 4.7 25.4 1.0
PA I:ADP600 4.7 26.0 1.0
O2A I:ADP600 4.9 25.9 1.0
CE2 I:PHE318 4.9 23.2 1.0

Magnesium binding site 7 out of 10 in 5ik2

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Magnesium binding site 7 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:23.2
occ:1.00
 O2B J:ADP600 2.2 23.4 1.0
OG1 J:THR176 2.2 24.0 1.0
CB J:THR176 3.3 25.0 1.0
PB J:ADP600 3.4 23.6 1.0
O1B J:ADP600 3.7 23.9 1.0
OD2 J:ASP261 3.9 22.5 1.0
OD1 J:ASP261 4.1 22.7 1.0
O1A J:ADP600 4.1 23.8 1.0
N J:THR176 4.2 25.7 1.0
CG2 J:THR176 4.3 25.0 1.0
OE1 J:GLN200 4.3 23.0 1.0
CA J:THR176 4.3 25.6 1.0
O J:HOH867 4.3 16.2 1.0
O3B J:ADP600 4.4 23.5 1.0
CG J:ASP261 4.5 22.6 1.0
O3A J:ADP600 4.5 24.0 1.0
O J:HOH814 4.6 17.3 1.0
PA J:ADP600 4.6 23.9 1.0
O2A J:ADP600 4.8 23.9 1.0
O J:HOH826 4.8 25.5 1.0

Magnesium binding site 8 out of 10 in 5ik2

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Magnesium binding site 8 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:20.8
occ:1.00
 O1B K:ADP600 2.2 20.9 1.0
OG1 K:THR176 2.2 21.3 1.0
CB K:THR176 3.3 22.0 1.0
PB K:ADP600 3.4 20.9 1.0
O3B K:ADP600 3.8 20.8 1.0
OD2 K:ASP261 4.0 20.8 1.0
OD1 K:ASP261 4.1 20.7 1.0
O2A K:ADP600 4.2 20.7 1.0
N K:THR176 4.2 22.3 1.0
O K:HOH865 4.2 27.2 1.0
CG2 K:THR176 4.3 21.9 1.0
CA K:THR176 4.3 22.2 1.0
O2B K:ADP600 4.4 20.7 1.0
CG K:ASP261 4.5 20.9 1.0
O3A K:ADP600 4.5 20.9 1.0
PA K:ADP600 4.7 20.7 1.0
O1A K:ADP600 4.8 20.8 1.0
CE2 K:PHE318 4.9 22.8 1.0

Magnesium binding site 9 out of 10 in 5ik2

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Magnesium binding site 9 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

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

b:25.3
occ:1.00
 OG1 L:THR158 2.2 25.2 1.0
O1B L:ADP600 2.2 25.5 1.0
CB L:THR158 3.3 25.0 1.0
PB L:ADP600 3.4 26.0 1.0
O3B L:ADP600 3.6 25.8 1.0
NH1 L:ARG184 3.7 28.5 1.0
OE1 L:GLU183 4.0 27.4 1.0
N L:THR158 4.1 24.6 1.0
O2A L:ADP600 4.1 25.8 1.0
O L:HOH856 4.2 20.0 1.0
OD1 L:ASP245 4.2 25.3 1.0
NH1 K:ARG365 4.2 29.3 1.0
OE1 L:GLU187 4.2 30.7 1.0
CA L:THR158 4.3 24.9 1.0
OE2 L:GLU187 4.3 31.5 1.0
OD2 L:ASP245 4.3 25.2 1.0
CG2 L:THR158 4.4 25.1 1.0
O3A L:ADP600 4.4 26.1 1.0
O2B L:ADP600 4.4 26.0 1.0
PA L:ADP600 4.6 26.0 1.0
CD L:GLU183 4.6 27.4 1.0
O L:HOH833 4.7 27.6 1.0
O1A L:ADP600 4.7 25.5 1.0
O L:HOH820 4.7 21.5 1.0
CD L:GLU187 4.7 31.2 1.0
CG L:ASP245 4.7 25.3 1.0
CE L:LYS157 4.9 24.4 1.0
CB L:LYS157 4.9 24.3 1.0
CZ L:ARG184 4.9 28.5 1.0

Magnesium binding site 10 out of 10 in 5ik2

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Magnesium binding site 10 out of 10 in the Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Caldalaklibacillus Thermarum F1-Atpase (Epsilon Mutant) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg602

b:22.4
occ:1.00
 O2B N:ADP600 2.2 22.3 1.0
OG1 N:THR158 2.2 22.7 1.0
CB N:THR158 3.4 23.0 1.0
PB N:ADP600 3.4 22.4 1.0
O1B N:ADP600 3.7 22.4 1.0
NH1 N:ARG184 3.8 25.2 1.0
OE1 N:GLU183 3.9 24.9 1.0
O1A N:ADP600 4.1 23.1 1.0
N N:THR158 4.2 23.0 1.0
OD2 N:ASP245 4.3 22.1 1.0
OE2 N:GLU187 4.3 30.6 1.0
CG2 N:THR158 4.3 22.9 1.0
CA N:THR158 4.4 23.1 1.0
O3A N:ADP600 4.4 22.6 1.0
O N:HOH873 4.4 19.5 1.0
OE1 N:GLU187 4.4 30.3 1.0
OD1 N:ASP245 4.4 22.8 1.0
PA N:ADP600 4.5 23.0 1.0
O3B N:ADP600 4.6 22.3 1.0
O N:HOH810 4.6 27.0 1.0
O2A N:ADP600 4.6 22.9 1.0
CD N:GLU183 4.7 25.2 1.0
O N:HOH872 4.7 21.0 1.0
CD N:GLU187 4.8 30.4 1.0
CG N:ASP245 4.8 22.6 1.0

Reference:

S.A.Ferguson, G.M.Cook, M.G.Montgomery, A.G.Leslie, J.E.Walker. Regulation of the Thermoalkaliphilic F1-Atpase From Caldalkalibacillus Thermarum. Proc.Natl.Acad.Sci.Usa V. 113 10860 2016.
ISSN: ESSN 1091-6490
PubMed: 27621435
DOI: 10.1073/PNAS.1612035113
Page generated: Sun Sep 29 16:43:02 2024

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