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Magnesium in PDB 5hkk: Caldalaklibacillus Thermarum F1-Atpase (Wild Type)

Enzymatic activity of Caldalaklibacillus Thermarum F1-Atpase (Wild Type)

All present enzymatic activity of Caldalaklibacillus Thermarum F1-Atpase (Wild Type):
3.6.3.14;

Protein crystallography data

The structure of Caldalaklibacillus Thermarum F1-Atpase (Wild Type), PDB code: 5hkk 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) 62.16 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 147.820, 130.790, 210.390, 90.00, 107.97, 90.00
R / Rfree (%) 20.3 / 24.6

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type) (pdb code 5hkk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type), PDB code: 5hkk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 5hkk

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Magnesium binding site 1 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:35.1
occ:1.00
 O A:HOH702 2.2 45.2 1.0
O2B A:ADP601 2.2 40.5 1.0
O A:HOH717 2.2 44.8 1.0
O A:HOH712 2.2 39.5 1.0
O A:HOH709 2.2 42.4 1.0
OG1 A:THR176 2.2 45.4 1.0
CB A:THR176 3.2 45.7 1.0
PB A:ADP601 3.4 41.1 1.0
O3B A:ADP601 3.7 41.0 1.0
O1A A:ADP601 3.8 45.0 1.0
N A:THR176 4.0 48.8 1.0
OD2 A:ASP261 4.0 44.0 1.0
OD1 A:ASP261 4.0 40.8 1.0
CA A:THR176 4.1 47.8 1.0
CG2 A:THR176 4.3 45.0 1.0
O1B A:ADP601 4.3 42.7 1.0
CG A:ASP261 4.4 44.1 1.0
O3A A:ADP601 4.5 43.3 1.0
PA A:ADP601 4.7 45.6 1.0
CE2 A:PHE318 4.9 52.0 1.0
CB A:LYS175 5.0 46.5 1.0

Magnesium binding site 2 out of 12 in 5hkk

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Magnesium binding site 2 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:26.8
occ:1.00
 O1B B:ADP600 2.2 32.5 1.0
O B:HOH717 2.2 28.0 1.0
OG1 B:THR176 2.2 29.6 1.0
O B:HOH714 2.2 26.2 1.0
O B:HOH715 2.2 29.5 1.0
O B:HOH701 2.2 26.9 1.0
CB B:THR176 3.1 32.1 1.0
PB B:ADP600 3.3 37.5 1.0
O3B B:ADP600 3.5 33.6 1.0
O2A B:ADP600 4.0 31.3 1.0
OD2 B:ASP261 4.1 34.9 1.0
N B:THR176 4.1 34.2 1.0
OD1 B:ASP261 4.1 41.3 1.0
CG2 B:THR176 4.2 31.0 1.0
CA B:THR176 4.2 33.6 1.0
O2B B:ADP600 4.3 33.6 1.0
O3A B:ADP600 4.4 34.8 1.0
O B:HOH706 4.5 34.3 1.0
CG B:ASP261 4.5 37.9 1.0
PA B:ADP600 4.6 35.1 1.0
OE1 B:GLN200 4.7 50.7 1.0

Magnesium binding site 3 out of 12 in 5hkk

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Magnesium binding site 3 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:33.9
occ:1.00
 OG1 C:THR176 2.2 33.3 1.0
O C:HOH710 2.2 31.5 1.0
O C:HOH712 2.2 34.7 1.0
O C:HOH718 2.2 37.5 1.0
O2B C:ADP600 2.2 33.6 1.0
O C:HOH721 2.2 34.9 1.0
CB C:THR176 3.1 33.8 1.0
PB C:ADP600 3.4 36.1 1.0
O1B C:ADP600 3.7 33.4 1.0
OD2 C:ASP261 4.0 40.3 1.0
N C:THR176 4.0 35.3 1.0
OD1 C:ASP261 4.1 44.4 1.0
CA C:THR176 4.1 33.6 1.0
CG2 C:THR176 4.2 33.6 1.0
O1A C:ADP600 4.3 28.1 1.0
O3B C:ADP600 4.4 34.5 1.0
CG C:ASP261 4.5 42.0 1.0
O3A C:ADP600 4.5 31.5 1.0
PA C:ADP600 4.7 30.9 1.0
O2A C:ADP600 4.9 31.2 1.0
CE2 C:PHE318 5.0 31.0 1.0

Magnesium binding site 4 out of 12 in 5hkk

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Magnesium binding site 4 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:67.8
occ:1.00
 OG1 D:THR158 2.2 55.6 1.0
O D:HOH717 2.2 56.7 1.0
O2B D:ADP600 2.2 53.0 1.0
O D:HOH702 2.2 64.0 1.0
O D:HOH712 2.2 57.7 1.0
O D:HOH714 2.2 61.1 1.0
NH1 D:ARG184 3.2 49.8 1.0
PB D:ADP600 3.3 48.7 1.0
CB D:THR158 3.4 50.4 1.0
O1B D:ADP600 3.6 50.5 1.0
OE1 D:GLU183 3.6 70.1 1.0
N D:THR158 4.0 46.6 1.0
CD D:GLU183 4.1 62.2 1.0
OE1 D:GLU187 4.2 98.7 1.0
O3A D:ADP600 4.2 67.1 1.0
OD1 D:ASP245 4.2 51.7 1.0
CA D:THR158 4.3 49.7 1.0
CZ D:ARG184 4.3 47.6 1.0
OD2 D:ASP245 4.3 53.5 1.0
CG2 D:THR158 4.4 53.6 1.0
O D:HOH726 4.4 22.3 1.0
NH2 D:ARG184 4.5 48.2 1.0
O3B D:ADP600 4.5 42.6 1.0
OE2 D:GLU183 4.5 59.7 1.0
O2A D:ADP600 4.6 83.3 1.0
CG D:GLU183 4.6 56.6 1.0
PA D:ADP600 4.7 82.9 1.0
CG D:ASP245 4.7 50.0 1.0
O1A D:ADP600 4.7 77.4 1.0
CE D:LYS157 4.7 52.5 1.0
CB D:LYS157 4.8 49.2 1.0
O D:HOH701 4.9 38.7 1.0

Magnesium binding site 5 out of 12 in 5hkk

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Magnesium binding site 5 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:32.5
occ:1.00
 O F:HOH718 2.2 28.3 1.0
O F:HOH711 2.2 31.5 1.0
OG1 F:THR158 2.2 33.9 1.0
O F:HOH708 2.2 34.0 1.0
O1B F:ADP600 2.2 32.3 1.0
O F:HOH725 2.2 34.6 1.0
CB F:THR158 3.3 32.9 1.0
PB F:ADP600 3.5 31.7 1.0
OE1 F:GLU183 3.9 62.1 1.0
O3B F:ADP600 3.9 30.6 1.0
NH1 F:ARG184 4.0 38.0 1.0
OE1 F:GLU187 4.0 48.5 1.0
O1A F:ADP600 4.1 39.2 1.0
N F:THR158 4.2 30.2 1.0
O F:HOH712 4.2 32.4 1.0
CG2 F:THR158 4.2 33.7 1.0
CD F:GLU183 4.3 55.8 1.0
OD2 F:ASP245 4.3 30.4 1.0
CA F:THR158 4.3 32.0 1.0
OD1 F:ASP245 4.3 28.4 1.0
O3A F:ADP600 4.5 33.6 1.0
OE2 F:GLU187 4.6 51.5 1.0
O F:HOH713 4.6 44.5 1.0
O2B F:ADP600 4.6 31.4 1.0
OE2 F:GLU183 4.7 57.0 1.0
PA F:ADP600 4.7 38.4 1.0
CD F:GLU187 4.8 50.4 1.0
CG F:ASP245 4.8 31.0 1.0
CG F:GLU183 4.8 49.8 1.0
O2A F:ADP600 4.9 39.6 1.0
CE F:LYS157 5.0 28.5 1.0
CB F:LYS157 5.0 27.3 1.0

Magnesium binding site 6 out of 12 in 5hkk

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Magnesium binding site 6 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:30.0
occ:1.00
 O1B H:ATP201 2.1 45.1 1.0
O H:HOH705 2.2 30.0 1.0
O1A H:ATP201 2.2 44.5 1.0
O H:HOH701 2.2 30.0 1.0
O H:HOH702 2.2 30.0 1.0
O H:HOH704 2.2 30.0 1.0
PB H:ATP201 3.2 43.0 1.0
PA H:ATP201 3.4 42.5 1.0
O3A H:ATP201 3.5 42.2 1.0
O3B H:ATP201 3.6 40.9 1.0
O1G H:ATP201 4.0 37.6 1.0
C5' H:ATP201 4.2 36.3 1.0
O5' H:ATP201 4.3 38.2 1.0
PG H:ATP201 4.4 38.8 1.0
O2B H:ATP201 4.5 45.9 1.0
O2A H:ATP201 4.6 42.6 1.0
O3G H:ATP201 4.6 39.9 1.0
NH2 H:ARG123 4.7 41.7 1.0
CB G:THR147 5.0 31.3 1.0

Magnesium binding site 7 out of 12 in 5hkk

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Magnesium binding site 7 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg601

b:30.2
occ:1.00
 O I:HOH709 2.2 30.2 1.0
O2B I:ADP600 2.2 33.0 1.0
O I:HOH712 2.2 31.1 1.0
O I:HOH703 2.2 29.8 1.0
O I:HOH711 2.2 32.8 1.0
OG1 I:THR176 2.2 33.2 1.0
CB I:THR176 3.2 32.1 1.0
PB I:ADP600 3.4 34.2 1.0
O3B I:ADP600 3.7 32.3 1.0
OD2 I:ASP261 4.0 33.4 1.0
OD1 I:ASP261 4.0 38.1 1.0
N I:THR176 4.1 32.5 1.0
CA I:THR176 4.2 31.5 1.0
O2A I:ADP600 4.2 31.8 1.0
CG2 I:THR176 4.2 33.0 1.0
O1B I:ADP600 4.3 33.7 1.0
CG I:ASP261 4.5 35.9 1.0
O3A I:ADP600 4.5 32.4 1.0
PA I:ADP600 4.7 33.8 1.0
O1A I:ADP600 4.9 33.1 1.0

Magnesium binding site 8 out of 12 in 5hkk

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Magnesium binding site 8 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg601

b:25.9
occ:1.00
 O2B J:ADP600 2.2 29.8 1.0
O J:HOH708 2.2 26.6 1.0
O J:HOH710 2.2 24.4 1.0
O J:HOH709 2.2 23.9 1.0
O J:HOH702 2.2 22.5 1.0
OG1 J:THR176 2.2 27.8 1.0
CB J:THR176 3.2 31.3 1.0
PB J:ADP600 3.4 33.3 1.0
O3B J:ADP600 3.6 32.9 1.0
O J:HOH704 4.0 13.5 1.0
OD2 J:ASP261 4.0 48.0 1.0
O2A J:ADP600 4.1 34.1 1.0
OD1 J:ASP261 4.1 41.1 1.0
CG2 J:THR176 4.1 30.1 1.0
N J:THR176 4.2 32.9 1.0
CA J:THR176 4.3 32.1 1.0
O3A J:ADP600 4.4 35.4 1.0
O1B J:ADP600 4.4 32.0 1.0
CG J:ASP261 4.5 41.1 1.0
PA J:ADP600 4.6 36.9 1.0
OE1 J:GLN200 4.6 41.7 1.0
O1A J:ADP600 4.9 36.7 1.0

Magnesium binding site 9 out of 12 in 5hkk

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Magnesium binding site 9 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg601

b:24.5
occ:1.00
 OG1 K:THR176 2.2 26.8 1.0
O K:HOH717 2.2 26.2 1.0
O2B K:ADP600 2.2 28.1 1.0
O K:HOH715 2.2 26.9 1.0
O K:HOH716 2.2 26.3 1.0
O K:HOH719 2.2 24.5 1.0
CB K:THR176 3.2 30.8 1.0
PB K:ADP600 3.5 31.0 1.0
OD1 K:ASP261 3.9 22.6 1.0
O K:HOH714 3.9 37.0 1.0
OD2 K:ASP261 3.9 22.6 1.0
O1B K:ADP600 4.0 31.4 1.0
N K:THR176 4.0 33.1 1.0
CA K:THR176 4.2 31.9 1.0
O3B K:ADP600 4.2 31.2 1.0
O1A K:ADP600 4.3 29.0 1.0
CG2 K:THR176 4.3 32.6 1.0
CG K:ASP261 4.3 23.3 1.0
O3A K:ADP600 4.6 29.5 1.0
PA K:ADP600 4.8 29.4 1.0
CE2 K:PHE318 4.9 31.0 1.0

Magnesium binding site 10 out of 12 in 5hkk

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Magnesium binding site 10 out of 12 in the Caldalaklibacillus Thermarum F1-Atpase (Wild Type)


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 (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg601

b:52.5
occ:1.00
 O2B L:ADP600 2.2 49.1 1.0
OG1 L:THR158 2.2 43.0 1.0
O L:HOH715 2.2 61.8 1.0
O L:HOH726 2.2 53.9 1.0
O L:HOH727 2.2 53.4 1.0
O L:HOH701 2.2 55.0 1.0
NH1 L:ARG184 3.1 45.1 1.0
CB L:THR158 3.3 38.6 1.0
PB L:ADP600 3.4 44.6 1.0
O3B L:ADP600 3.7 46.8 1.0
OE1 L:GLU183 3.7 46.8 1.0
N L:THR158 4.0 35.7 1.0
O L:HOH704 4.1 28.7 1.0
O3A L:ADP600 4.1 61.0 1.0
OE1 L:GLU187 4.2 49.0 1.0
CD L:GLU183 4.2 46.4 1.0
CZ L:ARG184 4.2 42.3 1.0
CA L:THR158 4.2 36.8 1.0
CG2 L:THR158 4.3 40.7 1.0
OD1 L:ASP245 4.4 36.2 1.0
OD2 L:ASP245 4.4 35.4 1.0
NH2 L:ARG184 4.4 42.4 1.0
O2A L:ADP600 4.5 80.0 1.0
O1A L:ADP600 4.5 79.7 1.0
PA L:ADP600 4.6 84.5 1.0
O1B L:ADP600 4.6 46.0 1.0
O L:HOH711 4.6 12.2 1.0
OE2 L:GLU183 4.7 53.0 1.0
CE L:LYS157 4.7 39.4 1.0
CB L:LYS157 4.7 36.8 1.0
CG L:GLU183 4.8 41.3 1.0
CG L:ASP245 4.9 36.8 1.0
NZ L:LYS157 5.0 38.4 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: Mon Dec 14 20:27:19 2020

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