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Sodium in PDB 2bl2: The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae

Enzymatic activity of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae

All present enzymatic activity of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae:
3.6.3.14;

Protein crystallography data

The structure of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae, PDB code: 2bl2 was solved by T.Murata, I.Yamato, Y.Kakinuma, 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) 61.00 / 2.1
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.136, 125.604, 210.866, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 20

Sodium Binding Sites:

The binding sites of Sodium atom in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae (pdb code 2bl2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae, PDB code: 2bl2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 2bl2

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Sodium binding site 1 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1157

b:23.7
occ:1.00
 OG1 A:THR64 2.2 23.9 1.0
OE1 A:GLU139 2.2 25.8 1.0
O A:LEU61 2.2 24.0 1.0
OE1 A:GLN110 2.2 23.2 1.0
OE1 A:GLN65 2.3 23.9 1.0
CD A:GLN65 3.1 23.5 1.0
CD A:GLN110 3.2 22.8 1.0
CD A:GLU139 3.2 27.9 1.0
NE2 A:GLN65 3.3 22.9 1.0
C A:LEU61 3.4 24.1 1.0
OE2 A:GLU139 3.5 28.3 1.0
NE2 A:GLN110 3.5 21.4 1.0
CB A:THR64 3.6 23.6 1.0
CA A:PRO62 3.6 23.6 1.0
N A:THR64 3.7 23.4 1.0
C A:PRO62 3.9 23.2 1.0
N A:PRO62 3.9 23.5 1.0
CG2 A:THR64 4.1 22.6 1.0
N A:GLN65 4.1 23.0 1.0
CA A:THR64 4.1 23.8 1.0
N A:GLY63 4.2 22.4 1.0
O A:PRO62 4.3 23.8 1.0
CG A:GLN65 4.4 23.0 1.0
C A:THR64 4.6 23.6 1.0
CG A:GLN110 4.6 21.7 1.0
CA A:LEU61 4.6 25.7 1.0
CG A:GLU139 4.6 26.5 1.0
C A:GLY63 4.8 23.6 1.0
CB A:GLU139 5.0 25.9 1.0

Sodium binding site 2 out of 10 in 2bl2

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Sodium binding site 2 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1157

b:23.2
occ:1.00
 OE1 B:GLN110 2.2 24.2 1.0
OG1 B:THR64 2.2 21.7 1.0
OE1 B:GLU139 2.2 24.5 1.0
O B:LEU61 2.3 24.1 1.0
OE1 B:GLN65 2.3 23.9 1.0
CD B:GLN65 3.1 22.9 1.0
CD B:GLN110 3.2 24.3 1.0
CD B:GLU139 3.2 26.7 1.0
NE2 B:GLN65 3.3 23.1 1.0
C B:LEU61 3.4 24.6 1.0
OE2 B:GLU139 3.5 28.5 1.0
NE2 B:GLN110 3.5 22.6 1.0
CB B:THR64 3.6 22.1 1.0
CA B:PRO62 3.6 22.6 1.0
N B:THR64 3.7 21.9 1.0
C B:PRO62 3.8 22.5 1.0
N B:PRO62 3.9 22.5 1.0
CG2 B:THR64 4.0 20.3 1.0
N B:GLN65 4.1 21.5 1.0
CA B:THR64 4.1 22.3 1.0
N B:GLY63 4.2 22.4 1.0
O B:PRO62 4.3 22.9 1.0
CG B:GLN65 4.4 22.1 1.0
CG B:GLN110 4.5 21.0 1.0
C B:THR64 4.5 22.7 1.0
CA B:LEU61 4.6 25.7 1.0
CG B:GLU139 4.6 27.1 1.0
C B:GLY63 4.8 22.4 1.0
CB B:GLU139 5.0 26.2 1.0

Sodium binding site 3 out of 10 in 2bl2

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Sodium binding site 3 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


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Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1157

b:22.4
occ:1.00
 OG1 C:THR64 2.2 22.9 1.0
O C:LEU61 2.2 23.7 1.0
OE1 C:GLN110 2.2 23.8 1.0
OE1 C:GLU139 2.2 24.5 1.0
OE1 C:GLN65 2.3 22.7 1.0
CD C:GLN65 3.1 22.1 1.0
CD C:GLN110 3.2 24.1 1.0
CD C:GLU139 3.2 27.5 1.0
NE2 C:GLN65 3.4 21.9 1.0
C C:LEU61 3.4 24.4 1.0
OE2 C:GLU139 3.5 28.0 1.0
CB C:THR64 3.6 23.1 1.0
NE2 C:GLN110 3.6 22.9 1.0
CA C:PRO62 3.7 24.4 1.0
N C:THR64 3.7 22.9 1.0
C C:PRO62 3.8 24.2 1.0
N C:PRO62 4.0 23.9 1.0
CG2 C:THR64 4.0 21.5 1.0
N C:GLN65 4.1 21.5 1.0
CA C:THR64 4.1 22.9 1.0
N C:GLY63 4.2 24.4 1.0
O C:PRO62 4.2 25.1 1.0
CG C:GLN65 4.5 21.4 1.0
C C:THR64 4.5 23.1 1.0
CG C:GLN110 4.6 22.1 1.0
CA C:LEU61 4.6 25.8 1.0
CG C:GLU139 4.6 25.8 1.0
C C:GLY63 4.8 23.5 1.0
CB C:GLU139 5.0 25.3 1.0

Sodium binding site 4 out of 10 in 2bl2

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Sodium binding site 4 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1157

b:24.1
occ:1.00
 OG1 D:THR64 2.2 22.7 1.0
OE1 D:GLN110 2.2 23.3 1.0
OE1 D:GLU139 2.2 25.4 1.0
O D:LEU61 2.2 25.7 1.0
OE1 D:GLN65 2.3 22.8 1.0
CD D:GLN65 3.1 23.0 1.0
CD D:GLN110 3.2 23.3 1.0
CD D:GLU139 3.2 27.4 1.0
NE2 D:GLN65 3.4 22.3 1.0
C D:LEU61 3.4 25.1 1.0
OE2 D:GLU139 3.5 27.8 1.0
CB D:THR64 3.6 22.8 1.0
NE2 D:GLN110 3.6 22.1 1.0
CA D:PRO62 3.6 23.7 1.0
N D:THR64 3.7 22.4 1.0
C D:PRO62 3.8 23.5 1.0
N D:PRO62 3.9 23.7 1.0
CG2 D:THR64 4.0 22.3 1.0
N D:GLN65 4.1 23.4 1.0
CA D:THR64 4.1 22.7 1.0
N D:GLY63 4.2 23.5 1.0
O D:PRO62 4.3 23.4 1.0
CG D:GLN65 4.4 22.4 1.0
C D:THR64 4.5 23.1 1.0
CG D:GLN110 4.6 21.3 1.0
CA D:LEU61 4.6 25.1 1.0
CG D:GLU139 4.6 26.3 1.0
C D:GLY63 4.8 22.3 1.0
CB D:GLU139 5.0 25.4 1.0

Sodium binding site 5 out of 10 in 2bl2

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Sodium binding site 5 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1157

b:23.7
occ:1.00
 OG1 E:THR64 2.2 23.1 1.0
OE1 E:GLU139 2.2 24.2 1.0
OE1 E:GLN110 2.2 23.4 1.0
O E:LEU61 2.2 25.1 1.0
OE1 E:GLN65 2.3 22.6 1.0
CD E:GLN65 3.1 23.8 1.0
CD E:GLU139 3.2 28.6 1.0
CD E:GLN110 3.2 24.1 1.0
NE2 E:GLN65 3.4 23.2 1.0
C E:LEU61 3.4 25.6 1.0
OE2 E:GLU139 3.5 29.1 1.0
NE2 E:GLN110 3.5 23.1 1.0
CB E:THR64 3.6 23.4 1.0
CA E:PRO62 3.7 24.8 1.0
N E:THR64 3.7 22.7 1.0
C E:PRO62 3.9 24.2 1.0
N E:PRO62 4.0 24.6 1.0
CG2 E:THR64 4.0 21.2 1.0
N E:GLN65 4.1 23.5 1.0
CA E:THR64 4.1 23.4 1.0
N E:GLY63 4.2 23.6 1.0
O E:PRO62 4.3 24.4 1.0
CG E:GLN65 4.5 23.3 1.0
C E:THR64 4.5 24.1 1.0
CG E:GLN110 4.6 22.1 1.0
CA E:LEU61 4.6 26.8 1.0
CG E:GLU139 4.6 26.6 1.0
C E:GLY63 4.8 23.6 1.0
CB E:GLU139 5.0 26.0 1.0

Sodium binding site 6 out of 10 in 2bl2

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Sodium binding site 6 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1157

b:22.4
occ:1.00
 OG1 F:THR64 2.2 23.7 1.0
OE1 F:GLU139 2.2 23.9 1.0
O F:LEU61 2.2 23.3 1.0
OE1 F:GLN110 2.3 22.5 1.0
OE1 F:GLN65 2.3 22.8 1.0
CD F:GLN65 3.1 23.1 1.0
CD F:GLU139 3.2 26.5 1.0
CD F:GLN110 3.2 22.2 1.0
NE2 F:GLN65 3.4 23.4 1.0
C F:LEU61 3.4 23.8 1.0
OE2 F:GLU139 3.4 27.4 1.0
NE2 F:GLN110 3.5 21.5 1.0
CB F:THR64 3.6 23.9 1.0
CA F:PRO62 3.7 22.6 1.0
N F:THR64 3.7 23.2 1.0
C F:PRO62 3.9 22.1 1.0
N F:PRO62 4.0 23.3 1.0
CG2 F:THR64 4.1 22.6 1.0
N F:GLN65 4.1 23.9 1.0
CA F:THR64 4.1 24.1 1.0
N F:GLY63 4.2 22.4 1.0
O F:PRO62 4.3 22.1 1.0
CG F:GLN65 4.4 21.6 1.0
C F:THR64 4.5 24.2 1.0
CG F:GLN110 4.6 20.1 1.0
CA F:LEU61 4.6 25.0 1.0
CG F:GLU139 4.6 25.6 1.0
C F:GLY63 4.8 23.3 1.0
CB F:GLU139 5.0 24.5 1.0

Sodium binding site 7 out of 10 in 2bl2

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Sodium binding site 7 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1157

b:23.4
occ:1.00
 OG1 G:THR64 2.2 22.9 1.0
O G:LEU61 2.2 25.3 1.0
OE1 G:GLN110 2.2 23.3 1.0
OE1 G:GLU139 2.2 26.6 1.0
OE1 G:GLN65 2.3 22.5 1.0
CD G:GLN65 3.1 22.8 1.0
CD G:GLN110 3.2 24.0 1.0
CD G:GLU139 3.2 28.2 1.0
C G:LEU61 3.4 25.2 1.0
NE2 G:GLN65 3.4 22.4 1.0
OE2 G:GLU139 3.5 28.4 1.0
CB G:THR64 3.6 24.6 1.0
NE2 G:GLN110 3.6 22.3 1.0
CA G:PRO62 3.6 24.0 1.0
N G:THR64 3.7 23.4 1.0
C G:PRO62 3.8 23.6 1.0
N G:PRO62 3.9 23.8 1.0
CG2 G:THR64 4.0 22.7 1.0
N G:GLN65 4.1 23.7 1.0
CA G:THR64 4.1 24.2 1.0
N G:GLY63 4.2 23.9 1.0
O G:PRO62 4.3 23.3 1.0
CG G:GLN65 4.5 22.7 1.0
C G:THR64 4.5 24.3 1.0
CG G:GLN110 4.5 22.6 1.0
CA G:LEU61 4.6 26.2 1.0
CG G:GLU139 4.6 25.7 1.0
C G:GLY63 4.8 24.4 1.0
CB G:GLU139 5.0 25.1 1.0

Sodium binding site 8 out of 10 in 2bl2

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Sodium binding site 8 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1157

b:23.7
occ:1.00
 OG1 H:THR64 2.2 22.9 1.0
OE1 H:GLN110 2.2 24.8 1.0
O H:LEU61 2.2 24.6 1.0
OE1 H:GLU139 2.2 28.0 1.0
OE1 H:GLN65 2.3 22.5 1.0
CD H:GLN65 3.1 22.7 1.0
CD H:GLN110 3.2 23.9 1.0
CD H:GLU139 3.2 28.1 1.0
NE2 H:GLN65 3.4 23.5 1.0
C H:LEU61 3.4 24.4 1.0
OE2 H:GLU139 3.5 29.3 1.0
NE2 H:GLN110 3.6 21.7 1.0
CB H:THR64 3.6 23.4 1.0
CA H:PRO62 3.6 23.9 1.0
N H:THR64 3.7 22.9 1.0
C H:PRO62 3.8 24.0 1.0
N H:PRO62 3.9 24.9 1.0
CG2 H:THR64 4.0 22.6 1.0
N H:GLN65 4.1 23.9 1.0
CA H:THR64 4.1 23.3 1.0
N H:GLY63 4.2 23.9 1.0
O H:PRO62 4.3 25.4 1.0
CG H:GLN65 4.4 21.8 1.0
C H:THR64 4.5 23.6 1.0
CG H:GLN110 4.5 21.1 1.0
CA H:LEU61 4.6 26.4 1.0
CG H:GLU139 4.6 25.5 1.0
C H:GLY63 4.8 23.5 1.0
CB H:GLU139 5.0 25.4 1.0

Sodium binding site 9 out of 10 in 2bl2

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Sodium binding site 9 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na1157

b:21.5
occ:1.00
 OE1 I:GLU139 2.2 25.6 1.0
OE1 I:GLN110 2.2 24.2 1.0
O I:LEU61 2.2 23.7 1.0
OG1 I:THR64 2.3 21.4 1.0
OE1 I:GLN65 2.3 21.8 1.0
CD I:GLN65 3.1 22.0 1.0
CD I:GLU139 3.2 27.5 1.0
CD I:GLN110 3.2 23.5 1.0
NE2 I:GLN65 3.3 21.5 1.0
C I:LEU61 3.4 23.7 1.0
OE2 I:GLU139 3.4 28.9 1.0
NE2 I:GLN110 3.6 21.4 1.0
CB I:THR64 3.6 22.3 1.0
CA I:PRO62 3.6 22.1 1.0
N I:THR64 3.7 21.1 1.0
C I:PRO62 3.9 22.3 1.0
N I:PRO62 3.9 23.1 1.0
CG2 I:THR64 4.1 21.6 1.0
N I:GLN65 4.1 22.9 1.0
CA I:THR64 4.1 22.4 1.0
N I:GLY63 4.2 21.5 1.0
O I:PRO62 4.3 22.1 1.0
CG I:GLN65 4.5 22.0 1.0
CG I:GLN110 4.6 22.1 1.0
CA I:LEU61 4.6 24.5 1.0
C I:THR64 4.6 23.4 1.0
CG I:GLU139 4.6 26.5 1.0
C I:GLY63 4.8 22.1 1.0
CB I:GLU139 5.0 25.8 1.0

Sodium binding site 10 out of 10 in 2bl2

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Sodium binding site 10 out of 10 in the The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Membrane Rotor of the V-Type Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na1157

b:22.1
occ:1.00
 OG1 J:THR64 2.2 21.2 1.0
OE1 J:GLU139 2.2 25.7 1.0
OE1 J:GLN110 2.2 20.4 1.0
O J:LEU61 2.2 24.1 1.0
OE1 J:GLN65 2.3 24.0 1.0
CD J:GLN65 3.1 24.7 1.0
CD J:GLN110 3.2 21.2 1.0
CD J:GLU139 3.2 26.4 1.0
NE2 J:GLN65 3.3 23.5 1.0
C J:LEU61 3.4 25.0 1.0
OE2 J:GLU139 3.5 26.4 1.0
NE2 J:GLN110 3.5 19.7 1.0
CB J:THR64 3.6 23.2 1.0
CA J:PRO62 3.7 24.2 1.0
N J:THR64 3.8 22.6 1.0
C J:PRO62 3.9 23.4 1.0
N J:PRO62 3.9 24.9 1.0
N J:GLN65 4.1 23.4 1.0
CG2 J:THR64 4.1 22.0 1.0
CA J:THR64 4.1 23.1 1.0
N J:GLY63 4.2 23.0 1.0
O J:PRO62 4.3 23.4 1.0
CG J:GLN65 4.4 23.6 1.0
CG J:GLN110 4.5 20.3 1.0
C J:THR64 4.6 23.1 1.0
CA J:LEU61 4.6 25.9 1.0
CG J:GLU139 4.6 26.1 1.0
C J:GLY63 4.8 23.5 1.0
CB J:GLU139 5.0 25.2 1.0

Reference:

T.Murata, I.Yamato, Y.Kakinuma, A.G.W.Leslie, J.E.Walker. Structure of the Rotor of the Vacuolar-Type Na- Atpase From Enterococcus Hirae Science V. 308 654 2005.
ISSN: ISSN 0036-8075
PubMed: 15802565
DOI: 10.1126/SCIENCE.1110064
Page generated: Tue Dec 15 05:46:04 2020

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