Atomistry » Sodium » PDB 2bii-2c8x » 2bl2
Atomistry »
  Sodium »
    PDB 2bii-2c8x »
      2bl2 »

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

Go back to Sodium Binding Sites List in 2bl2
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

Go back to Sodium Binding Sites List in 2bl2
Sodium binding site 2 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 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

Go back to Sodium Binding Sites List in 2bl2
Sodium binding site 3 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 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

Go back to Sodium Binding Sites List in 2bl2
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

Go back to Sodium Binding Sites List in 2bl2
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

Go back to Sodium Binding Sites List in 2bl2
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

Go back to Sodium Binding Sites List in 2bl2
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

Go back to Sodium Binding Sites List in 2bl2
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

Go back to Sodium Binding Sites List in 2bl2
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

Go back to Sodium Binding Sites List in 2bl2
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy