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Sodium in PDB 2db4: Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae

Enzymatic activity of Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae

All present enzymatic activity of Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae:
3.6.3.14;

Protein crystallography data

The structure of Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae, PDB code: 2db4 was solved by T.Murata, I.Yamato, Y.Kakinuma, M.Shirouzu, J.E.Walker, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.83 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 120.214, 125.229, 211.577, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 23.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae (pdb code 2db4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae, PDB code: 2db4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 2db4

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Sodium binding site 1 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:62.5
occ:1.00
 O A:LEU61 2.5 54.0 1.0
OG1 A:THR64 2.5 51.9 1.0
OE1 A:GLN65 2.7 51.5 1.0
OE1 A:GLN110 2.9 51.4 1.0
OE1 A:GLU139 3.0 63.0 1.0
N A:THR64 3.2 51.7 1.0
CB A:THR64 3.5 51.7 1.0
CD A:GLN65 3.5 51.3 1.0
C A:PRO62 3.6 52.7 1.0
C A:LEU61 3.6 53.9 1.0
N A:GLY63 3.6 52.4 1.0
CA A:PRO62 3.7 53.0 1.0
CD A:GLN110 3.7 51.1 1.0
CA A:THR64 3.8 51.7 1.0
CD A:GLU139 3.8 62.7 1.0
NE2 A:GLN110 3.9 51.3 1.0
NE2 A:GLN65 3.9 50.2 1.0
N A:GLN65 3.9 51.6 1.0
CG A:GLU139 3.9 59.1 1.0
CG2 A:THR64 4.0 51.2 1.0
O A:PRO62 4.1 52.6 1.0
N A:PRO62 4.1 53.4 1.0
C A:GLY63 4.2 52.0 1.0
C A:THR64 4.3 51.7 1.0
CA A:GLY63 4.4 52.0 1.0
O A:HOH325 4.6 53.9 1.0
C7 A:DCW201 4.7 64.7 1.0
CG A:GLN65 4.8 51.3 1.0
CA A:LEU61 4.8 54.1 1.0
CB A:GLU139 4.9 56.9 1.0

Sodium binding site 2 out of 10 in 2db4

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Sodium binding site 2 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:62.5
occ:1.00
 O B:LEU61 2.5 53.9 1.0
OG1 B:THR64 2.5 51.9 1.0
OE1 B:GLN65 2.6 52.0 1.0
OE1 B:GLN110 2.9 51.1 1.0
OE1 B:GLU139 3.0 62.9 1.0
N B:THR64 3.2 51.8 1.0
CD B:GLN65 3.5 51.4 1.0
C B:PRO62 3.5 52.7 1.0
CB B:THR64 3.5 51.8 1.0
C B:LEU61 3.6 53.9 1.0
N B:GLY63 3.6 52.4 1.0
CA B:PRO62 3.7 53.0 1.0
CD B:GLN110 3.7 51.0 1.0
CA B:THR64 3.8 51.6 1.0
NE2 B:GLN110 3.8 51.2 1.0
NE2 B:GLN65 3.8 50.0 1.0
CD B:GLU139 3.8 62.7 1.0
N B:GLN65 3.9 51.7 1.0
CG B:GLU139 4.0 59.1 1.0
O B:PRO62 4.0 52.6 1.0
CG2 B:THR64 4.1 51.3 1.0
N B:PRO62 4.1 53.4 1.0
C B:GLY63 4.2 52.1 1.0
C B:THR64 4.3 51.7 1.0
CA B:GLY63 4.4 52.1 1.0
O B:HOH322 4.7 55.3 1.0
CG B:GLN65 4.8 51.4 1.0
C7 B:DCW201 4.8 64.7 1.0
CA B:LEU61 4.9 54.2 1.0
CB B:GLU139 4.9 56.9 1.0

Sodium binding site 3 out of 10 in 2db4

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Sodium binding site 3 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na202

b:62.5
occ:1.00
 O C:LEU61 2.4 54.1 1.0
OG1 C:THR64 2.5 52.1 1.0
OE1 C:GLN65 2.6 51.4 1.0
OE1 C:GLN110 2.9 51.4 1.0
OE1 C:GLU139 3.0 63.1 1.0
N C:THR64 3.1 52.0 1.0
CB C:THR64 3.5 51.9 1.0
C C:PRO62 3.5 52.8 1.0
N C:GLY63 3.5 52.5 1.0
CD C:GLN65 3.6 51.3 1.0
C C:LEU61 3.6 53.9 1.0
CA C:PRO62 3.7 53.1 1.0
CA C:THR64 3.7 51.8 1.0
CD C:GLN110 3.8 51.1 1.0
N C:GLN65 3.8 51.6 1.0
CD C:GLU139 3.8 62.7 1.0
NE2 C:GLN110 4.0 51.3 1.0
NE2 C:GLN65 4.0 50.3 1.0
CG C:GLU139 4.0 59.0 1.0
CG2 C:THR64 4.0 51.1 1.0
O C:PRO62 4.0 52.6 1.0
N C:PRO62 4.1 53.5 1.0
C C:GLY63 4.2 52.2 1.0
C C:THR64 4.3 51.8 1.0
CA C:GLY63 4.4 52.2 1.0
O C:HOH314 4.6 62.4 1.0
C7 C:DCW201 4.8 64.7 1.0
CA C:LEU61 4.8 54.1 1.0
CG C:GLN65 4.8 51.2 1.0
CB C:GLU139 5.0 56.8 1.0
CA C:GLN65 5.0 51.6 1.0

Sodium binding site 4 out of 10 in 2db4

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Sodium binding site 4 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na202

b:62.6
occ:1.00
 OG1 D:THR64 2.5 52.0 1.0
O D:LEU61 2.5 54.0 1.0
OE1 D:GLN65 2.7 51.9 1.0
OE1 D:GLN110 2.9 51.3 1.0
OE1 D:GLU139 3.0 62.9 1.0
N D:THR64 3.2 51.8 1.0
CD D:GLN65 3.5 51.3 1.0
CB D:THR64 3.5 51.8 1.0
C D:PRO62 3.6 52.8 1.0
N D:GLY63 3.6 52.5 1.0
C D:LEU61 3.6 53.9 1.0
CA D:PRO62 3.7 53.1 1.0
CD D:GLN110 3.7 51.0 1.0
CA D:THR64 3.8 51.7 1.0
CD D:GLU139 3.8 62.7 1.0
NE2 D:GLN65 3.8 50.1 1.0
NE2 D:GLN110 3.9 51.2 1.0
N D:GLN65 3.9 51.9 1.0
CG D:GLU139 4.0 59.1 1.0
CG2 D:THR64 4.0 51.3 1.0
O D:PRO62 4.1 52.7 1.0
N D:PRO62 4.2 53.4 1.0
C D:GLY63 4.2 52.0 1.0
C D:THR64 4.3 51.8 1.0
CA D:GLY63 4.5 52.0 1.0
O D:HOH314 4.6 68.0 1.0
CG D:GLN65 4.7 51.4 1.0
C7 D:DCW201 4.8 64.7 1.0
CB D:GLU139 4.9 56.9 1.0
CA D:LEU61 4.9 54.1 1.0

Sodium binding site 5 out of 10 in 2db4

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Sodium binding site 5 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na202

b:62.6
occ:1.00
 OG1 E:THR64 2.5 52.0 1.0
O E:LEU61 2.5 54.0 1.0
OE1 E:GLN65 2.8 51.7 1.0
OE1 E:GLU139 2.9 62.8 1.0
OE1 E:GLN110 2.9 51.1 1.0
N E:THR64 3.2 51.9 1.0
CB E:THR64 3.5 51.8 1.0
CD E:GLN65 3.6 51.3 1.0
N E:GLY63 3.6 52.6 1.0
C E:PRO62 3.6 52.8 1.0
C E:LEU61 3.6 53.8 1.0
CA E:PRO62 3.7 53.0 1.0
CD E:GLN110 3.7 51.0 1.0
CA E:THR64 3.8 51.8 1.0
CD E:GLU139 3.8 62.7 1.0
NE2 E:GLN110 3.9 51.3 1.0
NE2 E:GLN65 3.9 50.1 1.0
N E:GLN65 3.9 51.8 1.0
CG E:GLU139 3.9 59.1 1.0
CG2 E:THR64 4.0 51.2 1.0
O E:PRO62 4.1 52.8 1.0
N E:PRO62 4.1 53.4 1.0
C E:GLY63 4.2 52.1 1.0
C E:THR64 4.3 51.7 1.0
CA E:GLY63 4.4 52.1 1.0
O E:HOH317 4.7 63.3 1.0
C7 E:DCW201 4.7 64.6 1.0
CG E:GLN65 4.8 51.4 1.0
CA E:LEU61 4.9 54.1 1.0
CB E:GLU139 4.9 56.9 1.0

Sodium binding site 6 out of 10 in 2db4

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Sodium binding site 6 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na202

b:62.5
occ:1.00
 O F:LEU61 2.4 54.0 1.0
OG1 F:THR64 2.6 52.0 1.0
OE1 F:GLN65 2.6 51.5 1.0
OE1 F:GLN110 2.9 51.5 1.0
OE1 F:GLU139 2.9 63.0 1.0
N F:THR64 3.2 52.0 1.0
C F:PRO62 3.5 52.8 1.0
C F:LEU61 3.5 54.0 1.0
CD F:GLN65 3.6 51.4 1.0
N F:GLY63 3.6 52.4 1.0
CB F:THR64 3.6 51.8 1.0
CA F:PRO62 3.7 53.1 1.0
CD F:GLN110 3.7 51.2 1.0
CD F:GLU139 3.8 62.8 1.0
CA F:THR64 3.8 51.9 1.0
NE2 F:GLN110 3.9 51.3 1.0
N F:GLN65 4.0 51.5 1.0
CG F:GLU139 4.0 58.9 1.0
NE2 F:GLN65 4.0 50.5 1.0
O F:PRO62 4.0 52.4 1.0
CG2 F:THR64 4.1 51.4 1.0
N F:PRO62 4.1 53.6 1.0
C F:GLY63 4.2 52.1 1.0
C F:THR64 4.4 51.9 1.0
CA F:GLY63 4.4 52.0 1.0
C7 F:DCW201 4.7 64.8 1.0
CA F:LEU61 4.8 54.1 1.0
O F:HOH320 4.8 72.2 1.0
CG F:GLN65 4.8 51.4 1.0
CB F:GLU139 4.9 56.9 1.0
O F:LEU60 5.0 54.2 1.0

Sodium binding site 7 out of 10 in 2db4

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Sodium binding site 7 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na202

b:62.7
occ:1.00
 OG1 G:THR64 2.5 51.9 1.0
O G:LEU61 2.5 54.0 1.0
OE1 G:GLN65 2.7 52.0 1.0
OE1 G:GLN110 2.9 51.2 1.0
OE1 G:GLU139 3.0 62.9 1.0
N G:THR64 3.2 51.8 1.0
CD G:GLN65 3.5 51.4 1.0
CB G:THR64 3.5 51.8 1.0
C G:PRO62 3.6 52.8 1.0
C G:LEU61 3.6 53.9 1.0
N G:GLY63 3.7 52.5 1.0
CA G:PRO62 3.7 53.0 1.0
CA G:THR64 3.8 51.7 1.0
CD G:GLN110 3.8 51.0 1.0
CD G:GLU139 3.8 62.7 1.0
NE2 G:GLN65 3.8 50.2 1.0
NE2 G:GLN110 3.9 51.3 1.0
N G:GLN65 3.9 51.9 1.0
CG G:GLU139 4.0 59.0 1.0
CG2 G:THR64 4.0 51.3 1.0
O G:PRO62 4.1 52.6 1.0
N G:PRO62 4.2 53.3 1.0
C G:GLY63 4.2 52.0 1.0
C G:THR64 4.3 51.7 1.0
CA G:GLY63 4.5 52.0 1.0
O G:HOH324 4.7 54.2 1.0
CG G:GLN65 4.7 51.3 1.0
C7 G:DCW201 4.7 64.7 1.0
CA G:LEU61 4.9 54.0 1.0
CB G:GLU139 4.9 56.9 1.0

Sodium binding site 8 out of 10 in 2db4

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Sodium binding site 8 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na202

b:62.5
occ:1.00
 O H:LEU61 2.5 54.1 1.0
OG1 H:THR64 2.5 52.0 1.0
OE1 H:GLN65 2.7 52.0 1.0
OE1 H:GLN110 2.9 51.4 1.0
OE1 H:GLU139 3.0 62.9 1.0
N H:THR64 3.2 51.7 1.0
CD H:GLN65 3.5 51.6 1.0
CB H:THR64 3.6 51.8 1.0
C H:PRO62 3.6 52.8 1.0
N H:GLY63 3.6 52.5 1.0
C H:LEU61 3.6 53.9 1.0
CA H:PRO62 3.7 53.2 1.0
CD H:GLN110 3.7 51.0 1.0
CA H:THR64 3.8 51.7 1.0
NE2 H:GLN65 3.8 50.0 1.0
NE2 H:GLN110 3.8 51.1 1.0
CD H:GLU139 3.8 62.7 1.0
N H:GLN65 3.9 51.8 1.0
CG H:GLU139 3.9 59.0 1.0
CG2 H:THR64 4.1 51.2 1.0
O H:PRO62 4.1 52.8 1.0
N H:PRO62 4.1 53.4 1.0
C H:GLY63 4.2 52.1 1.0
C H:THR64 4.3 51.7 1.0
CA H:GLY63 4.4 52.1 1.0
O H:HOH332 4.7 47.3 1.0
CG H:GLN65 4.7 51.4 1.0
C7 H:DCW201 4.8 64.7 1.0
CA H:LEU61 4.9 54.1 1.0
CB H:GLU139 4.9 56.9 1.0

Sodium binding site 9 out of 10 in 2db4

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Sodium binding site 9 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na202

b:63.3
occ:1.00
 OG1 I:THR64 2.4 52.0 1.0
O I:LEU61 2.5 54.1 1.0
OE1 I:GLN65 2.7 51.7 1.0
OE1 I:GLU139 2.9 63.1 1.0
OE1 I:GLN110 3.0 51.6 1.0
N I:THR64 3.1 51.6 1.0
CB I:THR64 3.5 51.8 1.0
CD I:GLN65 3.6 51.8 1.0
C I:LEU61 3.6 54.0 1.0
N I:GLY63 3.6 52.4 1.0
C I:PRO62 3.6 52.8 1.0
CD I:GLU139 3.7 62.9 1.0
CA I:PRO62 3.7 52.9 1.0
CA I:THR64 3.7 51.7 1.0
CD I:GLN110 3.8 51.2 1.0
CG I:GLU139 3.9 59.3 1.0
NE2 I:GLN110 3.9 51.8 1.0
CG2 I:THR64 4.0 51.0 1.0
N I:GLN65 4.0 51.7 1.0
NE2 I:GLN65 4.0 50.6 1.0
N I:PRO62 4.1 53.6 1.0
O I:PRO62 4.2 53.1 1.0
C I:GLY63 4.2 51.9 1.0
C I:THR64 4.3 51.8 1.0
CA I:GLY63 4.5 51.6 1.0
O I:HOH347 4.6 46.5 1.0
C7 I:DCW201 4.6 64.7 1.0
CG I:GLN65 4.8 51.5 1.0
CA I:LEU61 4.8 54.3 1.0
CB I:GLU139 4.9 57.1 1.0
N1 I:DCW201 4.9 64.4 1.0

Sodium binding site 10 out of 10 in 2db4

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Sodium binding site 10 out of 10 in the Crystal Structure of Rotor Ring with Dccd of the V- 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 Crystal Structure of Rotor Ring with Dccd of the V- Atpase From Enterococcus Hirae within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na202

b:61.7
occ:1.00
 O J:LEU61 2.4 53.6 1.0
OG1 J:THR64 2.6 51.7 1.0
OE1 J:GLN65 2.7 50.2 1.0
OE1 J:GLN110 2.9 51.4 1.0
OE1 J:GLU139 3.0 63.0 1.0
N J:THR64 3.1 51.4 1.0
C J:PRO62 3.5 52.4 1.0
CB J:THR64 3.5 51.4 1.0
C J:LEU61 3.5 53.5 1.0
N J:GLY63 3.5 52.1 1.0
CD J:GLN65 3.6 50.9 1.0
CA J:PRO62 3.7 52.9 1.0
CD J:GLN110 3.7 51.1 1.0
CA J:THR64 3.7 51.5 1.0
NE2 J:GLN110 3.8 51.0 1.0
CD J:GLU139 3.8 62.6 1.0
CG2 J:THR64 3.9 50.9 1.0
NE2 J:GLN65 3.9 49.7 1.0
CG J:GLU139 4.0 59.1 1.0
N J:GLN65 4.0 51.3 1.0
O J:PRO62 4.0 52.1 1.0
N J:PRO62 4.1 53.2 1.0
C J:GLY63 4.2 51.8 1.0
C J:THR64 4.3 51.3 1.0
CA J:GLY63 4.4 51.8 1.0
O J:HOH330 4.5 46.5 1.0
C7 J:DCW201 4.7 64.6 1.0
CA J:LEU61 4.8 53.9 1.0
CG J:GLN65 4.9 51.0 1.0
CB J:GLU139 4.9 56.8 1.0

Reference:

K.Mizutani, M.Yamamoto, K.Suzuki, I.Yamato, Y.Kakinuma, M.Shirouzu, J.E.Walker, S.Yokoyama, S.Iwata, T.Murata. Structure of the Rotor Ring Modified with N,N'-Dicyclohexylcarbodiimide of the Na+-Transporting Vacuolar Atpase. Proc.Natl.Acad.Sci.Usa V. 108 13474 2011.
ISSN: ISSN 0027-8424
PubMed: 21813759
DOI: 10.1073/PNAS.1103287108
Page generated: Mon Oct 7 02:12:02 2024

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