Atomistry » Sodium » PDB 1y5y-1z1q » 1yce
Atomistry »
  Sodium »
    PDB 1y5y-1z1q »
      1yce »

Sodium in PDB 1yce: Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus

Protein crystallography data

The structure of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus, PDB code: 1yce was solved by T.Meier, P.Polzer, K.Diederichs, W.Welte, P.Dimroth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 147.700, 140.000, 153.000, 90.00, 118.40, 90.00
R / Rfree (%) 20.1 / 24.6

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 44;

Binding sites:

The binding sites of Sodium atom in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus (pdb code 1yce). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 44 binding sites of Sodium where determined in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus, PDB code: 1yce:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 1 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:45.1
occ:1.00
 OE1 A:GLN32 2.3 41.1 1.0
OG K:SER66 2.4 36.9 1.0
O K:VAL63 2.4 42.9 1.0
OE2 A:GLU65 2.5 48.9 1.0
CD A:GLN32 3.3 44.8 1.0
CD A:GLU65 3.4 46.6 1.0
CB K:SER66 3.5 41.2 1.0
C K:VAL63 3.5 43.9 1.0
NE2 A:GLN32 3.7 38.2 1.0
OE1 A:GLU65 3.7 46.6 1.0
N K:SER66 3.8 43.5 1.0
CA K:ALA64 3.9 44.1 1.0
C K:ALA64 4.0 44.3 1.0
N K:THR67 4.0 43.0 1.0
CA K:SER66 4.1 42.6 1.0
O K:ALA64 4.1 44.2 1.0
N K:ALA64 4.2 44.0 1.0
CG2 K:THR67 4.2 43.4 1.0
CG1 K:VAL63 4.4 44.1 1.0
CB A:PRO28 4.5 45.6 1.0
C K:SER66 4.5 43.4 1.0
N K:GLU65 4.6 44.5 1.0
CG A:GLN32 4.6 46.5 1.0
CA K:VAL63 4.7 44.1 1.0
OG1 K:THR67 4.8 43.7 1.0
CG A:GLU65 4.8 45.0 1.0
C K:GLU65 4.8 44.1 1.0
CB K:THR67 4.9 43.6 1.0
O A:PRO28 5.0 46.3 1.0
C A:PRO28 5.0 45.6 1.0

Sodium binding site 2 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 2 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:41.9
occ:1.00
 OE2 B:GLU65 2.2 47.9 1.0
OG A:SER66 2.3 41.0 1.0
OE1 B:GLN32 2.4 45.8 1.0
O A:VAL63 2.5 44.5 1.0
CD B:GLU65 3.1 49.3 1.0
OE1 B:GLU65 3.3 51.9 1.0
CD B:GLN32 3.3 48.0 1.0
CB A:SER66 3.5 44.1 1.0
NE2 B:GLN32 3.6 44.2 1.0
C A:VAL63 3.7 44.2 1.0
N A:SER66 3.9 43.4 1.0
N A:THR67 4.1 44.0 1.0
CA A:ALA64 4.1 44.2 1.0
CG2 A:THR67 4.2 42.6 1.0
CA A:SER66 4.2 43.5 1.0
C A:ALA64 4.2 44.2 1.0
N A:ALA64 4.3 44.0 1.0
O A:ALA64 4.3 44.5 1.0
CB B:PRO28 4.4 45.2 1.0
CG1 A:VAL63 4.4 44.5 1.0
C A:SER66 4.6 44.1 1.0
CG B:GLU65 4.6 46.5 1.0
CG B:GLN32 4.7 44.9 1.0
N A:GLU65 4.7 44.5 1.0
CA A:VAL63 4.8 43.6 1.0
OG1 A:THR67 4.8 46.3 1.0
CB A:THR67 4.9 43.8 1.0
C A:GLU65 4.9 44.2 1.0
C B:PRO28 5.0 45.4 1.0
O B:PRO28 5.0 45.2 1.0

Sodium binding site 3 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 3 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:48.4
occ:1.00
 OG B:SER66 2.2 42.0 1.0
OE1 C:GLN32 2.3 43.4 1.0
O B:VAL63 2.4 44.4 1.0
OE2 C:GLU65 2.5 48.4 1.0
CD C:GLU65 3.4 48.2 1.0
CD C:GLN32 3.4 45.6 1.0
CB B:SER66 3.5 43.1 1.0
C B:VAL63 3.6 44.1 1.0
OE1 C:GLU65 3.6 48.2 1.0
N B:SER66 3.7 44.2 1.0
NE2 C:GLN32 3.9 45.8 1.0
CA B:ALA64 3.9 43.1 1.0
N B:THR67 3.9 44.4 1.0
C B:ALA64 3.9 43.8 1.0
CA B:SER66 4.0 43.5 1.0
O B:ALA64 4.1 45.1 1.0
N B:ALA64 4.2 44.2 1.0
CG2 B:THR67 4.3 44.9 1.0
CB C:PRO28 4.4 44.3 1.0
CG1 B:VAL63 4.4 42.6 1.0
C B:SER66 4.4 43.9 1.0
N B:GLU65 4.5 44.5 1.0
OG1 B:THR67 4.6 41.3 1.0
C B:GLU65 4.7 44.4 1.0
CA B:VAL63 4.7 43.5 1.0
CG C:GLN32 4.7 46.1 1.0
CG C:GLU65 4.8 46.4 1.0
CB B:THR67 4.8 44.1 1.0
C C:PRO28 4.9 45.3 1.0
CA B:THR67 4.9 44.1 1.0
O C:PRO28 4.9 45.1 1.0

Sodium binding site 4 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 4 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:50.8
occ:1.00
 OG C:SER66 2.3 38.8 1.0
O C:VAL63 2.3 44.5 1.0
OE2 D:GLU65 2.4 51.1 1.0
OE1 D:GLN32 2.5 42.4 1.0
CD D:GLU65 3.3 47.8 1.0
CB C:SER66 3.3 42.2 1.0
CD D:GLN32 3.4 45.8 1.0
C C:VAL63 3.5 44.5 1.0
OE1 D:GLU65 3.5 47.0 1.0
NE2 D:GLN32 3.6 44.5 1.0
N C:SER66 3.7 43.6 1.0
CA C:ALA64 3.9 44.4 1.0
CA C:SER66 4.0 42.9 1.0
N C:THR67 4.0 43.8 1.0
C C:ALA64 4.0 44.3 1.0
N C:ALA64 4.1 44.5 1.0
O C:ALA64 4.2 44.6 1.0
CG1 C:VAL63 4.3 46.4 1.0
CG2 C:THR67 4.3 43.7 1.0
C C:SER66 4.4 43.7 1.0
N C:GLU65 4.5 44.2 1.0
CA C:VAL63 4.6 44.3 1.0
CB D:PRO28 4.6 45.8 1.0
C C:GLU65 4.7 43.9 1.0
CG D:GLU65 4.7 46.7 1.0
CG D:GLN32 4.8 45.7 1.0
OG1 C:THR67 4.8 42.6 1.0
CB C:THR67 4.9 43.8 1.0

Sodium binding site 5 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 5 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:47.8
occ:1.00
 OG D:SER66 2.3 45.4 1.0
O D:VAL63 2.3 44.7 1.0
OE1 E:GLN32 2.3 51.2 1.0
OE2 E:GLU65 2.4 48.8 1.0
CD E:GLN32 3.3 48.0 1.0
CD E:GLU65 3.3 48.6 1.0
CB D:SER66 3.4 44.9 1.0
OE1 E:GLU65 3.5 48.9 1.0
C D:VAL63 3.5 44.5 1.0
NE2 E:GLN32 3.5 47.2 1.0
N D:SER66 3.8 44.7 1.0
CA D:ALA64 3.9 44.2 1.0
C D:ALA64 4.0 44.8 1.0
N D:THR67 4.0 44.4 1.0
CA D:SER66 4.1 44.6 1.0
N D:ALA64 4.1 44.5 1.0
O D:ALA64 4.2 44.7 1.0
CG2 D:THR67 4.3 42.2 1.0
CG1 D:VAL63 4.4 44.8 1.0
C D:SER66 4.5 44.8 1.0
CB E:PRO28 4.5 46.0 1.0
N D:GLU65 4.6 45.1 1.0
CA D:VAL63 4.6 44.1 1.0
CG E:GLN32 4.7 44.7 1.0
OG1 D:THR67 4.7 44.1 1.0
CG E:GLU65 4.7 46.0 1.0
C D:GLU65 4.8 44.1 1.0
CB D:THR67 4.9 44.9 1.0

Sodium binding site 6 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 6 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:49.5
occ:1.00
 OE1 F:GLN32 2.2 43.2 1.0
OE2 F:GLU65 2.2 46.9 1.0
OG E:SER66 2.4 39.8 1.0
O E:VAL63 2.6 45.4 1.0
CD F:GLU65 3.2 48.0 1.0
CD F:GLN32 3.3 46.1 1.0
OE1 F:GLU65 3.4 50.4 1.0
CB E:SER66 3.6 43.0 1.0
NE2 F:GLN32 3.6 41.7 1.0
C E:VAL63 3.7 44.1 1.0
N E:SER66 4.0 43.4 1.0
N E:THR67 4.0 44.3 1.0
CG2 E:THR67 4.0 42.7 1.0
CA E:ALA64 4.0 44.0 1.0
C E:ALA64 4.1 44.4 1.0
CA E:SER66 4.2 42.8 1.0
O E:ALA64 4.2 44.1 1.0
CB F:PRO28 4.2 45.1 1.0
N E:ALA64 4.3 43.6 1.0
CG1 E:VAL63 4.5 43.1 1.0
C E:SER66 4.5 43.5 1.0
CG F:GLN32 4.6 45.6 1.0
CG F:GLU65 4.6 45.8 1.0
N E:GLU65 4.7 44.3 1.0
OG1 E:THR67 4.8 40.6 1.0
CB E:THR67 4.8 43.5 1.0
C F:PRO28 4.8 45.3 1.0
O F:PRO28 4.9 46.4 1.0
CA E:VAL63 4.9 43.8 1.0
C E:GLU65 4.9 44.1 1.0
CA E:THR67 5.0 43.3 1.0

Sodium binding site 7 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 7 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:44.1
occ:1.00
 OG F:SER66 2.4 45.2 1.0
OE1 G:GLN32 2.4 46.5 1.0
OE2 G:GLU65 2.5 42.3 1.0
O F:VAL63 2.6 43.6 1.0
CD G:GLU65 3.4 44.9 1.0
CD G:GLN32 3.4 46.8 1.0
CB F:SER66 3.5 43.8 1.0
OE1 G:GLU65 3.6 47.8 1.0
N F:SER66 3.7 43.8 1.0
C F:VAL63 3.7 44.3 1.0
N F:THR67 3.7 44.2 1.0
NE2 G:GLN32 3.8 47.0 1.0
C F:ALA64 3.9 44.8 1.0
O F:ALA64 3.9 45.0 1.0
CA F:ALA64 3.9 44.7 1.0
CG2 F:THR67 4.0 44.3 1.0
CA F:SER66 4.0 43.8 1.0
CB G:PRO28 4.2 44.6 1.0
N F:ALA64 4.3 44.8 1.0
C F:SER66 4.3 44.0 1.0
OG1 F:THR67 4.4 42.4 1.0
N F:GLU65 4.5 44.5 1.0
CB F:THR67 4.6 44.1 1.0
C F:GLU65 4.6 44.7 1.0
CA F:THR67 4.7 44.2 1.0
C G:PRO28 4.7 45.5 1.0
CG G:GLN32 4.8 44.4 1.0
O G:PRO28 4.8 45.8 1.0
CG1 F:VAL63 4.8 44.5 1.0
N G:GLY29 4.9 46.0 1.0
CG G:GLU65 4.9 42.2 1.0
CA F:VAL63 4.9 43.9 1.0

Sodium binding site 8 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 8 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na201

b:43.9
occ:1.00
 OG G:SER66 2.2 39.2 1.0
OE2 H:GLU65 2.2 56.0 1.0
OE1 H:GLN32 2.5 52.8 1.0
O G:VAL63 2.5 45.0 1.0
CD H:GLU65 3.2 53.4 1.0
OE1 H:GLU65 3.4 57.2 1.0
CB G:SER66 3.4 42.4 1.0
CD H:GLN32 3.5 46.4 1.0
C G:VAL63 3.6 44.8 1.0
NE2 H:GLN32 3.8 46.5 1.0
N G:SER66 3.9 43.1 1.0
N G:THR67 4.0 44.7 1.0
CA G:SER66 4.1 43.0 1.0
CA G:ALA64 4.1 43.8 1.0
C G:ALA64 4.2 44.2 1.0
CG2 G:THR67 4.2 46.0 1.0
N G:ALA64 4.3 44.7 1.0
O G:ALA64 4.3 44.7 1.0
CG1 G:VAL63 4.4 43.5 1.0
CB H:PRO28 4.5 44.7 1.0
C G:SER66 4.5 44.1 1.0
CG H:GLU65 4.6 48.5 1.0
N G:GLU65 4.7 44.4 1.0
CA G:VAL63 4.7 44.1 1.0
OG1 G:THR67 4.8 42.7 1.0
CG H:GLN32 4.8 44.2 1.0
CB G:THR67 4.9 45.3 1.0
C G:GLU65 4.9 43.7 1.0

Sodium binding site 9 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 9 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na201

b:43.0
occ:1.00
 OG H:SER66 2.3 41.3 1.0
OE2 I:GLU65 2.3 49.2 1.0
OE1 I:GLN32 2.4 45.0 1.0
O H:VAL63 2.5 43.6 1.0
CD I:GLU65 3.3 47.7 1.0
CB H:SER66 3.4 43.5 1.0
OE1 I:GLU65 3.5 47.1 1.0
CD I:GLN32 3.5 45.7 1.0
C H:VAL63 3.6 44.1 1.0
N H:SER66 3.7 43.8 1.0
N H:THR67 3.8 44.0 1.0
NE2 I:GLN32 3.9 42.3 1.0
CA H:SER66 4.0 43.7 1.0
CA H:ALA64 4.0 44.1 1.0
C H:ALA64 4.0 44.6 1.0
CG2 H:THR67 4.1 45.6 1.0
O H:ALA64 4.1 44.6 1.0
N H:ALA64 4.2 44.6 1.0
C H:SER66 4.3 44.0 1.0
CB I:PRO28 4.4 44.5 1.0
N H:GLU65 4.5 45.4 1.0
CG1 H:VAL63 4.6 43.2 1.0
C H:GLU65 4.7 44.1 1.0
CG I:GLU65 4.7 46.5 1.0
OG1 H:THR67 4.7 40.0 1.0
CB H:THR67 4.7 44.3 1.0
CA H:VAL63 4.8 43.9 1.0
CG I:GLN32 4.8 44.8 1.0
CA H:THR67 4.8 43.9 1.0
C I:PRO28 5.0 45.6 1.0

Sodium binding site 10 out of 44 in 1yce

Go back to Sodium Binding Sites List in 1yce
Sodium binding site 10 out of 44 in the Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na201

b:34.7
occ:1.00
 O I:VAL63 2.3 45.5 1.0
OE2 J:GLU65 2.3 42.5 1.0
OG I:SER66 2.4 42.4 1.0
OE1 J:GLN32 2.5 52.5 1.0
CD J:GLU65 3.4 47.6 1.0
CD J:GLN32 3.4 48.4 1.0
C I:VAL63 3.5 44.8 1.0
CB I:SER66 3.5 42.5 1.0
NE2 J:GLN32 3.6 49.6 1.0
OE1 J:GLU65 3.6 44.4 1.0
N I:SER66 3.7 43.0 1.0
CA I:ALA64 3.9 44.2 1.0
C I:ALA64 3.9 44.0 1.0
N I:THR67 4.0 44.4 1.0
CA I:SER66 4.0 43.4 1.0
O I:ALA64 4.1 44.0 1.0
N I:ALA64 4.1 44.3 1.0
CG2 I:THR67 4.1 42.3 1.0
C I:SER66 4.4 44.5 1.0
CG1 I:VAL63 4.5 45.2 1.0
N I:GLU65 4.5 44.6 1.0
CB J:PRO28 4.6 45.1 1.0
CA I:VAL63 4.6 44.4 1.0
C I:GLU65 4.7 44.1 1.0
CG J:GLN32 4.8 45.3 1.0
CG J:GLU65 4.8 45.9 1.0
OG1 I:THR67 4.8 45.3 1.0
CB I:THR67 4.8 44.9 1.0
CA I:THR67 5.0 44.2 1.0

Reference:

T.Meier, P.Polzer, K.Diederichs, W.Welte, P.Dimroth. Structure of the Rotor Ring of F-Type Na+-Atpase From Ilyobacter Tartaricus. Science V. 308 659 2005.
ISSN: ISSN 0036-8075
PubMed: 15860619
DOI: 10.1126/SCIENCE.1111199
Page generated: Sun Aug 17 09:16:14 2025

Last articles

Na in 4Y9V
Na in 4Y96
Na in 4XTN
Na in 4Y8F
Na in 4Y7D
Na in 4Y0W
Na in 4Y6G
Na in 4Y5L
Na in 4Y23
Na in 4XTO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy