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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Oct 7 00:40:13 2024

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