Atomistry » Sodium » PDB 2wd0-2wof » 2wgm
Atomistry »
  Sodium »
    PDB 2wd0-2wof »
      2wgm »

Sodium in PDB 2wgm: Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase

Protein crystallography data

The structure of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase, PDB code: 2wgm was solved by T.Meier, D.Pogoryelov, K.Diederichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.678 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 146.690, 139.280, 151.910, 90.00, 118.40, 90.00
R / Rfree (%) 22.03 / 24.51

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 Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase (pdb code 2wgm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 44 binding sites of Sodium where determined in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase, PDB code: 2wgm:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 1 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:47.0
occ:1.00
OE1 A:GLN32 2.3 43.9 1.0
O K:HOH2015 2.4 34.8 1.0
O K:VAL63 2.4 49.6 1.0
OG K:SER66 2.4 40.8 1.0
OE2 A:GLU65 2.6 50.8 1.0
CD A:GLN32 3.2 45.8 1.0
C K:VAL63 3.5 56.2 1.0
CD A:GLU65 3.5 51.2 1.0
NE2 A:GLN32 3.5 35.6 1.0
CB K:SER66 3.5 36.1 1.0
OE1 A:GLU65 3.7 48.0 1.0
N K:SER66 3.8 45.1 1.0
CA K:ALA64 3.8 44.8 1.0
C K:ALA64 3.9 44.8 1.0
N K:THR67 4.0 44.5 1.0
O K:ALA64 4.1 45.7 1.0
CA K:SER66 4.1 48.4 1.0
N K:ALA64 4.1 48.8 1.0
CG2 K:THR67 4.2 37.6 1.0
CB A:PRO28 4.4 43.6 1.0
CG1 K:VAL63 4.4 35.1 1.0
N K:GLU65 4.4 43.6 1.0
C K:SER66 4.5 53.9 1.0
CG A:GLN32 4.6 49.7 1.0
OG1 K:THR67 4.7 38.1 1.0
CA K:VAL63 4.7 52.4 1.0
O A:PRO28 4.7 53.1 1.0
C K:GLU65 4.8 48.8 1.0
C A:PRO28 4.8 58.0 1.0
CB K:THR67 4.9 45.5 1.0
CG A:GLU65 4.9 46.5 1.0
CB A:GLN32 5.0 41.9 1.0
CA K:THR67 5.0 43.8 1.0

Sodium binding site 2 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 2 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:45.3
occ:1.00
OG A:SER66 2.2 46.2 1.0
OE2 B:GLU65 2.4 48.8 1.0
OE1 B:GLN32 2.4 46.8 1.0
O A:VAL63 2.5 50.4 1.0
O A:HOH2019 2.6 38.9 1.0
CD B:GLU65 3.2 51.8 1.0
CD B:GLN32 3.3 47.6 1.0
OE1 B:GLU65 3.4 51.5 1.0
CB A:SER66 3.4 42.2 1.0
NE2 B:GLN32 3.5 42.4 1.0
C A:VAL63 3.6 56.0 1.0
N A:SER66 3.9 42.9 1.0
N A:THR67 4.0 47.5 1.0
CA A:SER66 4.1 48.9 1.0
CA A:ALA64 4.1 45.3 1.0
CG2 A:THR67 4.2 34.7 1.0
C A:ALA64 4.2 46.7 1.0
N A:ALA64 4.3 41.5 1.0
CG1 A:VAL63 4.4 38.7 1.0
O A:ALA64 4.4 43.5 1.0
CB B:PRO28 4.4 41.2 1.0
C A:SER66 4.5 54.7 1.0
CG B:GLU65 4.7 46.5 1.0
N A:GLU65 4.7 46.6 1.0
CG B:GLN32 4.7 50.5 1.0
CA A:VAL63 4.7 47.9 1.0
OG1 A:THR67 4.8 44.7 1.0
CB A:THR67 4.9 43.4 1.0
O B:PRO28 4.9 52.7 1.0
C A:GLU65 4.9 50.3 1.0
C B:PRO28 5.0 57.1 1.0

Sodium binding site 3 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 3 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:55.6
occ:1.00
O B:VAL63 2.2 54.6 1.0
O B:HOH2016 2.3 48.6 1.0
OE1 C:GLN32 2.3 49.2 1.0
OG B:SER66 2.3 45.7 1.0
OE2 C:GLU65 2.6 46.4 1.0
CD C:GLN32 3.2 47.5 1.0
C B:VAL63 3.4 58.4 1.0
CB B:SER66 3.4 43.1 1.0
CD C:GLU65 3.5 54.7 1.0
NE2 C:GLN32 3.5 42.1 1.0
OE1 C:GLU65 3.7 52.5 1.0
N B:SER66 3.7 49.8 1.0
CA B:ALA64 3.8 42.5 1.0
C B:ALA64 3.9 46.0 1.0
N B:ALA64 4.0 46.3 1.0
CA B:SER66 4.0 47.6 1.0
N B:THR67 4.0 50.4 1.0
O B:ALA64 4.1 44.5 1.0
CG1 B:VAL63 4.2 40.6 1.0
CG2 B:THR67 4.4 37.9 1.0
N B:GLU65 4.4 45.4 1.0
CB C:PRO28 4.5 42.3 1.0
CA B:VAL63 4.5 51.8 1.0
C B:SER66 4.5 54.8 1.0
CG C:GLN32 4.6 52.8 1.0
C B:GLU65 4.8 52.5 1.0
O C:PRO28 4.8 55.1 1.0
OG1 B:THR67 4.8 43.6 1.0
CG C:GLU65 4.9 47.8 1.0
C C:PRO28 4.9 54.4 1.0
CB C:GLN32 4.9 40.2 1.0

Sodium binding site 4 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 4 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:60.2
occ:1.00
O C:HOH2015 2.3 59.4 1.0
OG C:SER66 2.3 52.4 1.0
O C:VAL63 2.3 55.4 1.0
OE1 D:GLN32 2.4 52.2 1.0
OE2 D:GLU65 2.6 53.0 1.0
CD D:GLN32 3.3 51.5 1.0
CB C:SER66 3.4 47.5 1.0
C C:VAL63 3.4 58.9 1.0
CD D:GLU65 3.5 58.4 1.0
NE2 D:GLN32 3.6 44.2 1.0
OE1 D:GLU65 3.7 54.6 1.0
N C:SER66 3.7 46.2 1.0
CA C:ALA64 3.8 49.8 1.0
C C:ALA64 3.9 46.7 1.0
CA C:SER66 4.0 50.2 1.0
N C:THR67 4.0 47.4 1.0
N C:ALA64 4.0 52.6 1.0
O C:ALA64 4.1 46.1 1.0
CG1 C:VAL63 4.2 46.6 1.0
CG2 C:THR67 4.4 37.9 1.0
N C:GLU65 4.4 45.7 1.0
C C:SER66 4.4 52.1 1.0
CB D:PRO28 4.5 39.8 1.0
CA C:VAL63 4.6 55.3 1.0
CG D:GLN32 4.7 53.1 1.0
C C:GLU65 4.7 51.5 1.0
OG1 C:THR67 4.8 46.1 1.0
O D:PRO28 4.8 57.0 1.0
CG D:GLU65 4.9 54.0 1.0
C D:PRO28 5.0 55.1 1.0
CB C:THR67 5.0 48.1 1.0

Sodium binding site 5 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 5 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:55.4
occ:1.00
OG D:SER66 2.1 60.6 1.0
O D:VAL63 2.2 59.5 1.0
OE1 E:GLN32 2.5 55.2 1.0
OE2 E:GLU65 2.5 51.6 1.0
O D:HOH2015 2.7 62.8 1.0
CB D:SER66 3.2 54.6 1.0
CD E:GLU65 3.3 59.6 1.0
CD E:GLN32 3.4 50.2 1.0
C D:VAL63 3.4 54.8 1.0
OE1 E:GLU65 3.5 57.6 1.0
NE2 E:GLN32 3.6 46.2 1.0
N D:SER66 3.6 51.6 1.0
CA D:SER66 3.9 51.5 1.0
N D:THR67 3.9 49.2 1.0
CA D:ALA64 3.9 44.5 1.0
C D:ALA64 4.0 49.5 1.0
N D:ALA64 4.1 53.5 1.0
O D:ALA64 4.2 55.4 1.0
CG1 D:VAL63 4.2 52.5 1.0
CG2 D:THR67 4.3 44.7 1.0
C D:SER66 4.3 53.5 1.0
N D:GLU65 4.5 50.6 1.0
CA D:VAL63 4.5 55.6 1.0
CB E:PRO28 4.6 47.2 1.0
C D:GLU65 4.7 51.3 1.0
CG E:GLU65 4.7 53.9 1.0
CG E:GLN32 4.8 50.0 1.0
OG1 D:THR67 4.9 46.1 1.0
CB D:THR67 5.0 52.6 1.0

Sodium binding site 6 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 6 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:54.4
occ:1.00
OG E:SER66 2.1 56.3 1.0
O E:HOH2014 2.3 48.9 1.0
O E:VAL63 2.3 64.3 1.0
OE1 F:GLN32 2.5 54.8 1.0
OE2 F:GLU65 2.6 52.1 1.0
CB E:SER66 3.2 51.2 1.0
C E:VAL63 3.4 53.9 1.0
CD F:GLN32 3.4 55.8 1.0
CD F:GLU65 3.5 56.2 1.0
N E:SER66 3.6 57.1 1.0
OE1 F:GLU65 3.6 59.6 1.0
NE2 F:GLN32 3.7 47.7 1.0
N E:THR67 3.8 46.8 1.0
CA E:ALA64 3.8 43.9 1.0
C E:ALA64 3.8 49.6 1.0
CA E:SER66 3.8 45.4 1.0
O E:ALA64 4.0 46.1 1.0
N E:ALA64 4.1 42.8 1.0
C E:SER66 4.2 53.8 1.0
CG2 E:THR67 4.3 43.2 1.0
N E:GLU65 4.3 48.3 1.0
CG1 E:VAL63 4.4 49.7 1.0
C E:GLU65 4.6 57.2 1.0
CB F:PRO28 4.6 43.0 1.0
CA E:VAL63 4.6 51.3 1.0
OG1 E:THR67 4.6 44.4 1.0
CG F:GLN32 4.8 47.8 1.0
CB E:THR67 4.8 48.6 1.0
CA E:THR67 4.9 46.5 1.0
CG F:GLU65 4.9 52.9 1.0
O F:PRO28 5.0 62.5 1.0

Sodium binding site 7 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 7 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:54.4
occ:1.00
O F:HOH2014 2.0 57.6 1.0
OG F:SER66 2.1 56.2 1.0
O F:VAL63 2.3 62.0 1.0
OE2 G:GLU65 2.5 51.9 1.0
OE1 G:GLN32 2.6 54.2 1.0
CB F:SER66 3.2 49.6 1.0
CD G:GLU65 3.3 53.8 1.0
OE1 G:GLU65 3.4 60.5 1.0
CD G:GLN32 3.5 50.6 1.0
C F:VAL63 3.5 56.9 1.0
NE2 G:GLN32 3.6 47.1 1.0
N F:SER66 3.7 54.9 1.0
N F:THR67 3.9 47.2 1.0
CA F:SER66 3.9 47.3 1.0
CA F:ALA64 4.0 46.7 1.0
C F:ALA64 4.1 47.5 1.0
N F:ALA64 4.2 50.9 1.0
O F:ALA64 4.2 49.1 1.0
CG2 F:THR67 4.3 44.1 1.0
C F:SER66 4.3 52.4 1.0
CG1 F:VAL63 4.3 47.8 1.0
N F:GLU65 4.5 42.5 1.0
CA F:VAL63 4.6 52.4 1.0
CB G:PRO28 4.6 41.2 1.0
CG G:GLU65 4.7 44.7 1.0
C F:GLU65 4.7 52.0 1.0
OG1 F:THR67 4.8 48.3 1.0
CG G:GLN32 4.9 50.7 1.0
CB F:THR67 4.9 50.8 1.0
CA F:THR67 5.0 47.0 1.0

Sodium binding site 8 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 8 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na201

b:57.2
occ:1.00
O G:HOH2013 2.2 53.0 1.0
OG G:SER66 2.2 45.0 1.0
O G:VAL63 2.3 52.9 1.0
OE1 H:GLN32 2.4 55.9 1.0
OE2 H:GLU65 2.5 57.4 1.0
CD H:GLN32 3.3 52.7 1.0
CB G:SER66 3.3 40.3 1.0
CD H:GLU65 3.4 59.0 1.0
C G:VAL63 3.5 59.0 1.0
NE2 H:GLN32 3.5 45.8 1.0
OE1 H:GLU65 3.6 58.0 1.0
N G:SER66 3.7 46.8 1.0
CA G:ALA64 3.9 46.5 1.0
CA G:SER66 4.0 48.2 1.0
C G:ALA64 4.0 46.9 1.0
N G:THR67 4.0 49.0 1.0
N G:ALA64 4.1 52.5 1.0
O G:ALA64 4.2 46.4 1.0
CG1 G:VAL63 4.3 43.2 1.0
CG2 G:THR67 4.3 42.4 1.0
C G:SER66 4.4 56.9 1.0
CB H:PRO28 4.5 47.1 1.0
N G:GLU65 4.5 48.4 1.0
CA G:VAL63 4.6 51.4 1.0
CG H:GLN32 4.7 47.5 1.0
OG1 G:THR67 4.7 46.7 1.0
C G:GLU65 4.8 52.9 1.0
CG H:GLU65 4.8 54.4 1.0
O H:PRO28 4.9 56.4 1.0
CB G:THR67 5.0 49.4 1.0
C H:PRO28 5.0 53.8 1.0

Sodium binding site 9 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 9 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na201

b:48.5
occ:1.00
OG H:SER66 2.2 47.7 1.0
O H:HOH2014 2.3 40.0 1.0
O H:VAL63 2.4 53.2 1.0
OE1 I:GLN32 2.4 49.0 1.0
OE2 I:GLU65 2.5 53.4 1.0
CB H:SER66 3.3 42.1 1.0
CD I:GLN32 3.4 49.8 1.0
CD I:GLU65 3.4 55.5 1.0
C H:VAL63 3.5 59.2 1.0
OE1 I:GLU65 3.6 54.4 1.0
NE2 I:GLN32 3.6 39.3 1.0
N H:SER66 3.6 52.1 1.0
N H:THR67 3.8 45.4 1.0
CA H:ALA64 3.9 44.1 1.0
CA H:SER66 3.9 45.8 1.0
C H:ALA64 3.9 48.3 1.0
O H:ALA64 4.0 44.8 1.0
N H:ALA64 4.1 51.3 1.0
CG2 H:THR67 4.2 37.0 1.0
C H:SER66 4.3 53.7 1.0
CG1 H:VAL63 4.4 43.1 1.0
N H:GLU65 4.4 46.7 1.0
CB I:PRO28 4.5 42.5 1.0
OG1 H:THR67 4.6 44.0 1.0
CA H:VAL63 4.7 50.0 1.0
C H:GLU65 4.7 48.9 1.0
CG I:GLN32 4.8 49.3 1.0
CB H:THR67 4.8 48.0 1.0
CG I:GLU65 4.8 50.3 1.0
CA H:THR67 4.9 47.5 1.0
O I:PRO28 4.9 53.5 1.0
C I:PRO28 5.0 59.6 1.0

Sodium binding site 10 out of 44 in 2wgm

Go back to Sodium Binding Sites List in 2wgm
Sodium binding site 10 out of 44 in the Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Complete Ion-Coordination Structure in the Rotor Ring of Na- Dependent F-Atp Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na201

b:51.1
occ:1.00
OG I:SER66 2.2 43.8 1.0
O I:HOH2011 2.2 40.0 1.0
OE2 J:GLU65 2.4 49.9 1.0
O I:VAL63 2.5 50.0 1.0
OE1 J:GLN32 2.6 50.7 1.0
CD J:GLU65 3.3 50.9 1.0
CB I:SER66 3.3 36.5 1.0
OE1 J:GLU65 3.4 49.7 1.0
CD J:GLN32 3.4 47.5 1.0
NE2 J:GLN32 3.6 39.4 1.0
C I:VAL63 3.7 58.3 1.0
N I:SER66 3.7 43.8 1.0
N I:THR67 3.8 46.8 1.0
CA I:SER66 3.9 49.5 1.0
CA I:ALA64 4.0 46.4 1.0
C I:ALA64 4.1 45.8 1.0
CG2 I:THR67 4.1 36.3 1.0
O I:ALA64 4.2 44.6 1.0
N I:ALA64 4.3 50.4 1.0
C I:SER66 4.3 54.0 1.0
CB J:PRO28 4.5 44.2 1.0
CG1 I:VAL63 4.6 39.1 1.0
OG1 I:THR67 4.6 46.8 1.0
N I:GLU65 4.6 45.3 1.0
CG J:GLU65 4.7 46.2 1.0
CB I:THR67 4.7 47.8 1.0
C I:GLU65 4.8 48.4 1.0
CA I:VAL63 4.8 50.4 1.0
CA I:THR67 4.8 45.9 1.0
CG J:GLN32 4.9 47.8 1.0
O J:PRO28 5.0 57.3 1.0

Reference:

T.Meier, A.Krah, P.J.Bond, D.Pogoryelov, K.Diederichs, J.D.Faraldo-Gomez. Complete Ion-Coordination Structure in the Rotor Ring of Na(+)-Dependent F-Atp Synthases. J.Mol.Biol. V. 391 498 2009.
ISSN: ISSN 0022-2836
PubMed: 19500592
DOI: 10.1016/J.JMB.2009.05.082
Page generated: Tue Dec 15 05:57:37 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy