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

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

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 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 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 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 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 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 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 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 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 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 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

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