Sodium in PDB 3zk1: Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3

The structure of Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3, PDB code: 3zk1 was solved by S.Schulz, T.Meier, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.747 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	135.770, 83.900, 150.990, 90.00, 112.85, 90.00
R / Rfree (%)	20.76 / 23.37

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3 (pdb code 3zk1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 22 binding sites of Sodium where determined in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3, PDB code: 3zk1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na90 b:29.1 occ:1.00 OG K:SER66 2.3 29.0 1.0 O K:VAL63 2.3 23.9 1.0 OE1 A:GLU32 2.4 28.3 1.0 OE1 A:GLU65 2.4 33.6 1.0 O A:HOH2007 2.5 23.8 1.0 CD A:GLU65 3.3 33.4 1.0 CD A:GLU32 3.3 27.4 1.0 C K:VAL63 3.4 24.5 1.0 CB K:SER66 3.4 24.3 1.0 OE2 A:GLU65 3.5 35.3 1.0 OE2 A:GLU32 3.5 31.2 1.0 N K:SER66 3.8 25.5 1.0 CA K:ALA64 3.9 22.2 1.0 C K:ALA64 3.9 22.7 1.0 O K:ALA64 4.0 23.9 1.0 N K:THR67 4.1 25.9 1.0 CA K:SER66 4.1 28.0 1.0 N K:ALA64 4.1 20.9 1.0 CG1 K:VAL63 4.3 23.3 1.0 CG2 K:THR67 4.3 18.9 1.0 C K:SER66 4.5 29.7 1.0 N K:GLU65 4.6 21.7 1.0 CA K:VAL63 4.6 25.3 1.0 CG A:GLU65 4.6 25.9 1.0 CG A:GLU32 4.7 27.9 1.0 OG1 K:THR67 4.8 22.9 1.0 C K:GLU65 4.8 25.2 1.0 CB A:GLU65 5.0 28.6 1.0 CB A:GLU32 5.0 24.4 1.0 CB A:PRO28 5.0 23.3 1.0

Sodium binding site 2 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na90 b:31.4 occ:1.00 OG A:SER66 2.3 26.5 1.0 OE1 B:GLU65 2.4 36.0 1.0 O A:VAL63 2.4 29.7 1.0 OE1 B:GLU32 2.4 33.0 1.0 O A:HOH2013 2.4 28.6 1.0 CD B:GLU32 3.2 27.3 1.0 CD B:GLU65 3.3 38.1 1.0 CB A:SER66 3.4 26.1 1.0 OE2 B:GLU32 3.4 30.1 1.0 C A:VAL63 3.4 30.3 1.0 OE2 B:GLU65 3.6 39.2 1.0 N A:SER66 3.8 25.3 1.0 CA A:ALA64 3.9 27.5 1.0 N A:THR67 4.0 27.5 1.0 C A:ALA64 4.0 28.4 1.0 CA A:SER66 4.0 27.5 1.0 N A:ALA64 4.1 26.7 1.0 CG1 A:VAL63 4.2 28.4 1.0 O A:ALA64 4.2 27.5 1.0 CG2 A:THR67 4.3 25.9 1.0 C A:SER66 4.5 28.8 1.0 CA A:VAL63 4.5 33.1 1.0 N A:GLU65 4.6 28.0 1.0 CG B:GLU65 4.6 35.6 1.0 CG B:GLU32 4.6 27.1 1.0 OG1 A:THR67 4.8 23.4 1.0 CB B:GLU65 4.9 30.8 1.0 C A:GLU65 4.9 28.4 1.0 CB B:GLU32 4.9 25.3 1.0 CB B:PRO28 4.9 23.2 1.0 CB A:VAL63 5.0 32.8 1.0

Sodium binding site 3 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na90 b:26.8 occ:1.00 O B:VAL63 2.3 30.1 1.0 OG B:SER66 2.3 31.0 1.0 OE1 C:GLU32 2.4 38.1 1.0 OE1 C:GLU65 2.4 35.4 1.0 O B:HOH2011 2.4 24.1 1.0 CD C:GLU32 3.2 35.0 1.0 CD C:GLU65 3.3 39.1 1.0 C B:VAL63 3.3 29.4 1.0 CB B:SER66 3.4 29.1 1.0 OE2 C:GLU32 3.5 38.4 1.0 OE2 C:GLU65 3.5 43.0 1.0 CA B:ALA64 3.8 28.9 1.0 N B:SER66 3.8 30.6 1.0 C B:ALA64 3.9 29.8 1.0 N B:ALA64 4.0 28.4 1.0 O B:ALA64 4.0 27.6 1.0 CA B:SER66 4.0 30.6 1.0 N B:THR67 4.0 31.3 1.0 CG1 B:VAL63 4.2 26.0 1.0 CG2 B:THR67 4.4 23.5 1.0 CA B:VAL63 4.5 31.5 1.0 N B:GLU65 4.5 29.2 1.0 C B:SER66 4.5 32.8 1.0 CG C:GLU32 4.6 28.6 1.0 CG C:GLU65 4.7 34.2 1.0 C B:GLU65 4.8 31.6 1.0 OG1 B:THR67 4.8 24.2 1.0 CB C:PRO28 4.8 26.6 1.0 CB C:GLU32 4.9 25.9 1.0 CB C:GLU65 5.0 31.5 1.0 CB B:VAL63 5.0 29.9 1.0

Sodium binding site 4 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na90 b:32.5 occ:1.00 OE1 D:GLU32 2.3 34.1 1.0 O C:VAL63 2.3 29.7 1.0 OG C:SER66 2.3 29.1 1.0 OE1 D:GLU65 2.5 34.2 1.0 O C:HOH2008 2.5 23.8 1.0 CD D:GLU32 3.1 31.1 1.0 OE2 D:GLU32 3.3 32.0 1.0 CD D:GLU65 3.3 38.1 1.0 CB C:SER66 3.4 28.7 1.0 C C:VAL63 3.4 30.5 1.0 OE2 D:GLU65 3.6 39.6 1.0 N C:SER66 3.9 29.7 1.0 CA C:ALA64 3.9 31.2 1.0 C C:ALA64 4.0 29.5 1.0 CA C:SER66 4.1 31.0 1.0 N C:THR67 4.1 30.1 1.0 O C:ALA64 4.1 33.7 1.0 N C:ALA64 4.1 30.9 1.0 CG1 C:VAL63 4.3 32.5 1.0 CG2 C:THR67 4.4 28.4 1.0 C C:SER66 4.5 29.1 1.0 CG D:GLU32 4.5 26.7 1.0 CA C:VAL63 4.6 30.6 1.0 N C:GLU65 4.6 29.4 1.0 CG D:GLU65 4.6 35.1 1.0 OG1 C:THR67 4.7 28.0 1.0 CB D:PRO28 4.8 28.7 1.0 CB D:GLU32 4.9 28.3 1.0 C C:GLU65 4.9 29.1 1.0 CB D:GLU65 4.9 31.7 1.0

Sodium binding site 5 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na90 b:31.3 occ:1.00 O D:VAL63 2.3 27.7 1.0 OG D:SER66 2.3 32.7 1.0 OE1 E:GLU32 2.4 31.4 1.0 OE1 E:GLU65 2.4 31.6 1.0 O D:HOH2009 2.4 29.1 1.0 CD E:GLU65 3.2 32.9 1.0 CD E:GLU32 3.3 34.7 1.0 OE2 E:GLU65 3.3 35.2 1.0 C D:VAL63 3.4 30.7 1.0 CB D:SER66 3.4 29.8 1.0 OE2 E:GLU32 3.5 37.6 1.0 CA D:ALA64 3.8 29.6 1.0 N D:SER66 3.8 31.4 1.0 C D:ALA64 3.9 32.3 1.0 N D:THR67 4.0 27.7 1.0 N D:ALA64 4.0 28.2 1.0 CA D:SER66 4.1 30.5 1.0 O D:ALA64 4.1 32.3 1.0 CG2 D:THR67 4.2 26.0 1.0 CG1 D:VAL63 4.2 30.6 1.0 N D:GLU65 4.5 33.5 1.0 C D:SER66 4.5 31.4 1.0 CA D:VAL63 4.5 33.4 1.0 CG E:GLU65 4.6 27.5 1.0 CG E:GLU32 4.7 31.2 1.0 OG1 D:THR67 4.7 31.8 1.0 CB E:PRO28 4.8 30.7 1.0 C D:GLU65 4.8 31.3 1.0 CB D:THR67 4.9 26.7 1.0 CB E:GLU65 4.9 27.3 1.0 CB E:GLU32 5.0 28.8 1.0 O E:PRO28 5.0 23.3 1.0

Sodium binding site 6 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Na90 b:32.7 occ:1.00 OG E:SER66 2.3 25.9 1.0 O E:VAL63 2.3 34.5 1.0 OE1 F:GLU32 2.3 33.6 1.0 O E:HOH2007 2.3 22.5 1.0 OE1 F:GLU65 2.4 32.0 1.0 CD F:GLU32 3.2 31.1 1.0 CD F:GLU65 3.3 33.6 1.0 C E:VAL63 3.4 35.1 1.0 OE2 F:GLU32 3.4 31.3 1.0 CB E:SER66 3.4 26.1 1.0 OE2 F:GLU65 3.5 36.0 1.0 CA E:ALA64 3.8 29.5 1.0 N E:SER66 3.8 22.0 1.0 C E:ALA64 4.0 28.1 1.0 N E:ALA64 4.0 31.2 1.0 N E:THR67 4.1 27.5 1.0 CA E:SER66 4.1 27.7 1.0 O E:ALA64 4.2 27.3 1.0 CG1 E:VAL63 4.2 32.4 1.0 CG2 E:THR67 4.3 22.2 1.0 N E:GLU65 4.5 30.6 1.0 CA E:VAL63 4.5 31.6 1.0 C E:SER66 4.5 30.1 1.0 CG F:GLU32 4.6 29.0 1.0 CG F:GLU65 4.6 31.0 1.0 OG1 E:THR67 4.8 32.2 1.0 C E:GLU65 4.9 27.1 1.0 CB F:PRO28 4.9 29.8 1.0 CB F:GLU32 4.9 28.9 1.0 CB F:GLU65 4.9 25.6 1.0

Sodium binding site 7 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ G:Na90 b:36.5 occ:1.00 OG F:SER66 2.3 28.1 1.0 OE1 G:GLU32 2.3 34.7 1.0 O F:VAL63 2.3 31.5 1.0 O F:HOH2012 2.4 31.0 1.0 OE1 G:GLU65 2.4 32.2 1.0 CD G:GLU65 3.2 34.3 1.0 CB F:SER66 3.3 23.0 1.0 CD G:GLU32 3.3 32.0 1.0 OE2 G:GLU65 3.4 39.1 1.0 C F:VAL63 3.4 32.8 1.0 OE2 G:GLU32 3.5 34.0 1.0 N F:SER66 3.8 23.2 1.0 CA F:ALA64 3.9 28.1 1.0 N F:THR67 4.0 26.1 1.0 CA F:SER66 4.0 25.3 1.0 C F:ALA64 4.0 26.4 1.0 N F:ALA64 4.1 29.5 1.0 O F:ALA64 4.2 24.0 1.0 CG2 F:THR67 4.3 22.9 1.0 CG1 F:VAL63 4.3 33.5 1.0 C F:SER66 4.4 28.8 1.0 CA F:VAL63 4.6 31.0 1.0 CG G:GLU65 4.6 26.5 1.0 N F:GLU65 4.6 26.4 1.0 CG G:GLU32 4.7 30.1 1.0 OG1 F:THR67 4.7 27.6 1.0 C F:GLU65 4.9 27.7 1.0 CB G:PRO28 4.9 27.0 1.0 CB G:GLU65 4.9 23.3 1.0 CB F:THR67 4.9 26.9 1.0 CB G:GLU32 5.0 24.4 1.0

Sodium binding site 8 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na90 b:31.9 occ:1.00 OG G:SER66 2.3 25.8 1.0 O G:VAL63 2.3 30.4 1.0 OE1 H:GLU32 2.4 30.9 1.0 OE1 H:GLU65 2.4 33.7 1.0 O G:HOH2008 2.4 22.3 1.0 CD H:GLU65 3.3 33.9 1.0 CD H:GLU32 3.3 30.3 1.0 CB G:SER66 3.4 26.7 1.0 C G:VAL63 3.4 30.2 1.0 OE2 H:GLU65 3.5 37.8 1.0 OE2 H:GLU32 3.5 34.1 1.0 N G:SER66 3.8 24.9 1.0 CA G:ALA64 3.9 29.6 1.0 C G:ALA64 3.9 25.2 1.0 O G:ALA64 3.9 26.0 1.0 N G:THR67 4.0 24.7 1.0 CA G:SER66 4.0 28.0 1.0 N G:ALA64 4.1 29.1 1.0 CG2 G:THR67 4.3 27.4 1.0 CG1 G:VAL63 4.3 22.8 1.0 C G:SER66 4.5 24.9 1.0 N G:GLU65 4.5 19.3 1.0 CA G:VAL63 4.6 26.6 1.0 CG H:GLU65 4.6 29.9 1.0 CG H:GLU32 4.7 28.9 1.0 OG1 G:THR67 4.7 29.1 1.0 C G:GLU65 4.8 24.5 1.0 CB H:PRO28 4.8 26.4 1.0 CB G:THR67 4.9 28.8 1.0 O H:PRO28 4.9 21.6 1.0 CB H:GLU65 5.0 28.1 1.0 CB H:GLU32 5.0 26.7 1.0

Sodium binding site 9 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ I:Na90 b:28.4 occ:1.00 OG H:SER66 2.3 25.1 1.0 O H:VAL63 2.3 26.1 1.0 O H:HOH2005 2.3 24.5 1.0 OE1 I:GLU32 2.4 30.5 1.0 OE1 I:GLU65 2.4 32.5 1.0 CD I:GLU32 3.2 26.6 1.0 CD I:GLU65 3.3 27.7 1.0 CB H:SER66 3.3 24.8 1.0 C H:VAL63 3.4 28.9 1.0 OE2 I:GLU32 3.4 31.9 1.0 OE2 I:GLU65 3.5 28.2 1.0 N H:SER66 3.8 20.8 1.0 CA H:ALA64 3.8 26.1 1.0 C H:ALA64 3.9 25.4 1.0 N H:THR67 4.0 22.1 1.0 CA H:SER66 4.0 24.1 1.0 N H:ALA64 4.0 25.4 1.0 O H:ALA64 4.1 25.8 1.0 CG1 H:VAL63 4.3 28.0 1.0 CG2 H:THR67 4.3 24.0 1.0 C H:SER66 4.4 26.1 1.0 N H:GLU65 4.5 23.0 1.0 CA H:VAL63 4.5 30.5 1.0 CG I:GLU32 4.6 20.2 1.0 CG I:GLU65 4.7 24.2 1.0 OG1 H:THR67 4.8 22.1 1.0 C H:GLU65 4.8 26.2 1.0 CB I:PRO28 4.8 20.6 1.0 CB I:GLU32 4.9 20.7 1.0 CB H:THR67 4.9 22.2 1.0 CB I:GLU65 5.0 22.3 1.0

Sodium binding site 10 out of 22 in the Crystal Structure of the Sodium Binding Rotor Ring at pH 5.3


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 the Sodium Binding Rotor Ring at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ J:Na90 b:26.8 occ:1.00 OG I:SER66 2.3 23.7 1.0 OE1 J:GLU32 2.4 29.1 1.0 O I:VAL63 2.4 26.2 1.0 O I:HOH2008 2.4 18.2 1.0 OE1 J:GLU65 2.5 31.7 1.0 CD J:GLU32 3.3 26.2 1.0 CD J:GLU65 3.4 30.9 1.0 CB I:SER66 3.4 22.6 1.0 C I:VAL63 3.5 24.9 1.0 OE2 J:GLU32 3.6 27.6 1.0 OE2 J:GLU65 3.6 30.6 1.0 N I:SER66 3.8 18.3 1.0 CA I:ALA64 3.8 25.6 1.0 C I:ALA64 3.9 27.8 1.0 N I:THR67 4.0 21.4 1.0 CA I:SER66 4.0 23.4 1.0 N I:ALA64 4.1 22.3 1.0 O I:ALA64 4.1 29.5 1.0 CG2 I:THR67 4.3 20.5 1.0 CG1 I:VAL63 4.3 20.2 1.0 N I:GLU65 4.5 23.1 1.0 C I:SER66 4.5 24.7 1.0 CA I:VAL63 4.6 24.0 1.0 CG J:GLU32 4.7 25.2 1.0 OG1 I:THR67 4.7 20.2 1.0 CG J:GLU65 4.7 26.6 1.0 C I:GLU65 4.8 23.0 1.0 CB I:THR67 4.9 21.8 1.0 CB J:PRO28 4.9 21.3 1.0 CB J:GLU32 4.9 21.8 1.0

S.Schulz, M.Iglesias-Cans, A.Krah, O.Yildiz, V.Leone, D.Matthies, G.M.Cook, J.D.Faraldo-Gomez, T.Meier. A New Type of Na(+)-Driven Atp Synthase Membrane Rotor with A Two-Carboxylate Ion-Coupling Motif. Plos Biol. V. 11 01596 2013.
ISSN: ISSN 1544-9173
PubMed: 23824040
DOI: 10.1371/JOURNAL.PBIO.1001596