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Sodium in PDB 4bem: Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.

Protein crystallography data

The structure of Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii., PDB code: 4bem was solved by D.Matthies, T.Meier, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.200 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.170, 121.170, 150.570, 90.00, 90.00, 90.00
R / Rfree (%) 18.18 / 21.98

Other elements in 4bem:

The structure of Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii. also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii. (pdb code 4bem). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii., PDB code: 4bem:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 4bem

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Sodium binding site 1 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:45.9
occ:1.00
 O A:HOH2008 2.3 33.9 1.0
OE1 A:GLN29 2.3 43.9 1.0
OG1 J:THR163 2.4 51.6 1.0
OE1 A:GLU62 2.4 42.6 1.0
O J:VAL160 2.4 39.4 1.0
CD A:GLN29 3.2 39.2 1.0
CD A:GLU62 3.3 47.3 1.0
NE2 A:GLN29 3.3 41.4 1.0
OE2 A:GLU62 3.5 54.4 1.0
C J:VAL160 3.6 44.8 1.0
CB J:THR163 3.7 46.5 1.0
N J:THR163 3.8 45.2 1.0
N J:THR164 4.0 41.6 1.0
CG2 J:THR164 4.0 43.1 1.0
CA J:ALA161 4.1 39.2 1.0
C J:ALA161 4.1 35.5 1.0
CA J:THR163 4.2 44.1 1.0
CG2 J:THR163 4.2 49.1 1.0
O J:ALA161 4.3 37.2 1.0
N J:ALA161 4.3 43.2 1.0
CG1 J:VAL160 4.4 42.2 1.0
CB A:PRO25 4.4 37.6 1.0
C J:THR163 4.5 46.6 1.0
N J:GLN162 4.5 43.1 1.0
CG A:GLN29 4.6 35.1 1.0
OG1 J:THR164 4.7 46.7 1.0
CA J:VAL160 4.7 45.5 1.0
CG A:GLU62 4.7 47.3 1.0
C J:GLN162 4.8 42.8 1.0
CB J:THR164 4.8 45.4 1.0
O A:PRO25 4.9 43.7 1.0
C A:PRO25 5.0 45.3 1.0
CB A:GLN29 5.0 36.6 1.0

Sodium binding site 2 out of 10 in 4bem

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Sodium binding site 2 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:52.8
occ:1.00
 O A:HOH2017 2.2 39.3 1.0
OE1 B:GLN29 2.3 51.2 1.0
OG1 A:THR63 2.3 52.6 1.0
OE1 B:GLU62 2.4 51.2 1.0
O A:VAL60 2.4 48.6 1.0
CD B:GLN29 3.2 48.7 1.0
CD B:GLU62 3.3 60.6 1.0
OE2 B:GLU62 3.5 59.7 1.0
C A:VAL60 3.5 49.0 1.0
NE2 B:GLN29 3.5 42.7 1.0
CB A:THR63 3.6 55.1 1.0
N A:THR63 3.9 49.9 1.0
CA A:ALA61 4.0 40.5 1.0
CG2 A:THR64 4.0 59.0 1.0
N A:THR64 4.0 49.8 1.0
CG2 A:THR63 4.0 54.8 1.0
C A:ALA61 4.1 43.2 1.0
N A:ALA61 4.2 46.5 1.0
CA A:THR63 4.2 53.3 1.0
O A:ALA61 4.3 44.8 1.0
CG1 A:VAL60 4.3 48.9 1.0
CB B:PRO25 4.4 42.5 1.0
C A:THR63 4.6 52.8 1.0
OG1 A:THR64 4.6 48.6 1.0
N A:GLU62 4.6 46.4 1.0
CA A:VAL60 4.6 50.1 1.0
CG B:GLN29 4.6 38.6 1.0
CG B:GLU62 4.7 53.5 1.0
CB A:THR64 4.7 53.5 1.0
C A:GLU62 4.8 55.3 1.0
CA A:THR64 5.0 51.5 1.0
O B:PRO25 5.0 41.1 1.0
CB B:GLN29 5.0 44.5 1.0
C B:PRO25 5.0 42.2 1.0

Sodium binding site 3 out of 10 in 4bem

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Sodium binding site 3 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:48.1
occ:1.00
 OE1 C:GLN29 2.2 44.9 1.0
O B:HOH2010 2.3 43.6 1.0
O B:VAL60 2.4 52.6 1.0
OG1 B:THR63 2.4 53.0 1.0
OE1 C:GLU62 2.4 53.9 1.0
CD C:GLN29 3.1 47.2 1.0
CD C:GLU62 3.3 58.8 1.0
NE2 C:GLN29 3.3 47.2 1.0
OE2 C:GLU62 3.5 59.1 1.0
C B:VAL60 3.5 52.1 1.0
CB B:THR63 3.7 54.6 1.0
N B:THR63 4.0 59.7 1.0
CA B:ALA61 4.1 46.6 1.0
N B:THR64 4.1 49.9 1.0
CG1 B:VAL60 4.2 49.6 1.0
CG2 B:THR64 4.2 47.7 1.0
C B:ALA61 4.2 46.8 1.0
N B:ALA61 4.2 51.2 1.0
CG2 B:THR63 4.3 49.9 1.0
CA B:THR63 4.3 55.3 1.0
O B:ALA61 4.4 45.9 1.0
CB C:PRO25 4.4 39.8 1.0
CG C:GLN29 4.5 40.3 1.0
CA B:VAL60 4.6 49.0 1.0
C B:THR63 4.7 57.4 1.0
CG C:GLU62 4.7 54.7 1.0
OG1 B:THR64 4.7 51.5 1.0
N B:GLU62 4.7 46.8 1.0
O C:PRO25 4.9 45.1 1.0
CB B:THR64 4.9 49.5 1.0
CB C:GLN29 5.0 38.1 1.0
C B:GLU62 5.0 58.3 1.0

Sodium binding site 4 out of 10 in 4bem

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Sodium binding site 4 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:52.7
occ:1.00
 OE1 D:GLN29 2.2 50.2 1.0
O C:HOH2009 2.3 44.1 1.0
O C:VAL60 2.3 57.3 1.0
OG1 C:THR63 2.4 46.3 1.0
OE1 D:GLU62 2.4 52.8 1.0
CD D:GLN29 3.2 47.7 1.0
CD D:GLU62 3.4 58.3 1.0
C C:VAL60 3.4 57.5 1.0
NE2 D:GLN29 3.4 48.6 1.0
CB C:THR63 3.6 59.2 1.0
OE2 D:GLU62 3.6 57.7 1.0
N C:THR63 3.8 55.6 1.0
CA C:ALA61 3.9 48.7 1.0
C C:ALA61 3.9 50.9 1.0
N C:THR64 3.9 50.8 1.0
CG2 C:THR63 4.0 49.8 1.0
N C:ALA61 4.0 47.5 1.0
O C:ALA61 4.0 46.1 1.0
CA C:THR63 4.1 54.9 1.0
CG2 C:THR64 4.2 52.1 1.0
CG1 C:VAL60 4.2 52.3 1.0
N C:GLU62 4.5 52.3 1.0
C C:THR63 4.5 57.0 1.0
CB D:PRO25 4.5 40.0 1.0
CA C:VAL60 4.5 54.8 1.0
CG D:GLN29 4.6 41.9 1.0
OG1 C:THR64 4.6 48.1 1.0
C C:GLU62 4.8 58.1 1.0
CG D:GLU62 4.8 57.8 1.0
CB C:THR64 4.8 48.6 1.0
CB D:GLN29 4.9 40.1 1.0
O D:PRO25 4.9 42.7 1.0
CA C:THR64 5.0 50.1 1.0

Sodium binding site 5 out of 10 in 4bem

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Sodium binding site 5 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na201

b:48.8
occ:1.00
 OE1 E:GLN29 2.3 44.9 1.0
OG1 D:THR63 2.3 46.7 1.0
O D:HOH2010 2.3 40.4 1.0
OE1 E:GLU62 2.4 54.5 1.0
O D:VAL60 2.4 49.1 1.0
CD E:GLN29 3.2 45.7 1.0
CD E:GLU62 3.2 54.0 1.0
OE2 E:GLU62 3.4 54.6 1.0
C D:VAL60 3.4 54.5 1.0
NE2 E:GLN29 3.5 44.5 1.0
CB D:THR63 3.6 56.0 1.0
CA D:ALA61 3.9 47.9 1.0
N D:THR63 3.9 53.3 1.0
N D:THR64 4.0 54.7 1.0
C D:ALA61 4.0 54.6 1.0
CG2 D:THR64 4.1 49.0 1.0
N D:ALA61 4.1 45.8 1.0
CG2 D:THR63 4.1 58.3 1.0
CG1 D:VAL60 4.1 51.0 1.0
O D:ALA61 4.2 47.2 1.0
CA D:THR63 4.2 59.0 1.0
CB E:PRO25 4.5 43.5 1.0
CA D:VAL60 4.6 53.3 1.0
N D:GLU62 4.6 51.8 1.0
C D:THR63 4.6 60.3 1.0
CG E:GLN29 4.6 40.5 1.0
CG E:GLU62 4.7 52.9 1.0
OG1 D:THR64 4.7 48.8 1.0
CB D:THR64 4.8 48.7 1.0
C D:GLU62 4.9 51.1 1.0
O E:PRO25 4.9 46.2 1.0
CA D:THR64 5.0 54.3 1.0

Sodium binding site 6 out of 10 in 4bem

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Sodium binding site 6 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na201

b:43.2
occ:1.00
 OE1 F:GLN29 2.3 41.0 1.0
OG1 E:THR63 2.3 44.5 1.0
O E:VAL60 2.3 48.8 1.0
OE1 F:GLU62 2.4 47.6 1.0
O E:HOH2010 2.5 38.1 1.0
CD F:GLN29 3.2 45.0 1.0
CD F:GLU62 3.3 48.9 1.0
NE2 F:GLN29 3.5 44.6 1.0
C E:VAL60 3.5 53.9 1.0
OE2 F:GLU62 3.5 53.0 1.0
CB E:THR63 3.6 47.7 1.0
N E:THR63 3.9 43.2 1.0
CA E:ALA61 3.9 44.3 1.0
C E:ALA61 4.0 44.8 1.0
CG2 E:THR63 4.0 46.4 1.0
N E:THR64 4.1 44.3 1.0
N E:ALA61 4.1 43.8 1.0
CA E:THR63 4.1 51.4 1.0
O E:ALA61 4.2 46.4 1.0
CG2 E:THR64 4.3 41.4 1.0
CG1 E:VAL60 4.3 45.4 1.0
CB F:PRO25 4.5 33.8 1.0
N E:GLU62 4.6 46.2 1.0
C E:THR63 4.6 51.2 1.0
CG F:GLN29 4.6 41.4 1.0
CA E:VAL60 4.6 53.4 1.0
OG1 E:THR64 4.7 48.8 1.0
CG F:GLU62 4.7 49.9 1.0
C E:GLU62 4.9 48.5 1.0
O F:PRO25 4.9 45.1 1.0
CB E:THR64 5.0 45.8 1.0
C7' F:HTG1083 5.0 80.2 1.0

Sodium binding site 7 out of 10 in 4bem

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Sodium binding site 7 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na201

b:38.6
occ:1.00
 OE1 G:GLN29 2.2 37.2 1.0
OG1 F:THR63 2.3 44.2 1.0
O F:VAL60 2.3 43.3 1.0
OE1 G:GLU62 2.4 38.0 1.0
O F:HOH2009 2.4 39.2 1.0
CD G:GLN29 3.1 39.1 1.0
NE2 G:GLN29 3.3 40.6 1.0
CD G:GLU62 3.4 46.6 1.0
C F:VAL60 3.4 46.0 1.0
CB F:THR63 3.6 48.5 1.0
OE2 G:GLU62 3.6 47.6 1.0
CA F:ALA61 3.9 38.3 1.0
N F:THR63 3.9 38.7 1.0
C F:ALA61 4.0 42.9 1.0
N F:ALA61 4.0 39.1 1.0
CG2 F:THR63 4.1 49.2 1.0
N F:THR64 4.1 44.4 1.0
O F:ALA61 4.1 39.0 1.0
CA F:THR63 4.2 49.4 1.0
CG1 F:VAL60 4.2 40.6 1.0
CG2 F:THR64 4.3 36.4 1.0
CB G:PRO25 4.5 36.2 1.0
CG G:GLN29 4.5 34.9 1.0
CA F:VAL60 4.5 46.0 1.0
C F:THR63 4.6 49.6 1.0
N F:GLU62 4.6 40.2 1.0
OG1 F:THR64 4.7 37.2 1.0
CG G:GLU62 4.8 39.9 1.0
O G:PRO25 4.9 39.0 1.0
C F:GLU62 4.9 44.5 1.0
CB G:GLN29 4.9 35.3 1.0
CB F:VAL60 5.0 46.7 1.0
CB F:THR64 5.0 42.2 1.0
C G:PRO25 5.0 39.3 1.0

Sodium binding site 8 out of 10 in 4bem

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Sodium binding site 8 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na201

b:38.4
occ:1.00
 OE1 H:GLN29 2.3 41.2 1.0
OG1 G:THR63 2.3 40.0 1.0
O G:VAL60 2.3 43.7 1.0
O G:HOH2010 2.4 34.8 1.0
OE1 H:GLU62 2.5 41.4 1.0
CD H:GLN29 3.3 39.3 1.0
CD H:GLU62 3.4 43.7 1.0
C G:VAL60 3.4 47.5 1.0
NE2 H:GLN29 3.6 34.2 1.0
OE2 H:GLU62 3.6 42.1 1.0
CB G:THR63 3.6 41.2 1.0
N G:THR63 3.8 39.2 1.0
CA G:ALA61 4.0 37.5 1.0
N G:THR64 4.0 35.8 1.0
C G:ALA61 4.0 35.8 1.0
CG2 G:THR63 4.1 38.8 1.0
N G:ALA61 4.1 38.9 1.0
CA G:THR63 4.1 41.6 1.0
O G:ALA61 4.2 40.9 1.0
CG2 G:THR64 4.2 36.4 1.0
CG1 G:VAL60 4.2 38.0 1.0
N G:GLU62 4.5 33.8 1.0
C G:THR63 4.5 43.7 1.0
CA G:VAL60 4.5 44.7 1.0
CB H:PRO25 4.6 30.3 1.0
CG H:GLN29 4.7 36.1 1.0
OG1 G:THR64 4.7 43.9 1.0
CG H:GLU62 4.8 37.6 1.0
C G:GLU62 4.8 44.0 1.0
CB G:THR64 4.9 41.6 1.0
O H:PRO25 4.9 34.0 1.0

Sodium binding site 9 out of 10 in 4bem

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Sodium binding site 9 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na201

b:39.4
occ:1.00
 OG1 H:THR63 2.3 36.9 1.0
O H:VAL60 2.3 37.5 1.0
OE1 I:GLN29 2.3 37.8 1.0
O H:HOH2015 2.4 35.0 1.0
OE1 I:GLU62 2.4 38.0 1.0
CD I:GLN29 3.3 37.8 1.0
CD I:GLU62 3.3 40.3 1.0
C H:VAL60 3.4 39.8 1.0
OE2 I:GLU62 3.5 40.9 1.0
CB H:THR63 3.5 41.9 1.0
NE2 I:GLN29 3.6 33.4 1.0
N H:THR63 3.7 35.2 1.0
CA H:ALA61 3.9 33.4 1.0
C H:ALA61 4.0 36.4 1.0
N H:THR64 4.0 35.5 1.0
CG2 H:THR63 4.0 36.0 1.0
CA H:THR63 4.0 36.5 1.0
N H:ALA61 4.1 32.3 1.0
CG1 H:VAL60 4.1 37.1 1.0
CG2 H:THR64 4.1 36.3 1.0
O H:ALA61 4.2 37.7 1.0
C H:THR63 4.5 41.0 1.0
N H:GLU62 4.5 34.0 1.0
CA H:VAL60 4.5 40.6 1.0
CB I:PRO25 4.5 28.0 1.0
CG I:GLN29 4.7 30.6 1.0
OG1 H:THR64 4.7 36.6 1.0
C H:GLU62 4.7 39.6 1.0
CG I:GLU62 4.8 36.6 1.0
CB H:THR64 4.9 37.2 1.0
O I:PRO25 4.9 35.6 1.0
CB H:VAL60 5.0 39.9 1.0

Sodium binding site 10 out of 10 in 4bem

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Sodium binding site 10 out of 10 in the Crystal Structure of the F-Type Atp Synthase C-Ring From Acetobacterium Woodii.


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 F-Type Atp Synthase C-Ring From Acetobacterium Woodii. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na201

b:38.7
occ:1.00
 OG1 I:THR63 2.3 38.3 1.0
OE1 J:GLN46 2.3 36.6 1.0
O I:VAL60 2.3 36.6 1.0
O I:HOH2011 2.4 35.4 1.0
OE1 J:GLU79 2.4 40.3 1.0
CD J:GLN46 3.2 35.4 1.0
CD J:GLU79 3.3 45.5 1.0
C I:VAL60 3.4 41.8 1.0
NE2 J:GLN46 3.5 35.9 1.0
OE2 J:GLU79 3.5 41.4 1.0
CB I:THR63 3.5 41.3 1.0
N I:THR63 3.7 34.1 1.0
CA I:ALA61 3.9 31.0 1.0
N I:THR64 4.0 36.0 1.0
C I:ALA61 4.0 37.3 1.0
CA I:THR63 4.0 39.6 1.0
N I:ALA61 4.1 31.4 1.0
CG2 I:THR63 4.1 34.9 1.0
O I:ALA61 4.2 37.3 1.0
CG2 I:THR64 4.2 34.9 1.0
CG1 I:VAL60 4.3 42.5 1.0
C I:THR63 4.5 39.4 1.0
CB J:PRO42 4.5 35.3 1.0
N I:GLU62 4.5 33.8 1.0
CA I:VAL60 4.6 45.4 1.0
CG J:GLN46 4.6 29.3 1.0
OG1 I:THR64 4.7 38.0 1.0
CG J:GLU79 4.7 39.2 1.0
C I:GLU62 4.7 43.3 1.0
CB I:THR64 4.9 37.7 1.0
O J:PRO42 5.0 36.7 1.0
CB J:GLN46 5.0 28.9 1.0

Reference:

D.Matthies, W.Zhou, A.L.Klyszejko, C.Anselmi, O.Yildiz, K.Brandt, V.Muller, J.D.Faraldo-Gomez, T.Meier. High-Resolution Structure and Mechanism of An F/V-Hybrid Rotor Ring in A Na+-Coupled Atp Synthase Nat.Commun. 2014.
ISSN: ESSN 2041-1723
DOI: 10.1038/NCOMMS6286
Page generated: Mon Oct 7 14:31:04 2024

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