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Sodium in PDB 4cbk: The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology

Protein crystallography data

The structure of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology, PDB code: 4cbk was solved by L.Preiss, O.Yildiz, T.Meier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.004 / 2.42
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.790, 96.750, 118.330, 90.00, 105.38, 90.00
R / Rfree (%) 19.49 / 22.83

Sodium Binding Sites:

The binding sites of Sodium atom in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology (pdb code 4cbk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology, PDB code: 4cbk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 4cbk

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Sodium binding site 1 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:78.0
occ:1.00
 OE1 B:GLU30 2.5 60.8 1.0
OE2 C:GLU30 2.6 55.2 1.0
O B:HOH2002 3.1 49.3 1.0
CD C:GLU30 3.5 60.1 1.0
CG C:GLU30 3.5 51.3 1.0
CD B:GLU30 3.6 60.8 1.0
CA B:ALA27 3.9 42.4 1.0
CB B:GLU30 4.0 36.7 1.0
CE C:LYS26 4.1 59.3 1.0
CB B:ALA27 4.1 28.6 1.0
CG B:GLU30 4.3 58.9 1.0
O C:HOH2004 4.4 50.3 1.0
OE2 B:GLU30 4.4 58.3 1.0
O B:ALA27 4.5 37.4 1.0
O B:HOH2001 4.6 53.9 1.0
CG C:LYS26 4.7 45.1 1.0
OE1 C:GLU30 4.7 62.3 1.0
C B:ALA27 4.7 48.5 1.0
N B:ALA27 4.8 41.1 1.0
C7 B:DPV200 4.9 0.4 1.0
CB C:GLU30 5.0 33.4 1.0
O B:LYS26 5.0 44.0 1.0

Sodium binding site 2 out of 10 in 4cbk

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Sodium binding site 2 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:77.4
occ:1.00
 OE1 C:GLU30 2.5 62.3 1.0
OE2 D:GLU30 2.8 62.0 1.0
O C:HOH2003 2.8 39.3 1.0
CA C:ALA27 3.4 48.4 1.0
CG D:GLU30 3.4 45.4 1.0
CD D:GLU30 3.5 65.1 1.0
CD C:GLU30 3.6 60.1 1.0
CB C:ALA27 3.7 30.2 1.0
CB C:GLU30 3.9 33.4 1.0
CE D:LYS26 4.0 61.1 1.0
O C:ALA27 4.0 41.4 1.0
C C:ALA27 4.2 48.7 1.0
CG C:GLU30 4.2 51.3 1.0
O C:HOH2002 4.2 56.3 1.0
N C:ALA27 4.3 36.5 1.0
CG D:LYS26 4.4 49.1 1.0
O C:HOH2001 4.5 42.6 1.0
OE2 C:GLU30 4.5 55.2 1.0
O C:LYS26 4.6 42.1 1.0
C7 C:DPV200 4.6 98.5 1.0
C6 C:DPV200 4.6 80.1 1.0
CD D:LYS26 4.7 58.8 1.0
OE1 D:GLU30 4.8 78.3 1.0
C C:LYS26 4.8 50.5 1.0
CB D:GLU30 4.9 33.2 1.0

Sodium binding site 3 out of 10 in 4cbk

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Sodium binding site 3 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:62.7
occ:1.00
 OE1 D:GLU30 2.5 78.3 1.0
OE2 E:GLU30 2.5 60.6 1.0
O D:HOH2002 2.7 34.5 1.0
CG E:GLU30 3.3 45.0 1.0
CD E:GLU30 3.3 59.2 1.0
CD D:GLU30 3.6 65.1 1.0
CA D:ALA27 3.6 35.9 1.0
C7 D:DPV200 3.8 84.7 1.0
CB D:ALA27 3.8 33.4 1.0
CB D:GLU30 3.8 33.2 1.0
O E:HOH2005 4.1 50.1 1.0
O D:ALA27 4.2 32.0 1.0
CG D:GLU30 4.2 45.4 1.0
C D:ALA27 4.4 37.3 1.0
O D:HOH2001 4.4 59.9 1.0
CE E:LYS26 4.4 61.1 1.0
OE1 E:GLU30 4.5 58.0 1.0
OE2 D:GLU30 4.5 62.0 1.0
N D:ALA27 4.6 36.0 1.0
N D:DPV200 4.7 98.7 1.0
C6 D:DPV200 4.7 80.3 1.0
CB E:GLU30 4.7 35.1 1.0
C8 D:DPV200 4.8 0.5 1.0
CG E:LYS26 4.8 40.7 1.0
O D:LYS26 4.9 42.3 1.0

Sodium binding site 4 out of 10 in 4cbk

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Sodium binding site 4 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na101

b:58.5
occ:1.00
 OE2 F:GLU30 2.5 59.1 1.0
O E:HOH2003 2.7 40.4 1.0
OE1 E:GLU30 2.8 58.0 1.0
CG F:GLU30 3.2 48.3 1.0
CD F:GLU30 3.2 62.8 1.0
CA E:ALA27 3.9 34.9 1.0
CD E:GLU30 3.9 59.2 1.0
CB E:ALA27 4.1 33.6 1.0
CE F:LYS26 4.1 54.1 1.0
CB E:GLU30 4.1 35.1 1.0
O E:HOH2001 4.1 46.6 1.0
O E:ALA27 4.4 37.8 1.0
OE1 F:GLU30 4.4 70.3 1.0
CG E:GLU30 4.5 45.0 1.0
O E:HOH2002 4.5 52.8 1.0
CG F:LYS26 4.6 38.9 1.0
CB F:GLU30 4.7 34.5 1.0
C E:ALA27 4.7 39.2 1.0
N E:ALA27 4.8 29.1 1.0
OE2 E:GLU30 4.9 60.6 1.0
CD F:LYS26 4.9 60.1 1.0

Sodium binding site 5 out of 10 in 4cbk

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Sodium binding site 5 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na101

b:70.3
occ:1.00
 OE2 G:GLU30 2.5 51.8 1.0
OE1 F:GLU30 2.7 70.3 1.0
O F:HOH2002 3.0 37.1 1.0
C7 F:DPV200 3.2 86.0 1.0
NZ G:LYS26 3.3 75.0 1.0
CD G:GLU30 3.3 56.9 1.0
CG G:GLU30 3.4 45.0 1.0
CD F:GLU30 3.8 62.8 1.0
CA F:ALA27 3.9 35.7 1.0
CB F:GLU30 4.1 34.5 1.0
CB F:ALA27 4.1 24.9 1.0
O G:HOH2004 4.2 44.0 1.0
O F:ALA27 4.4 36.5 1.0
CE G:LYS26 4.4 54.0 1.0
OE1 G:GLU30 4.5 57.1 1.0
CG F:GLU30 4.5 48.3 1.0
N F:DPV200 4.5 0.9 1.0
O F:HOH2001 4.6 55.0 1.0
C F:ALA27 4.7 32.7 1.0
CG G:LYS26 4.7 38.6 1.0
OE2 F:GLU30 4.7 59.1 1.0
N F:ALA27 4.8 30.0 1.0
CB G:GLU30 4.9 35.6 1.0
C8 F:DPV200 4.9 95.3 1.0
O F:LYS26 5.0 35.8 1.0

Sodium binding site 6 out of 10 in 4cbk

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Sodium binding site 6 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na101

b:71.4
occ:1.00
 OE1 G:GLU30 2.5 57.1 1.0
O G:HOH2003 2.9 36.7 1.0
OE2 H:GLU30 3.2 63.9 1.0
CG H:GLU30 3.3 53.9 1.0
CD G:GLU30 3.5 56.9 1.0
CD H:GLU30 3.6 64.9 1.0
CB G:GLU30 3.8 35.6 1.0
CA G:ALA27 3.8 32.1 1.0
CB G:ALA27 4.1 34.0 1.0
O G:HOH2001 4.1 49.8 1.0
C7 G:DPV200 4.2 86.9 1.0
CG G:GLU30 4.2 45.0 1.0
CE H:LYS26 4.3 66.2 1.0
O G:ALA27 4.3 35.1 1.0
OE2 G:GLU30 4.5 51.8 1.0
C8 G:DPV200 4.5 85.4 1.0
C G:ALA27 4.6 33.0 1.0
OE1 H:GLU30 4.6 80.8 1.0
CG H:LYS26 4.7 46.8 1.0
N G:ALA27 4.8 27.6 1.0
CB H:GLU30 4.8 46.1 1.0
O G:HOH2002 4.8 52.9 1.0
N G:DPV200 4.8 0.2 1.0
O G:LYS26 4.9 36.5 1.0

Sodium binding site 7 out of 10 in 4cbk

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Sodium binding site 7 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na101

b:60.4
occ:1.00
 OE1 H:GLU30 2.9 80.8 1.0
O H:HOH2002 3.0 38.5 1.0
OE2 I:GLU30 3.0 59.8 1.0
CD H:GLU30 3.2 64.9 1.0
NZ I:LYS26 3.2 90.5 1.0
CB H:GLU30 3.6 46.1 1.0
OE2 H:GLU30 3.6 63.9 1.0
CG I:GLU30 3.7 42.1 1.0
CA H:ALA27 3.7 39.1 1.0
CD I:GLU30 3.8 58.6 1.0
CG H:GLU30 3.8 53.9 1.0
CB H:ALA27 4.1 38.2 1.0
O H:HOH2004 4.2 50.4 1.0
C8 H:DPV200 4.2 99.4 1.0
O H:ALA27 4.3 36.5 1.0
C H:ALA27 4.5 36.1 1.0
N H:ALA27 4.5 33.1 1.0
O H:HOH2001 4.6 54.4 1.0
CE I:LYS26 4.6 62.7 1.0
O H:LYS26 4.7 35.6 1.0
C5 H:DPV200 4.8 90.2 1.0
NH1 H:ARG34 4.9 74.8 1.0
CG I:LYS26 4.9 37.1 1.0
C H:LYS26 4.9 39.2 1.0
CA H:GLU30 5.0 40.0 1.0
OE1 I:GLU30 5.0 63.1 1.0

Sodium binding site 8 out of 10 in 4cbk

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Sodium binding site 8 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na101

b:63.6
occ:1.00
 OE1 I:GLU30 2.7 63.1 1.0
OE2 J:GLU30 2.7 58.4 1.0
O I:HOH2002 2.7 42.9 1.0
CG J:GLU30 3.2 49.9 1.0
CD J:GLU30 3.3 55.9 1.0
CA I:ALA27 3.7 35.7 1.0
CD I:GLU30 3.8 58.6 1.0
CB I:ALA27 3.8 31.4 1.0
CB I:GLU30 4.1 34.6 1.0
O I:ALA27 4.1 35.6 1.0
O I:HOH2003 4.2 50.1 1.0
CE J:LYS26 4.3 58.1 1.0
C I:ALA27 4.4 34.3 1.0
CG I:GLU30 4.5 42.1 1.0
CG J:LYS26 4.5 34.2 1.0
OE1 J:GLU30 4.6 74.0 1.0
CB J:GLU30 4.6 35.4 1.0
OE2 I:GLU30 4.7 59.8 1.0
N I:ALA27 4.7 39.8 1.0
NH1 I:ARG34 4.8 83.8 1.0
O I:HOH2001 4.8 53.2 1.0
O I:LYS26 5.0 34.8 1.0
CD J:LYS26 5.0 59.6 1.0

Sodium binding site 9 out of 10 in 4cbk

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Sodium binding site 9 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na101

b:66.1
occ:1.00
 OE2 L:GLU30 2.5 60.0 1.0
OE1 K:GLU30 2.7 57.3 1.0
O K:HOH2003 2.8 44.5 1.0
CG L:GLU30 3.0 54.3 1.0
CD L:GLU30 3.1 63.0 1.0
NZ L:LYS26 3.6 59.0 1.0
CD K:GLU30 3.9 59.6 1.0
CA K:ALA27 4.1 36.8 1.0
CB K:GLU30 4.1 39.6 1.0
O K:HOH2001 4.1 53.1 1.0
CB K:ALA27 4.2 32.0 1.0
OE1 L:GLU30 4.3 70.2 1.0
O K:ALA27 4.4 38.2 1.0
CB L:GLU30 4.5 43.9 1.0
CG K:GLU30 4.6 54.2 1.0
C6 K:DPV200 4.6 98.0 1.0
CG L:LYS26 4.6 40.8 1.0
C K:ALA27 4.8 41.6 1.0
O K:HOH2002 4.8 49.9 1.0
CE L:LYS26 4.8 58.9 1.0
OE2 K:GLU30 4.8 63.6 1.0
CD L:LYS26 4.9 66.1 1.0

Sodium binding site 10 out of 10 in 4cbk

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Sodium binding site 10 out of 10 in the The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The C-Ring Ion Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Cell Physiology within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na101

b:71.3
occ:1.00
 OE1 L:GLU30 2.5 70.2 1.0
OE2 M:GLU30 2.5 69.1 1.0
O L:HOH2002 2.8 55.3 1.0
CG M:GLU30 3.2 65.0 1.0
CD M:GLU30 3.2 61.6 1.0
CD L:GLU30 3.6 63.0 1.0
CB L:GLU30 3.8 43.9 1.0
CA L:ALA27 4.0 38.6 1.0
O L:HOH2001 4.2 42.0 1.0
CE M:LYS26 4.2 74.3 1.0
CB L:ALA27 4.2 27.6 1.0
CG L:GLU30 4.2 54.3 1.0
O L:ALA27 4.4 41.3 1.0
OE2 L:GLU30 4.5 60.0 1.0
OE1 M:GLU30 4.5 63.4 1.0
CB M:GLU30 4.6 33.4 1.0
C L:ALA27 4.7 41.7 1.0
CG M:LYS26 4.8 56.1 1.0
N L:ALA27 4.9 36.7 1.0

Reference:

L.Preiss, J.D.Langer, D.B.Hicks, J.Liu, O.Yildiz, T.A.Krulwich, T.Meier. The C-Ring Ion-Binding Site of the Atp Synthase From Bacillus Pseudofirmus OF4 Is Adapted to Alkaliphilic Lifestyle. Mol.Microbiol. V. 92 973 2014.
ISSN: ISSN 0950-382X
PubMed: 24707994
DOI: 10.1111/MMI.12605
Page generated: Tue Dec 15 06:35:30 2020

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