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Sodium in PDB 2x2v: Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring

Protein crystallography data

The structure of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring, PDB code: 2x2v was solved by L.Preiss, O.Yildiz, D.B.Hicks, T.A.Krulwich, T.Meier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.951 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.180, 97.340, 121.240, 90.00, 104.73, 90.00
R / Rfree (%) 18.76 / 23.45

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring (pdb code 2x2v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring, PDB code: 2x2v:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 2x2v

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Sodium binding site 1 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:71.1
occ:1.00
 O B:HOH2002 3.0 43.9 1.0
OE2 C:GLU30 3.0 61.6 1.0
O B:HOH2006 3.0 62.6 1.0
OE2 B:GLU30 3.1 66.5 1.0
CG C:GLU30 3.6 48.5 1.0
CA B:ALA27 3.6 34.2 1.0
CD C:GLU30 3.6 58.5 1.0
CB B:ALA27 3.9 26.8 1.0
CB B:GLU30 4.0 41.5 1.0
CD B:GLU30 4.1 70.1 1.0
CE C:LYS26 4.1 52.7 1.0
O B:ALA27 4.2 41.8 1.0
CG B:GLU30 4.3 57.4 1.0
C B:ALA27 4.4 42.7 1.0
O C:HOH2003 4.4 48.8 1.0
N B:ALA27 4.5 41.6 1.0
O B:HOH2001 4.5 53.1 1.0
CG C:LYS26 4.7 50.8 1.0
OE1 C:GLU30 4.8 62.7 1.0
C7 B:DPV200 4.8 0.7 1.0
C8 B:DPV200 4.8 0.2 1.0
O B:LYS26 4.8 37.6 1.0
NZ C:LYS26 4.9 58.9 1.0
CB C:GLU30 5.0 40.2 1.0

Sodium binding site 2 out of 10 in 2x2v

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Sodium binding site 2 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na101

b:78.5
occ:1.00
 OE1 C:GLU30 2.9 62.7 1.0
OE2 D:GLU30 2.9 58.7 1.0
O C:HOH2002 3.0 39.4 1.0
CG D:GLU30 3.4 46.3 1.0
CD D:GLU30 3.5 61.9 1.0
CA C:ALA27 3.6 41.1 1.0
CD C:GLU30 3.7 58.5 1.0
CE D:LYS26 3.7 55.3 1.0
CB C:ALA27 3.9 36.3 1.0
CB C:GLU30 4.0 40.2 1.0
O C:ALA27 4.2 37.8 1.0
CG C:GLU30 4.3 48.5 1.0
CG D:LYS26 4.4 41.4 1.0
O C:HOH2001 4.4 59.6 1.0
O D:HOH2002 4.4 39.5 1.0
C C:ALA27 4.4 43.3 1.0
N C:ALA27 4.4 42.0 1.0
OE2 C:GLU30 4.5 61.6 1.0
OE1 D:GLU30 4.5 78.1 1.0
CD D:LYS26 4.7 46.9 1.0
NZ D:LYS26 4.8 63.0 1.0
O C:LYS26 4.8 49.5 1.0
C7 C:DPV200 4.9 0.6 1.0
CB D:GLU30 4.9 32.8 1.0
C C:LYS26 5.0 46.5 1.0

Sodium binding site 3 out of 10 in 2x2v

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Sodium binding site 3 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na101

b:78.8
occ:1.00
 OE1 D:GLU30 2.9 78.1 1.0
OE2 E:GLU30 3.0 55.8 1.0
O D:HOH2001 3.1 43.3 1.0
CD D:GLU30 3.4 61.9 1.0
CA D:ALA27 3.6 38.3 1.0
CD E:GLU30 3.7 55.1 1.0
CG E:GLU30 3.8 44.5 1.0
CB D:GLU30 3.8 32.8 1.0
C7 D:DPV200 3.9 0.3 1.0
OE2 D:GLU30 3.9 58.7 1.0
CE E:LYS26 3.9 47.8 1.0
CG D:GLU30 4.0 46.3 1.0
CB D:ALA27 4.0 30.0 1.0
O D:HOH2004 4.1 67.1 1.0
O D:ALA27 4.2 42.7 1.0
C6 D:DPV200 4.4 0.6 1.0
N D:ALA27 4.4 43.9 1.0
C D:ALA27 4.4 43.0 1.0
O E:HOH2003 4.6 44.7 1.0
CG E:LYS26 4.7 38.8 1.0
O D:LYS26 4.7 53.0 1.0
N D:DPV200 4.7 0.9 1.0
OE1 E:GLU30 4.8 59.7 1.0
C D:LYS26 4.9 49.1 1.0
CD E:LYS26 4.9 38.5 1.0
NZ E:LYS26 5.0 57.8 1.0

Sodium binding site 4 out of 10 in 2x2v

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Sodium binding site 4 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na101

b:56.8
occ:1.00
 OE1 E:GLU30 2.8 59.7 1.0
OE2 F:GLU30 2.9 54.3 1.0
O E:HOH2008 3.1 73.5 1.0
O E:HOH2002 3.1 45.5 1.0
CD E:GLU30 3.5 55.1 1.0
CA E:ALA27 3.6 38.0 1.0
CD F:GLU30 3.7 56.1 1.0
CG F:GLU30 3.8 51.2 1.0
CE F:LYS26 3.8 49.6 1.0
CB E:GLU30 4.0 36.3 1.0
CB E:ALA27 4.0 37.0 1.0
OE2 E:GLU30 4.2 55.8 1.0
CG E:GLU30 4.3 44.5 1.0
O E:ALA27 4.4 36.3 1.0
N E:ALA27 4.5 37.5 1.0
C E:ALA27 4.5 40.8 1.0
O E:HOH2001 4.5 46.4 1.0
CG F:LYS26 4.6 34.4 1.0
C6 E:DPV200 4.6 0.9 1.0
O E:LYS26 4.7 50.0 1.0
NZ F:LYS26 4.8 59.9 1.0
CD F:LYS26 4.8 41.6 1.0
OE1 F:GLU30 4.9 64.2 1.0
C E:LYS26 4.9 43.8 1.0

Sodium binding site 5 out of 10 in 2x2v

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Sodium binding site 5 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na101

b:69.1
occ:1.00
 OE1 F:GLU30 2.8 64.2 1.0
OE2 G:GLU30 2.8 53.2 1.0
O F:HOH2002 3.1 43.2 1.0
CA F:ALA27 3.5 30.6 1.0
CG G:GLU30 3.6 48.7 1.0
CD G:GLU30 3.6 57.6 1.0
CB F:ALA27 3.7 26.2 1.0
CD F:GLU30 3.7 56.1 1.0
CE G:LYS26 3.8 56.0 1.0
CB F:GLU30 4.0 37.6 1.0
O F:ALA27 4.3 39.5 1.0
O F:HOH2001 4.4 65.4 1.0
CG G:LYS26 4.4 32.9 1.0
C F:ALA27 4.4 37.7 1.0
CG F:GLU30 4.5 51.2 1.0
N F:ALA27 4.5 29.6 1.0
OE2 F:GLU30 4.5 54.3 1.0
O F:HOH2003 4.6 41.7 1.0
NZ G:LYS26 4.7 66.1 1.0
CD G:LYS26 4.8 40.0 1.0
O F:LYS26 4.8 39.5 1.0
C8 F:DPV200 4.8 0.3 1.0
OE1 G:GLU30 4.9 69.0 1.0
C F:LYS26 5.0 36.0 1.0
C6 F:DPV200 5.0 0.1 1.0

Sodium binding site 6 out of 10 in 2x2v

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Sodium binding site 6 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na101

b:58.3
occ:1.00
 OE2 H:GLU30 2.9 80.3 1.0
O H:HOH2001 2.9 42.8 1.0
OE2 I:GLU30 3.0 56.0 1.0
CG I:GLU30 3.5 40.7 1.0
CD I:GLU30 3.6 56.3 1.0
CA H:ALA27 3.6 32.2 1.0
CD H:GLU30 3.8 68.7 1.0
CB H:GLU30 3.9 33.6 1.0
CB H:ALA27 3.9 30.9 1.0
CE I:LYS26 4.0 50.4 1.0
O H:ALA27 4.2 33.6 1.0
C8 H:DPV200 4.3 0.1 1.0
O I:HOH2005 4.3 44.2 1.0
CG H:GLU30 4.4 49.4 1.0
C H:ALA27 4.5 34.8 1.0
N H:ALA27 4.5 30.2 1.0
CG I:LYS26 4.6 31.6 1.0
OE1 H:GLU30 4.7 76.3 1.0
O H:LYS26 4.8 36.7 1.0
OE1 I:GLU30 4.8 60.8 1.0
C5 H:DPV200 4.8 0.7 1.0
CB I:GLU30 4.9 29.2 1.0
CD I:LYS26 5.0 34.6 1.0

Sodium binding site 7 out of 10 in 2x2v

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Sodium binding site 7 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na101

b:74.4
occ:1.00
 OE1 I:GLU30 2.8 60.8 1.0
OE2 J:GLU30 3.0 58.4 1.0
O I:HOH2002 3.0 46.7 1.0
O I:HOH2001 3.1 70.7 1.0
CG J:GLU30 3.4 48.0 1.0
CA I:ALA27 3.5 29.6 1.0
CD J:GLU30 3.5 56.7 1.0
CD I:GLU30 3.6 56.3 1.0
CB I:ALA27 3.7 30.8 1.0
CE J:LYS26 3.9 51.0 1.0
O I:HOH2004 4.0 58.7 1.0
CB I:GLU30 4.0 29.2 1.0
O I:ALA27 4.1 33.9 1.0
C I:ALA27 4.3 34.8 1.0
CG I:GLU30 4.3 40.7 1.0
O J:HOH2005 4.4 73.2 1.0
OE2 I:GLU30 4.4 56.0 1.0
O J:HOH2004 4.5 44.7 1.0
CG J:LYS26 4.5 33.3 1.0
O I:HOH2011 4.5 58.7 1.0
N I:ALA27 4.5 36.2 1.0
OE1 J:GLU30 4.6 71.1 1.0
CB J:GLU30 4.8 39.6 1.0
CD J:LYS26 4.8 40.3 1.0
O I:LYS26 4.9 34.4 1.0
NZ J:LYS26 4.9 61.9 1.0

Sodium binding site 8 out of 10 in 2x2v

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Sodium binding site 8 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na101

b:94.8
occ:1.00
 OE2 K:GLU30 2.9 60.7 1.0
OE1 J:GLU30 3.0 71.1 1.0
O J:HOH2002 3.1 39.7 1.0
CA J:ALA27 3.4 32.1 1.0
CG K:GLU30 3.5 47.1 1.0
CD K:GLU30 3.5 54.0 1.0
CD J:GLU30 3.6 56.7 1.0
CB J:ALA27 3.7 26.2 1.0
CB J:GLU30 3.8 39.6 1.0
O J:ALA27 4.1 32.9 1.0
O J:HOH2003 4.1 63.5 1.0
CE K:LYS26 4.1 51.0 1.0
CG J:GLU30 4.1 48.0 1.0
OE2 J:GLU30 4.2 58.4 1.0
C J:ALA27 4.2 35.5 1.0
C6 J:DPV200 4.3 0.4 1.0
N J:ALA27 4.3 33.5 1.0
O J:HOH2001 4.3 44.1 1.0
O J:HOH2009 4.4 71.4 1.0
O J:LYS26 4.6 36.7 1.0
OE1 K:GLU30 4.7 53.2 1.0
CG K:LYS26 4.7 37.0 1.0
C J:LYS26 4.8 36.4 1.0
CB K:GLU30 5.0 38.4 1.0

Sodium binding site 9 out of 10 in 2x2v

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Sodium binding site 9 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na101

b:76.3
occ:1.00
 OE1 K:GLU30 2.8 53.2 1.0
O K:HOH2003 2.9 49.8 1.0
OE2 L:GLU30 3.1 61.3 1.0
CD L:GLU30 3.3 61.7 1.0
CG L:GLU30 3.4 50.3 1.0
NZ L:LYS26 3.5 55.9 1.0
CA K:ALA27 3.8 30.8 1.0
CD K:GLU30 3.9 54.0 1.0
CB K:ALA27 4.0 27.9 1.0
CB K:GLU30 4.0 38.4 1.0
OE1 L:GLU30 4.1 82.2 1.0
C6 K:DPV200 4.2 0.2 1.0
O K:HOH2001 4.3 46.7 1.0
O K:ALA27 4.4 37.2 1.0
CG L:LYS26 4.6 44.0 1.0
CG K:GLU30 4.6 47.1 1.0
O K:HOH2002 4.6 64.8 1.0
C K:ALA27 4.7 35.9 1.0
CE L:LYS26 4.8 53.8 1.0
C8 K:DPV200 4.8 0.4 1.0
N K:ALA27 4.8 34.2 1.0
OE2 K:GLU30 4.8 60.7 1.0
CB L:GLU30 4.8 45.0 1.0

Sodium binding site 10 out of 10 in 2x2v

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Sodium binding site 10 out of 10 in the Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structural Basis of A Novel Proton-Coordination Type in An F1FO-Atp Synthase Rotor Ring within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na101

b:65.5
occ:1.00
 OE1 M:GLU30 2.9 55.4 1.0
OE1 L:GLU30 2.9 82.2 1.0
O L:HOH2003 3.0 55.5 1.0
CD L:GLU30 3.4 61.7 1.0
CG M:GLU30 3.5 48.9 1.0
CD M:GLU30 3.6 57.3 1.0
NZ M:LYS26 3.7 64.4 1.0
CB L:GLU30 3.7 45.0 1.0
OE2 L:GLU30 3.9 61.3 1.0
CA L:ALA27 4.0 34.4 1.0
CG L:GLU30 4.1 50.3 1.0
O L:HOH2001 4.3 51.8 1.0
CB L:ALA27 4.3 34.2 1.0
O L:ALA27 4.5 41.6 1.0
CE M:LYS26 4.6 55.3 1.0
O L:HOH2002 4.7 63.3 1.0
C L:ALA27 4.8 38.6 1.0
OE2 M:GLU30 4.8 65.7 1.0
N L:ALA27 4.9 41.7 1.0
CG M:LYS26 4.9 41.3 1.0
CB M:GLU30 5.0 34.5 1.0
O L:LYS26 5.0 44.1 1.0

Reference:

L.Preiss, O.Yildiz, D.B.Hicks, T.A.Krulwich, T.Meier. A New Type of Proton Coordination in An F(1)F(O)- Atp Synthase Rotor Ring. Plos Biol. V. 8 443 2010.
ISSN: ISSN 1544-9173
PubMed: 20689804
DOI: 10.1371/JOURNAL.PBIO.1000443
Page generated: Tue Dec 15 05:58:47 2020

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