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Sodium in PDB 5a1s: Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica.

Protein crystallography data

The structure of Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica., PDB code: 5a1s was solved by D.Woehlert, M.J.Groetzinger, W.Kuhlbrandt, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.98 / 2.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 86.382, 89.935, 91.843, 90.44, 113.79, 99.55
R / Rfree (%) 20.8 / 24.6

Other elements in 5a1s:

The structure of Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica. also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica. (pdb code 5a1s). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica., PDB code: 5a1s:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 5a1s

Go back to Sodium Binding Sites List in 5a1s
Sodium binding site 1 out of 7 in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica.


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-Dependent Citrate Symporter Secits Form Salmonella Enterica. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:39.2
occ:1.00
 OG A:SER427 2.2 42.8 1.0
OD1 A:ASN401 2.3 37.6 1.0
O A:CYS398 2.4 44.4 1.0
OD1 A:ASP407 2.4 38.4 1.0
O A:HOH2007 2.5 33.5 0.8
O A:GLY403 3.1 33.8 1.0
CG A:ASN401 3.2 42.9 1.0
CG A:ASP407 3.2 39.7 1.0
C A:CYS398 3.3 41.8 1.0
OD2 A:ASP407 3.4 30.1 1.0
ND2 A:ASN401 3.5 44.9 1.0
CB A:SER427 3.5 34.0 1.0
C A:GLY403 3.7 43.9 1.0
CA A:GLY403 3.7 42.2 1.0
CA A:SER427 3.9 37.6 1.0
N A:GLY403 3.9 34.6 1.0
CA A:CYS398 3.9 42.3 1.0
O A:ALA423 4.1 44.9 1.0
N A:SER427 4.2 38.0 1.0
CB A:CYS398 4.2 46.6 1.0
O A:ASN401 4.3 33.1 1.0
N A:MET399 4.4 39.9 1.0
O A:HOH2006 4.5 37.8 1.0
CB A:ASN401 4.5 47.4 1.0
CB A:ASP407 4.5 36.2 1.0
C A:ASN401 4.6 37.2 1.0
N A:ASP407 4.6 34.4 1.0
CA A:MET399 4.6 50.1 1.0
CA A:ASP407 4.8 50.3 1.0
N A:GLY404 4.8 40.2 1.0
C A:ARG402 4.9 42.8 1.0
N A:ASN401 4.9 43.6 1.0
CA A:ASN401 4.9 38.0 1.0
C A:MET399 4.9 40.6 1.0
O A:MET399 5.0 41.8 1.0

Sodium binding site 2 out of 7 in 5a1s

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Sodium binding site 2 out of 7 in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica.


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-Dependent Citrate Symporter Secits Form Salmonella Enterica. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:42.2
occ:1.00
 O A:ASN401 2.3 33.1 1.0
O A:GLY183 2.3 35.1 1.0
O A:MET399 2.4 41.8 1.0
O A:ILE181 2.4 37.8 1.0
O A:HOH2004 2.4 35.4 1.0
O A:HOH2007 3.2 33.5 0.8
C A:ASN401 3.4 37.2 1.0
C A:MET399 3.4 40.6 1.0
C A:ILE181 3.4 47.6 1.0
C A:ALA400 3.5 42.7 1.0
C A:GLY183 3.5 39.7 1.0
N A:ASN401 3.5 43.6 1.0
C A:MET182 3.7 43.8 1.0
N A:GLY183 3.8 43.9 1.0
CA A:ALA400 3.8 43.8 1.0
O A:HOH2014 3.8 28.1 0.8
O A:HOH2006 3.9 37.8 1.0
O A:ALA400 3.9 51.6 1.0
N A:GLY185 4.0 35.5 1.0
N A:ALA400 4.0 38.7 1.0
CA A:MET182 4.0 48.4 1.0
CA A:ASN401 4.1 38.0 1.0
O A:MET182 4.1 45.5 1.0
N A:MET182 4.1 49.8 1.0
CA A:GLY183 4.2 35.5 1.0
O A:PRO180 4.3 45.6 1.0
N A:ARG402 4.5 36.6 1.0
OD1 A:ASN401 4.5 37.6 1.0
CA A:ILE181 4.5 49.3 1.0
N A:GLY184 4.6 35.7 1.0
CA A:GLY185 4.6 34.6 1.0
CA A:MET399 4.6 50.1 1.0
N A:GLY403 4.6 34.6 1.0
O A:HOH2005 4.7 28.2 0.8
CA A:ARG402 4.7 36.5 1.0
CA A:GLY184 4.8 27.7 1.0
C A:GLY184 4.8 31.1 1.0

Sodium binding site 3 out of 7 in 5a1s

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Sodium binding site 3 out of 7 in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica.


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-Dependent Citrate Symporter Secits Form Salmonella Enterica. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:72.0
occ:1.00
 O B:MET399 2.3 78.9 1.0
O B:ILE181 2.3 72.7 1.0
O B:HOH2007 2.3 62.4 1.0
O B:GLY183 2.3 72.4 1.0
O B:ASN401 2.4 74.5 1.0
C B:MET399 3.4 72.6 1.0
C B:ILE181 3.4 77.9 1.0
C B:GLY183 3.4 67.4 1.0
C B:ALA400 3.4 75.3 1.0
C B:ASN401 3.5 70.2 1.0
C B:MET182 3.5 80.5 1.0
N B:GLY183 3.6 75.1 1.0
N B:ASN401 3.6 78.3 1.0
CA B:ALA400 3.8 68.7 1.0
O B:ALA400 3.8 81.4 1.0
CA B:MET182 3.9 76.4 1.0
O B:MET182 3.9 81.6 1.0
N B:ALA400 4.0 70.9 1.0
N B:MET182 4.0 69.2 1.0
CA B:GLY183 4.1 68.5 1.0
N B:GLY185 4.1 60.8 1.0
CA B:ASN401 4.1 81.1 1.0
O B:PRO180 4.3 68.0 1.0
OD1 B:ASN401 4.4 73.8 1.0
N B:GLY184 4.5 69.3 1.0
CA B:ILE181 4.5 76.5 1.0
CA B:MET399 4.6 67.0 1.0
N B:ARG402 4.6 77.5 1.0
CA B:GLY185 4.7 57.7 1.0
CA B:GLY184 4.8 46.1 1.0
N B:GLY403 4.8 71.1 1.0
C B:GLY184 4.8 67.4 1.0
O B:HOH2008 4.9 58.7 1.0
CA B:ARG402 4.9 70.2 1.0

Sodium binding site 4 out of 7 in 5a1s

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Sodium binding site 4 out of 7 in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica.


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-Dependent Citrate Symporter Secits Form Salmonella Enterica. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:54.8
occ:1.00
 OD1 C:ASN401 2.3 50.8 1.0
OG C:SER427 2.3 46.6 1.0
O C:CYS398 2.5 52.4 1.0
OD1 C:ASP407 2.6 39.0 1.0
O C:HOH2005 3.0 60.1 1.0
CG C:ASN401 3.2 48.3 1.0
C C:CYS398 3.3 55.6 1.0
CB C:SER427 3.3 45.2 1.0
O C:GLY403 3.3 44.9 1.0
CG C:ASP407 3.5 44.4 1.0
ND2 C:ASN401 3.6 47.1 1.0
CA C:SER427 3.7 58.1 1.0
N C:GLY403 3.8 53.3 1.0
OD2 C:ASP407 3.8 47.1 1.0
C C:GLY403 3.9 56.1 1.0
CA C:GLY403 3.9 51.9 1.0
CA C:CYS398 4.0 45.3 1.0
N C:MET399 4.1 64.3 1.0
N C:SER427 4.1 58.7 1.0
O C:ASN401 4.1 51.2 1.0
CA C:MET399 4.2 55.8 1.0
C C:ASN401 4.4 57.2 1.0
O C:ALA423 4.4 43.1 1.0
CB C:CYS398 4.5 40.6 1.0
CB C:ASN401 4.5 47.0 1.0
O C:MET399 4.6 58.5 1.0
C C:MET399 4.6 54.2 1.0
C C:ARG402 4.6 56.2 1.0
N C:ASP407 4.8 51.3 1.0
CB C:ASP407 4.8 38.0 1.0
N C:ASN401 4.8 44.2 1.0
CA C:ASN401 4.9 47.8 1.0
N C:ARG402 4.9 57.7 1.0
C C:SER426 4.9 57.5 1.0

Sodium binding site 5 out of 7 in 5a1s

Go back to Sodium Binding Sites List in 5a1s
Sodium binding site 5 out of 7 in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica.


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-Dependent Citrate Symporter Secits Form Salmonella Enterica. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:56.3
occ:1.00
 O C:ASN401 2.3 51.2 1.0
O C:GLY183 2.3 60.0 1.0
O C:ILE181 2.3 58.8 1.0
O C:MET399 2.3 58.5 1.0
O C:HOH2003 2.4 53.1 1.0
O C:HOH2005 3.4 60.1 1.0
C C:ILE181 3.4 61.2 1.0
C C:GLY183 3.4 59.2 1.0
C C:ASN401 3.5 57.2 1.0
C C:MET399 3.5 54.2 1.0
N C:GLY183 3.7 67.7 1.0
C C:MET182 3.7 61.1 1.0
C C:ALA400 3.7 46.2 1.0
N C:GLY185 3.8 49.3 1.0
N C:ASN401 3.9 44.2 1.0
CA C:ALA400 3.9 59.4 1.0
O C:PRO180 4.0 56.6 1.0
CA C:MET182 4.0 59.0 1.0
N C:MET182 4.1 57.0 1.0
O C:ALA400 4.1 54.5 1.0
N C:ALA400 4.1 52.3 1.0
O C:MET182 4.1 65.7 1.0
CA C:GLY183 4.2 56.8 1.0
CA C:ASN401 4.3 47.8 1.0
CA C:GLY185 4.3 50.0 1.0
CA C:ARG402 4.4 55.3 1.0
N C:ARG402 4.4 57.7 1.0
CA C:ILE181 4.4 63.6 1.0
N C:GLY184 4.5 53.3 1.0
OD1 C:ASN401 4.6 50.8 1.0
C C:GLY184 4.6 54.8 1.0
CA C:MET399 4.6 55.8 1.0
CA C:GLY184 4.7 45.7 1.0
O C:HOH2004 4.7 58.7 1.0
N C:GLY403 4.9 53.3 1.0
C C:PRO180 4.9 62.1 1.0

Sodium binding site 6 out of 7 in 5a1s

Go back to Sodium Binding Sites List in 5a1s
Sodium binding site 6 out of 7 in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica.


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-Dependent Citrate Symporter Secits Form Salmonella Enterica. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:54.6
occ:1.00
 OD1 D:ASN401 2.3 49.4 1.0
OG D:SER427 2.3 48.2 1.0
O D:CYS398 2.4 59.2 1.0
O D:HOH2009 2.4 44.3 1.0
OD1 D:ASP407 2.4 60.7 1.0
C D:CYS398 3.2 53.2 1.0
O D:GLY403 3.3 57.6 1.0
CG D:ASN401 3.3 54.1 1.0
CG D:ASP407 3.3 56.2 1.0
CB D:SER427 3.5 53.2 1.0
OD2 D:ASP407 3.6 58.5 1.0
ND2 D:ASN401 3.7 54.1 1.0
C D:GLY403 3.8 58.1 1.0
CA D:CYS398 3.8 58.9 1.0
CA D:SER427 3.9 62.1 1.0
CA D:GLY403 3.9 45.2 1.0
N D:GLY403 4.0 51.9 1.0
O D:HOH2008 4.1 55.7 1.0
N D:MET399 4.1 63.7 1.0
N D:SER427 4.2 60.2 1.0
O D:ASN401 4.2 43.8 1.0
CB D:CYS398 4.2 53.2 1.0
CA D:MET399 4.3 52.0 1.0
O D:ALA423 4.6 63.7 1.0
C D:ASN401 4.6 51.3 1.0
CB D:ASN401 4.7 54.3 1.0
C D:MET399 4.7 41.0 1.0
O D:MET399 4.7 50.6 1.0
CB D:ASP407 4.7 42.2 1.0
N D:ASP407 4.8 52.1 1.0
N D:GLY404 4.8 57.5 1.0
N D:ASN401 4.9 50.4 1.0
C D:SER426 4.9 54.7 1.0
CA D:ASN401 4.9 42.6 1.0

Sodium binding site 7 out of 7 in 5a1s

Go back to Sodium Binding Sites List in 5a1s
Sodium binding site 7 out of 7 in the Crystal Structure of the Sodium-Dependent Citrate Symporter Secits Form Salmonella Enterica.


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-Dependent Citrate Symporter Secits Form Salmonella Enterica. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:50.0
occ:1.00
 O D:HOH2006 2.2 47.6 1.0
O D:MET399 2.3 50.6 1.0
O D:ILE181 2.3 54.7 1.0
O D:GLY183 2.3 39.5 1.0
O D:ASN401 2.5 43.8 1.0
C D:ILE181 3.3 47.0 1.0
C D:MET399 3.4 41.0 1.0
C D:GLY183 3.4 58.4 1.0
C D:ALA400 3.5 58.2 1.0
C D:MET182 3.5 52.7 1.0
C D:ASN401 3.5 51.3 1.0
N D:GLY183 3.5 50.7 1.0
O D:HOH2009 3.6 44.3 1.0
N D:ASN401 3.7 50.4 1.0
O D:ALA400 3.7 50.6 1.0
CA D:MET182 3.8 52.3 1.0
CA D:ALA400 3.9 51.9 1.0
N D:MET182 3.9 51.2 1.0
O D:PRO180 4.0 54.5 1.0
O D:MET182 4.0 49.3 1.0
O D:HOH2008 4.0 55.7 1.0
N D:ALA400 4.1 46.2 1.0
CA D:GLY183 4.1 47.7 1.0
CA D:ASN401 4.2 42.6 1.0
N D:GLY185 4.3 43.0 1.0
CA D:ILE181 4.3 49.5 1.0
N D:GLY184 4.5 51.0 1.0
N D:ARG402 4.6 47.0 1.0
CD2 D:LEU216 4.6 71.0 1.0
CA D:MET399 4.6 52.0 1.0
OD1 D:ASN401 4.7 49.4 1.0
N D:GLY403 4.8 51.9 1.0
CA D:ARG402 4.8 40.5 1.0
CA D:GLY184 4.8 55.6 1.0
O D:HOH2007 4.9 42.3 1.0
C D:PRO180 4.9 53.1 1.0
C D:GLY184 4.9 51.8 1.0
CA D:GLY185 5.0 40.5 1.0

Reference:

D.Wohlert, M.J.Grotzinger, W.Kuhlbrandt, O.Yildiz. Mechanism of Na(+)-Dependent Citrate Transport From the Structure of An Asymmetrical Cits Dimer. Elife V. 4 09375 2015.
ISSN: ESSN 2050-084X
PubMed: 26636752
DOI: 10.7554/ELIFE.09375
Page generated: Tue Dec 15 10:11:05 2020

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