Atomistry » Sodium » PDB 5uka-5v0d » 5ul9
Atomistry »
  Sodium »
    PDB 5uka-5v0d »
      5ul9 »

Sodium in PDB 5ul9: Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant

Protein crystallography data

The structure of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant, PDB code: 5ul9 was solved by M.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.78
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.125, 102.112, 167.991, 90.00, 99.52, 90.00
R / Rfree (%) 24.2 / 26.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant (pdb code 5ul9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant, PDB code: 5ul9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5ul9

Go back to Sodium Binding Sites List in 5ul9
Sodium binding site 1 out of 8 in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:72.5
occ:1.00
 O A:SER146 2.4 61.4 1.0
OD1 A:ASN151 2.6 65.3 1.0
OG A:SER146 2.6 54.4 1.0
O A:SER150 2.7 58.7 1.0
O A:GLY199 2.8 76.5 1.0
C A:SER150 3.1 59.5 1.0
C A:GLY199 3.2 69.7 1.0
C A:SER146 3.3 64.1 1.0
CA A:GLY199 3.4 70.6 1.0
CA A:GLY193 3.5 66.0 1.0
CG A:ASN151 3.5 68.9 1.0
N A:SER150 3.7 60.1 1.0
CA A:SER150 3.7 57.2 1.0
CB A:SER146 3.7 58.3 1.0
N A:ASN151 3.8 63.8 1.0
CA A:SER146 3.8 57.4 1.0
ND2 A:ASN151 4.1 72.8 1.0
N A:GLY193 4.2 66.2 1.0
N A:SER200 4.2 66.6 1.0
CA A:ASN151 4.3 66.2 1.0
O A:ALA189 4.4 80.4 1.0
N A:MET147 4.5 65.7 1.0
CB A:ASN151 4.5 69.2 1.0
C A:GLY193 4.7 66.5 1.0
N A:GLY199 4.7 73.7 1.0
C A:GLY192 4.7 65.2 1.0
C A:ILE149 4.8 68.5 1.0
O A:GLY192 4.8 64.8 1.0
O A:GLY193 4.9 68.3 1.0
CA A:MET147 5.0 62.0 1.0
CA A:SER200 5.0 64.7 1.0
N A:ILE149 5.0 62.1 1.0

Sodium binding site 2 out of 8 in 5ul9

Go back to Sodium Binding Sites List in 5ul9
Sodium binding site 2 out of 8 in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:68.2
occ:1.00
 O A:THR373 2.3 58.2 1.0
O A:ALA420 2.4 81.7 1.0
O A:ALA376 2.5 56.8 1.0
OD1 A:ASN378 2.6 62.3 1.0
OG1 A:THR373 2.7 36.3 1.0
N A:ASN378 3.0 68.7 1.0
C A:THR373 3.4 55.3 1.0
CG A:ASN378 3.4 71.8 1.0
C A:ALA420 3.5 75.8 1.0
CA A:ASN378 3.5 71.2 1.0
C A:SER377 3.5 69.2 1.0
C A:ALA376 3.6 63.9 1.0
CA A:THR373 3.8 51.3 1.0
CB A:THR373 3.8 44.1 1.0
CB A:ALA414 4.0 73.0 1.0
CA A:SER377 4.0 72.2 1.0
OG1 A:THR421 4.0 78.9 1.0
CB A:ASN378 4.0 72.3 1.0
CA A:ALA420 4.1 70.8 1.0
O A:SER377 4.2 64.9 1.0
N A:SER377 4.2 66.4 1.0
ND2 A:ASN378 4.3 76.6 1.0
CB A:ALA420 4.5 66.3 1.0
N A:THR421 4.5 76.4 1.0
O A:ALA411 4.5 61.6 1.0
N A:GLU374 4.6 56.5 1.0
CG2 A:THR373 4.7 42.2 1.0
CA A:ALA376 4.8 65.4 1.0
N A:ALA376 4.9 66.5 1.0
O5 A:CIT503 4.9 0.3 1.0
CA A:THR421 4.9 72.1 1.0
C A:ASN378 4.9 71.1 1.0

Sodium binding site 3 out of 8 in 5ul9

Go back to Sodium Binding Sites List in 5ul9
Sodium binding site 3 out of 8 in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:90.4
occ:1.00
 O B:SER146 2.3 87.8 1.0
OD1 B:ASN151 2.7 81.6 1.0
OG B:SER146 2.7 90.5 1.0
O B:SER150 2.7 85.3 1.0
O B:GLY199 2.8 75.9 1.0
C B:SER150 3.1 81.9 1.0
C B:GLY199 3.2 70.4 1.0
C B:SER146 3.3 91.8 1.0
CA B:GLY199 3.4 70.6 1.0
CA B:GLY193 3.5 92.9 1.0
CG B:ASN151 3.5 81.0 1.0
CA B:SER150 3.6 80.1 1.0
N B:SER150 3.6 83.8 1.0
N B:ASN151 3.7 81.7 1.0
CB B:SER146 3.8 91.5 1.0
CA B:SER146 3.8 91.2 1.0
ND2 B:ASN151 4.2 82.9 1.0
N B:GLY193 4.2 96.8 1.0
N B:SER200 4.2 69.3 1.0
CA B:ASN151 4.3 78.2 1.0
O B:ALA189 4.4 0.6 1.0
N B:MET147 4.5 94.3 1.0
CB B:ASN151 4.5 79.4 1.0
C B:ILE149 4.7 92.9 1.0
N B:GLY199 4.7 75.1 1.0
C B:GLY193 4.8 88.8 1.0
C B:GLY192 4.8 93.6 1.0
O B:GLY192 4.8 96.9 1.0
N B:ILE149 4.9 88.1 1.0
O B:GLY193 4.9 89.5 1.0
CA B:MET147 5.0 96.0 1.0
OG1 B:THR154 5.0 91.5 1.0
CA B:SER200 5.0 70.1 1.0
C B:MET147 5.0 96.0 1.0

Sodium binding site 4 out of 8 in 5ul9

Go back to Sodium Binding Sites List in 5ul9
Sodium binding site 4 out of 8 in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:87.8
occ:1.00
 O B:THR373 2.3 84.8 1.0
O B:ALA420 2.4 0.1 1.0
O B:ALA376 2.5 68.3 1.0
OD1 B:ASN378 2.6 90.1 1.0
OG1 B:THR373 2.8 78.7 1.0
N B:ASN378 3.1 71.8 1.0
C B:THR373 3.3 83.6 1.0
C B:ALA420 3.4 0.1 1.0
CG B:ASN378 3.4 88.5 1.0
CA B:ASN378 3.6 75.8 1.0
C B:SER377 3.6 73.4 1.0
C B:ALA376 3.7 73.2 1.0
CA B:THR373 3.8 80.7 1.0
CB B:THR373 3.8 78.9 1.0
CB B:ALA414 3.9 80.2 1.0
OG1 B:THR421 4.0 0.7 1.0
CA B:ALA420 4.0 0.8 1.0
CA B:SER377 4.0 74.0 1.0
CB B:ASN378 4.1 84.6 1.0
O B:SER377 4.3 76.6 1.0
N B:SER377 4.3 72.0 1.0
ND2 B:ASN378 4.4 95.1 1.0
CB B:ALA420 4.4 0.6 1.0
N B:THR421 4.5 0.8 1.0
N B:GLU374 4.5 84.0 1.0
O B:ALA411 4.5 67.4 1.0
CG2 B:THR373 4.7 77.6 1.0
CA B:ALA376 4.9 75.5 1.0
CA B:THR421 4.9 0.6 1.0
N B:ALA376 4.9 77.2 1.0
O6 B:CIT503 4.9 0.1 1.0
CA B:GLU374 5.0 79.5 1.0
C B:ASN378 5.0 71.9 1.0

Sodium binding site 5 out of 8 in 5ul9

Go back to Sodium Binding Sites List in 5ul9
Sodium binding site 5 out of 8 in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:70.0
occ:1.00
 O C:SER146 2.4 66.9 1.0
OD1 C:ASN151 2.6 68.6 1.0
OG C:SER146 2.7 71.8 1.0
O C:SER150 2.7 77.1 1.0
O C:GLY199 2.8 63.2 1.0
C C:SER150 3.1 63.5 1.0
C C:GLY199 3.2 57.3 1.0
CA C:GLY199 3.4 57.5 1.0
C C:SER146 3.4 68.5 1.0
CG C:ASN151 3.5 69.6 1.0
CA C:GLY193 3.5 74.9 1.0
CA C:SER150 3.6 57.3 1.0
N C:SER150 3.7 59.4 1.0
N C:ASN151 3.7 64.0 1.0
CB C:SER146 3.8 68.2 1.0
CA C:SER146 3.8 68.6 1.0
ND2 C:ASN151 4.1 76.1 1.0
N C:GLY193 4.2 74.0 1.0
N C:SER200 4.2 50.5 1.0
CA C:ASN151 4.3 63.4 1.0
O C:ALA189 4.4 59.5 1.0
CB C:ASN151 4.5 66.0 1.0
N C:MET147 4.5 69.6 1.0
C C:GLY193 4.7 74.3 1.0
N C:GLY199 4.7 62.3 1.0
C C:ILE149 4.7 70.8 1.0
C C:GLY192 4.8 68.8 1.0
O C:GLY192 4.8 72.4 1.0
O C:GLY193 4.9 77.7 1.0
CA C:SER200 4.9 51.2 1.0
N C:ILE149 5.0 70.0 1.0
CA C:MET147 5.0 68.8 1.0

Sodium binding site 6 out of 8 in 5ul9

Go back to Sodium Binding Sites List in 5ul9
Sodium binding site 6 out of 8 in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:89.8
occ:1.00
 O C:THR373 2.3 77.6 1.0
O C:ALA420 2.4 84.5 1.0
O C:ALA376 2.5 58.8 1.0
OD1 C:ASN378 2.6 64.5 1.0
OG1 C:THR373 2.8 68.2 1.0
N C:ASN378 3.0 65.8 1.0
C C:THR373 3.4 72.2 1.0
CG C:ASN378 3.4 66.4 1.0
C C:ALA420 3.4 76.0 1.0
CA C:ASN378 3.5 64.1 1.0
C C:SER377 3.5 63.1 1.0
C C:ALA376 3.6 62.6 1.0
CA C:THR373 3.8 71.6 1.0
CB C:THR373 3.9 68.2 1.0
CB C:ALA414 4.0 56.9 1.0
CA C:SER377 4.0 61.3 1.0
OG1 C:THR421 4.0 66.7 1.0
CB C:ASN378 4.0 69.2 1.0
CA C:ALA420 4.1 75.6 1.0
O C:SER377 4.2 62.6 1.0
N C:SER377 4.2 59.6 1.0
ND2 C:ASN378 4.4 66.2 1.0
N C:THR421 4.5 69.2 1.0
CB C:ALA420 4.5 72.4 1.0
O C:ALA411 4.5 48.4 1.0
N C:GLU374 4.6 65.7 1.0
CG2 C:THR373 4.7 65.1 1.0
CA C:ALA376 4.8 63.4 1.0
O5 C:CIT503 4.8 0.8 1.0
N C:ALA376 4.9 62.6 1.0
CA C:THR421 4.9 67.6 1.0
C C:ASN378 4.9 59.5 1.0

Sodium binding site 7 out of 8 in 5ul9

Go back to Sodium Binding Sites List in 5ul9
Sodium binding site 7 out of 8 in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:98.7
occ:1.00
 O D:SER146 2.3 45.7 1.0
OD1 D:ASN151 2.6 56.0 1.0
OG D:SER146 2.6 32.2 1.0
O D:SER150 2.7 58.5 1.0
O D:GLY199 2.8 68.7 1.0
C D:SER150 3.1 59.3 1.0
C D:GLY199 3.2 64.5 1.0
C D:SER146 3.3 47.9 1.0
CA D:GLY199 3.4 65.2 1.0
CG D:ASN151 3.5 63.9 1.0
CA D:GLY193 3.5 61.6 1.0
CA D:SER150 3.6 56.5 1.0
N D:SER150 3.6 56.7 1.0
N D:ASN151 3.7 62.1 1.0
CB D:SER146 3.8 38.9 1.0
CA D:SER146 3.8 41.6 1.0
ND2 D:ASN151 4.1 70.0 1.0
N D:GLY193 4.2 56.1 1.0
CA D:ASN151 4.2 60.5 1.0
N D:SER200 4.2 62.6 1.0
O D:ALA189 4.4 68.7 1.0
CB D:ASN151 4.5 65.5 1.0
N D:MET147 4.5 52.5 1.0
C D:ILE149 4.7 63.4 1.0
N D:GLY199 4.7 66.7 1.0
C D:GLY193 4.8 68.0 1.0
C D:GLY192 4.8 55.3 1.0
O D:GLY192 4.8 51.7 1.0
N D:ILE149 4.9 55.6 1.0
O D:GLY193 4.9 73.8 1.0
OG1 D:THR154 5.0 49.4 1.0
CA D:MET147 5.0 55.8 1.0
CA D:SER200 5.0 63.2 1.0

Sodium binding site 8 out of 8 in 5ul9

Go back to Sodium Binding Sites List in 5ul9
Sodium binding site 8 out of 8 in the Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure and Function of the Divalent Anion/Na+ Symporter From Vibrio Cholerae and A Humanized Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:75.9
occ:1.00
 O D:THR373 2.3 70.7 1.0
O D:ALA420 2.5 52.2 1.0
O D:ALA376 2.5 66.5 1.0
OD1 D:ASN378 2.6 58.3 1.0
OG1 D:THR373 2.7 60.9 1.0
N D:ASN378 3.0 60.3 1.0
C D:THR373 3.4 66.4 1.0
CG D:ASN378 3.4 65.2 1.0
C D:ALA420 3.5 56.3 1.0
CA D:ASN378 3.5 61.7 1.0
C D:SER377 3.5 63.9 1.0
C D:ALA376 3.6 67.0 1.0
CA D:THR373 3.8 64.6 1.0
CB D:THR373 3.8 63.5 1.0
CA D:SER377 4.0 66.4 1.0
CB D:ALA414 4.0 55.4 1.0
CB D:ASN378 4.0 67.2 1.0
OG1 D:THR421 4.1 69.0 1.0
CA D:ALA420 4.1 54.9 1.0
O D:SER377 4.2 68.5 1.0
N D:SER377 4.2 68.4 1.0
ND2 D:ASN378 4.4 68.0 1.0
O D:ALA411 4.5 56.8 1.0
CB D:ALA420 4.5 47.6 1.0
N D:THR421 4.5 62.2 1.0
N D:GLU374 4.6 67.8 1.0
CG2 D:THR373 4.7 64.0 1.0
CA D:ALA376 4.8 65.0 1.0
N D:ALA376 4.9 67.1 1.0
O6 D:CIT503 4.9 0.1 1.0
C D:ASN378 4.9 59.8 1.0
CA D:THR421 4.9 62.3 1.0

Reference:

R.Nie, S.Stark, J.Symersky, R.S.Kaplan, M.Lu. Structure and Function of the Divalent Anion/Na(+) Symporter From Vibrio Cholerae and A Humanized Variant. Nat Commun V. 8 15009 2017.
ISSN: ESSN 2041-1723
PubMed: 28436435
DOI: 10.1038/NCOMMS15009
Page generated: Tue Oct 8 00:35:35 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy