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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

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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

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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

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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

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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

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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

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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

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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

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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

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