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Sodium in PDB 5uld: 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: 5uld 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 (°) 106.087, 101.535, 168.882, 90.00, 99.73, 90.00
R / Rfree (%) 25.2 / 26.8

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 5uld). 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: 5uld:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5uld

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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:63.0
occ:1.00
 OG A:SER146 2.5 87.6 1.0
OD1 A:ASN151 2.5 75.4 1.0
O A:SER146 2.5 85.0 1.0
O A:GLY199 2.7 93.4 1.0
O A:SER150 2.8 71.1 1.0
C A:SER150 3.1 70.7 1.0
C A:GLY199 3.3 82.2 1.0
C A:SER146 3.3 85.1 1.0
CA A:GLY193 3.4 73.5 1.0
CG A:ASN151 3.5 77.2 1.0
CA A:GLY199 3.5 80.1 1.0
N A:ASN151 3.6 73.8 1.0
CA A:SER150 3.6 67.1 1.0
CB A:SER146 3.7 90.5 1.0
N A:SER150 3.7 70.1 1.0
CA A:SER146 3.8 85.3 1.0
N A:GLY193 3.9 72.4 1.0
O A:ALA189 4.1 88.4 1.0
CA A:ASN151 4.2 75.2 1.0
ND2 A:ASN151 4.2 79.2 1.0
N A:THR200 4.4 78.9 1.0
C A:GLY192 4.4 71.9 1.0
N A:MET147 4.4 83.1 1.0
CB A:ASN151 4.4 76.8 1.0
O A:GLY192 4.5 70.5 1.0
C A:GLY193 4.7 75.0 1.0
CA A:MET147 4.9 79.3 1.0
CB A:THR200 4.9 80.8 1.0
C A:ILE149 4.9 80.1 1.0
N A:GLY199 5.0 85.4 1.0
C A:MET147 5.0 76.0 1.0
O A:GLY193 5.0 78.5 1.0

Sodium binding site 2 out of 8 in 5uld

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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:70.5
occ:1.00
 O A:ALA420 2.5 78.1 1.0
OD1 A:ASN378 2.5 74.9 1.0
O A:THR373 2.5 76.7 1.0
O A:THR376 2.5 85.6 1.0
OG1 A:THR373 2.7 59.3 1.0
N A:ASN378 3.1 77.5 1.0
CG A:ASN378 3.4 76.8 1.0
C A:ALA420 3.4 71.8 1.0
C A:THR373 3.6 70.3 1.0
C A:SER377 3.6 80.2 1.0
CA A:ASN378 3.6 76.6 1.0
C A:THR376 3.7 88.7 1.0
OG1 A:THR421 3.9 70.9 1.0
CB A:THR373 3.9 62.9 1.0
CB A:ALA414 3.9 70.4 1.0
CA A:SER377 3.9 87.6 1.0
CA A:THR373 4.0 67.2 1.0
CB A:ASN378 4.1 77.0 1.0
CA A:ALA420 4.1 66.8 1.0
N A:SER377 4.2 87.3 1.0
O A:ALA411 4.3 67.9 1.0
O A:SER377 4.3 72.2 1.0
ND2 A:ASN378 4.4 73.4 1.0
N A:THR421 4.4 71.9 1.0
CB A:ALA420 4.5 61.5 1.0
O5 A:CIT503 4.6 73.0 1.0
N A:GLU374 4.8 69.6 1.0
CG2 A:THR373 4.8 63.7 1.0
CA A:THR421 4.8 68.0 1.0
CA A:THR376 4.9 92.6 1.0
CB A:THR421 5.0 64.4 1.0

Sodium binding site 3 out of 8 in 5uld

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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:95.0
occ:1.00
 O B:SER146 2.5 84.0 1.0
OG B:SER146 2.6 93.5 1.0
OD1 B:ASN151 2.6 0.8 1.0
O B:GLY199 2.7 90.8 1.0
O B:SER150 2.8 92.3 1.0
C B:SER150 3.1 87.5 1.0
C B:GLY199 3.3 84.1 1.0
C B:SER146 3.3 89.9 1.0
CA B:GLY193 3.4 0.7 1.0
CA B:GLY199 3.5 82.1 1.0
CG B:ASN151 3.5 99.7 1.0
CA B:SER150 3.6 82.1 1.0
N B:ASN151 3.7 90.4 1.0
CB B:SER146 3.7 91.0 1.0
N B:SER150 3.7 85.4 1.0
CA B:SER146 3.8 89.0 1.0
N B:GLY193 3.9 0.5 1.0
O B:ALA189 4.2 0.1 1.0
CA B:ASN151 4.2 91.6 1.0
ND2 B:ASN151 4.2 98.9 1.0
N B:THR200 4.3 81.5 1.0
N B:MET147 4.4 93.5 1.0
C B:GLY192 4.4 0.3 1.0
CB B:ASN151 4.5 97.0 1.0
O B:GLY192 4.5 0.0 1.0
C B:GLY193 4.7 0.1 1.0
CA B:MET147 4.9 95.6 1.0
C B:ILE149 4.9 96.1 1.0
N B:GLY199 4.9 87.2 1.0
CB B:THR200 4.9 92.8 1.0
C B:MET147 4.9 96.9 1.0
O B:GLY193 5.0 0.3 1.0
CA B:THR200 5.0 83.5 1.0

Sodium binding site 4 out of 8 in 5uld

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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:0.1
occ:1.00
 O B:ALA420 2.4 1.0 1.0
O B:THR373 2.5 91.3 1.0
O B:THR376 2.5 83.5 1.0
OD1 B:ASN378 2.6 87.3 1.0
OG1 B:THR373 2.8 91.5 1.0
N B:ASN378 3.1 75.9 1.0
C B:ALA420 3.4 0.9 1.0
CG B:ASN378 3.5 83.0 1.0
C B:THR373 3.6 88.2 1.0
C B:SER377 3.6 78.6 1.0
C B:THR376 3.6 87.1 1.0
CA B:ASN378 3.7 76.0 1.0
OG1 B:THR421 3.8 99.5 1.0
CB B:ALA414 3.9 89.5 1.0
CA B:SER377 3.9 80.8 1.0
CB B:THR373 4.0 86.7 1.0
CA B:THR373 4.0 85.9 1.0
CA B:ALA420 4.0 0.3 1.0
CB B:ASN378 4.1 79.4 1.0
N B:SER377 4.2 82.4 1.0
O B:SER377 4.3 77.5 1.0
O B:ALA411 4.4 79.6 1.0
N B:THR421 4.4 0.9 1.0
CB B:ALA420 4.4 0.1 1.0
ND2 B:ASN378 4.5 84.6 1.0
O6 B:CIT503 4.5 87.5 1.0
N B:GLU374 4.7 88.8 1.0
CA B:THR421 4.8 99.9 1.0
CG2 B:THR373 4.8 86.6 1.0
CA B:THR376 4.9 92.5 1.0
CB B:THR421 4.9 96.4 1.0
N B:THR376 5.0 91.6 1.0

Sodium binding site 5 out of 8 in 5uld

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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:72.4
occ:1.00
 OD1 C:ASN151 2.5 88.0 1.0
O C:SER146 2.5 72.8 1.0
OG C:SER146 2.6 85.7 1.0
O C:GLY199 2.8 83.0 1.0
O C:SER150 2.8 90.3 1.0
C C:SER150 3.1 74.1 1.0
C C:GLY199 3.3 73.4 1.0
C C:SER146 3.4 73.6 1.0
CA C:GLY193 3.4 80.1 1.0
CG C:ASN151 3.5 84.7 1.0
CA C:GLY199 3.5 73.6 1.0
CA C:SER150 3.6 62.5 1.0
N C:ASN151 3.7 77.2 1.0
CB C:SER146 3.7 81.1 1.0
N C:SER150 3.8 63.1 1.0
CA C:SER146 3.8 78.6 1.0
N C:GLY193 3.9 83.6 1.0
ND2 C:ASN151 4.2 83.5 1.0
O C:ALA189 4.2 64.4 1.0
CA C:ASN151 4.2 78.9 1.0
N C:THR200 4.3 71.0 1.0
C C:GLY192 4.4 76.3 1.0
N C:MET147 4.4 72.7 1.0
CB C:ASN151 4.4 82.9 1.0
O C:GLY192 4.5 82.0 1.0
C C:GLY193 4.7 81.3 1.0
CB C:THR200 4.9 81.2 1.0
CA C:MET147 4.9 75.6 1.0
N C:GLY199 4.9 84.8 1.0
C C:ILE149 4.9 73.7 1.0
CA C:THR200 5.0 73.4 1.0
O C:GLY193 5.0 77.6 1.0
C C:MET147 5.0 77.9 1.0

Sodium binding site 6 out of 8 in 5uld

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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:69.1
occ:1.00
 O C:ALA420 2.4 87.5 1.0
OD1 C:ASN378 2.5 61.2 1.0
O C:THR376 2.5 73.7 1.0
O C:THR373 2.6 93.1 1.0
OG1 C:THR373 2.8 79.5 1.0
N C:ASN378 3.1 68.7 1.0
C C:ALA420 3.4 87.7 1.0
CG C:ASN378 3.5 62.7 1.0
C C:SER377 3.6 69.6 1.0
C C:THR373 3.6 82.7 1.0
CA C:ASN378 3.6 63.5 1.0
C C:THR376 3.6 76.8 1.0
OG1 C:THR421 3.8 76.8 1.0
CB C:ALA414 3.9 64.3 1.0
CA C:SER377 3.9 68.0 1.0
CB C:THR373 4.0 75.6 1.0
CA C:THR373 4.0 79.7 1.0
CA C:ALA420 4.0 90.6 1.0
CB C:ASN378 4.1 67.2 1.0
N C:SER377 4.2 68.5 1.0
O C:SER377 4.3 67.5 1.0
O C:ALA411 4.4 55.2 1.0
N C:THR421 4.4 81.8 1.0
ND2 C:ASN378 4.4 61.4 1.0
CB C:ALA420 4.5 86.2 1.0
O5 C:CIT503 4.5 70.3 1.0
CA C:THR421 4.8 74.0 1.0
N C:GLU374 4.8 76.2 1.0
CG2 C:THR373 4.8 70.4 1.0
CA C:THR376 4.9 84.4 1.0
CB C:THR421 4.9 72.9 1.0

Sodium binding site 7 out of 8 in 5uld

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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:72.6
occ:1.00
 O D:SER146 2.5 54.0 1.0
OG D:SER146 2.5 47.4 1.0
OD1 D:ASN151 2.5 59.4 1.0
O D:GLY199 2.8 56.6 1.0
O D:SER150 2.8 59.0 1.0
C D:SER150 3.1 54.1 1.0
C D:SER146 3.3 52.1 1.0
C D:GLY199 3.3 54.0 1.0
CA D:GLY193 3.4 52.8 1.0
CG D:ASN151 3.5 59.6 1.0
CA D:GLY199 3.5 53.1 1.0
CA D:SER150 3.6 50.9 1.0
CB D:SER146 3.6 50.2 1.0
N D:ASN151 3.7 53.5 1.0
N D:SER150 3.7 50.4 1.0
CA D:SER146 3.8 50.4 1.0
N D:GLY193 3.9 50.5 1.0
O D:ALA189 4.2 72.6 1.0
CA D:ASN151 4.2 54.9 1.0
ND2 D:ASN151 4.2 63.5 1.0
N D:MET147 4.4 51.8 1.0
N D:THR200 4.4 55.5 1.0
C D:GLY192 4.4 51.3 1.0
CB D:ASN151 4.4 58.7 1.0
O D:GLY192 4.5 51.8 1.0
C D:GLY193 4.7 56.0 1.0
CA D:MET147 4.9 53.5 1.0
C D:ILE149 4.9 56.4 1.0
CB D:THR200 4.9 65.6 1.0
N D:GLY199 4.9 54.6 1.0
C D:MET147 5.0 55.2 1.0
OG1 D:THR154 5.0 53.3 1.0
O D:GLY193 5.0 56.9 1.0

Sodium binding site 8 out of 8 in 5uld

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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:57.5
occ:1.00
 O D:ALA420 2.4 61.7 1.0
O D:THR376 2.5 66.0 1.0
O D:THR373 2.5 55.0 1.0
OD1 D:ASN378 2.6 51.0 1.0
OG1 D:THR373 2.8 44.8 1.0
N D:ASN378 3.1 51.2 1.0
C D:ALA420 3.4 58.1 1.0
CG D:ASN378 3.5 53.6 1.0
C D:SER377 3.5 54.6 1.0
C D:THR373 3.6 52.4 1.0
C D:THR376 3.6 66.7 1.0
CA D:ASN378 3.6 51.2 1.0
OG1 D:THR421 3.8 61.8 1.0
CA D:SER377 3.9 60.2 1.0
CB D:ALA414 3.9 52.2 1.0
CB D:THR373 4.0 46.6 1.0
CA D:THR373 4.0 49.0 1.0
CA D:ALA420 4.1 55.4 1.0
CB D:ASN378 4.1 54.6 1.0
N D:SER377 4.1 65.2 1.0
O D:SER377 4.3 53.1 1.0
O D:ALA411 4.4 49.1 1.0
N D:THR421 4.4 58.6 1.0
CB D:ALA420 4.5 51.0 1.0
ND2 D:ASN378 4.5 54.0 1.0
O6 D:CIT503 4.6 83.0 1.0
N D:GLU374 4.8 55.6 1.0
CA D:THR421 4.8 55.7 1.0
CG2 D:THR373 4.8 47.4 1.0
CA D:THR376 4.9 67.8 1.0
CB D:THR421 4.9 55.0 1.0
N D:THR376 5.0 67.9 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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