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Sodium in PDB 5ul7: 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: 5ul7 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 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 106.694, 101.918, 167.755, 90.00, 98.97, 90.00
R / Rfree (%) 26 / 27

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 5ul7). 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: 5ul7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5ul7

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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:67.2
occ:1.00
 OG A:SER146 2.4 0.3 1.0
O A:SER146 2.5 89.7 1.0
OD1 A:ASN151 2.6 88.5 1.0
O A:GLY199 2.7 95.1 1.0
O A:SER150 2.9 80.3 1.0
CA A:GLY193 3.2 78.5 1.0
C A:SER146 3.3 92.6 1.0
C A:SER150 3.3 77.8 1.0
C A:GLY199 3.5 90.1 1.0
CB A:SER146 3.6 99.9 1.0
N A:GLY193 3.7 77.6 1.0
CG A:ASN151 3.7 89.0 1.0
CA A:GLY199 3.7 90.8 1.0
CA A:SER146 3.7 94.8 1.0
N A:ASN151 3.8 75.7 1.0
O A:ALA189 3.9 96.0 1.0
CA A:SER150 3.9 78.1 1.0
N A:SER150 4.0 81.0 1.0
CA A:ASN151 4.2 78.3 1.0
C A:GLY192 4.2 76.8 1.0
N A:MET147 4.3 89.5 1.0
O A:GLY192 4.3 77.0 1.0
C A:GLY193 4.5 80.5 1.0
CB A:ASN151 4.6 83.9 1.0
ND2 A:ASN151 4.6 97.1 1.0
N A:SER200 4.6 86.6 1.0
CA A:MET147 4.7 85.3 1.0
O A:GLY193 4.8 82.0 1.0
C A:MET147 4.9 83.5 1.0
CB A:SER200 5.0 90.5 1.0

Sodium binding site 2 out of 8 in 5ul7

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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:64.7
occ:1.00
 O A:ALA420 2.5 86.7 1.0
O A:THR373 2.5 77.7 1.0
OD1 A:ASN378 2.5 66.6 1.0
OG1 A:THR373 2.6 71.9 1.0
O A:ALA376 2.6 70.4 1.0
N A:ASN378 2.9 75.4 1.0
C A:SER377 3.3 79.1 1.0
CA A:ASN378 3.4 75.3 1.0
CG A:ASN378 3.4 73.3 1.0
C A:ALA420 3.5 79.5 1.0
C A:THR373 3.5 74.9 1.0
C A:ALA376 3.7 72.2 1.0
CB A:ALA414 3.7 82.3 1.0
OG1 A:THR421 3.7 83.5 1.0
CB A:THR373 3.7 71.2 1.0
O A:SER377 3.7 81.5 1.0
CA A:THR373 3.9 73.5 1.0
CA A:SER377 3.9 78.0 1.0
O A:ALA411 3.9 71.3 1.0
CB A:ASN378 4.0 75.0 1.0
CA A:ALA420 4.1 74.5 1.0
N A:SER377 4.2 74.8 1.0
ND2 A:ASN378 4.4 76.5 1.0
CB A:ALA420 4.5 68.9 1.0
N A:THR421 4.5 81.4 1.0
CG2 A:THR373 4.5 72.1 1.0
N A:GLU374 4.7 74.9 1.0
C A:ASN378 4.8 77.0 1.0
CA A:THR421 4.8 80.0 1.0
CB A:THR421 4.9 77.9 1.0
O1 A:SIN503 4.9 80.3 1.0
CA A:ALA376 5.0 72.5 1.0
CA A:ALA414 5.0 85.3 1.0

Sodium binding site 3 out of 8 in 5ul7

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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:99.1
occ:1.00
 OG B:SER146 2.4 1.0 1.0
O B:SER146 2.5 0.1 1.0
OD1 B:ASN151 2.6 97.3 1.0
O B:GLY199 2.6 91.5 1.0
O B:SER150 2.8 0.8 1.0
C B:SER150 3.2 0.3 1.0
C B:SER146 3.3 0.4 1.0
CA B:GLY193 3.3 0.1 1.0
C B:GLY199 3.4 85.1 1.0
CB B:SER146 3.6 0.3 1.0
CA B:GLY199 3.7 85.4 1.0
CA B:SER146 3.7 0.9 1.0
N B:ASN151 3.7 0.5 1.0
CG B:ASN151 3.7 98.0 1.0
N B:GLY193 3.8 0.7 1.0
CA B:SER150 3.8 0.4 1.0
N B:SER150 3.9 0.1 1.0
O B:ALA189 4.0 0.0 1.0
CA B:ASN151 4.1 0.9 1.0
C B:GLY192 4.2 0.7 1.0
N B:MET147 4.3 0.8 1.0
O B:GLY192 4.3 1.0 1.0
CB B:ASN151 4.6 0.9 1.0
N B:SER200 4.6 82.4 1.0
C B:GLY193 4.6 0.9 1.0
ND2 B:ASN151 4.7 99.3 1.0
CA B:MET147 4.7 0.6 1.0
O B:GLY193 4.9 0.7 1.0
C B:MET147 4.9 0.5 1.0
OG1 B:THR154 5.0 0.5 1.0
C B:ILE149 5.0 0.6 1.0
CB B:SER200 5.0 92.2 1.0

Sodium binding site 4 out of 8 in 5ul7

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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:87.4
occ:1.00
 O B:THR373 2.4 0.8 1.0
O B:ALA420 2.5 0.2 1.0
OG1 B:THR373 2.5 98.5 1.0
OD1 B:ASN378 2.6 0.1 1.0
O B:ALA376 2.6 83.1 1.0
N B:ASN378 3.1 93.5 1.0
C B:SER377 3.4 89.8 1.0
C B:THR373 3.4 0.3 1.0
C B:ALA420 3.4 0.2 1.0
CA B:ASN378 3.5 97.6 1.0
CG B:ASN378 3.5 0.7 1.0
CB B:ALA414 3.7 96.9 1.0
CB B:THR373 3.7 100.0 1.0
C B:ALA376 3.7 86.9 1.0
OG1 B:THR421 3.8 0.8 1.0
O B:SER377 3.8 93.8 1.0
CA B:THR373 3.8 98.8 1.0
CA B:SER377 3.9 86.7 1.0
O B:ALA411 4.0 0.6 1.0
CA B:ALA420 4.1 0.1 1.0
CB B:ASN378 4.1 0.2 1.0
N B:SER377 4.2 86.4 1.0
CB B:ALA420 4.4 0.9 1.0
CG2 B:THR373 4.4 98.0 1.0
N B:THR421 4.5 0.5 1.0
ND2 B:ASN378 4.5 0.5 1.0
N B:GLU374 4.6 98.4 1.0
CA B:THR421 4.8 0.6 1.0
C B:ASN378 4.8 96.5 1.0
CB B:THR421 4.9 0.4 1.0
CA B:ALA414 4.9 97.6 1.0
O1 B:SIN503 5.0 98.8 1.0
CA B:ALA376 5.0 87.5 1.0

Sodium binding site 5 out of 8 in 5ul7

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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:90.0
occ:1.00
 OG C:SER146 2.5 80.9 1.0
O C:SER146 2.5 82.1 1.0
OD1 C:ASN151 2.6 95.8 1.0
O C:GLY199 2.6 89.0 1.0
O C:SER150 2.9 92.1 1.0
CA C:GLY193 3.2 91.3 1.0
C C:SER150 3.3 79.2 1.0
C C:SER146 3.3 79.4 1.0
C C:GLY199 3.4 84.5 1.0
CB C:SER146 3.6 79.4 1.0
CA C:GLY199 3.7 83.7 1.0
N C:GLY193 3.7 91.2 1.0
CG C:ASN151 3.7 90.5 1.0
CA C:SER146 3.8 80.4 1.0
N C:ASN151 3.8 78.8 1.0
CA C:SER150 3.9 72.1 1.0
O C:ALA189 4.0 79.5 1.0
N C:SER150 4.0 74.1 1.0
CA C:ASN151 4.2 79.9 1.0
C C:GLY192 4.2 84.3 1.0
O C:GLY192 4.3 92.1 1.0
N C:MET147 4.3 77.9 1.0
C C:GLY193 4.5 91.7 1.0
N C:SER200 4.6 78.8 1.0
CB C:ASN151 4.6 84.7 1.0
ND2 C:ASN151 4.6 94.2 1.0
CA C:MET147 4.7 80.8 1.0
O C:GLY193 4.8 92.2 1.0
C C:MET147 4.9 80.2 1.0
CB C:SER200 4.9 77.4 1.0

Sodium binding site 6 out of 8 in 5ul7

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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:74.3
occ:1.00
 O C:ALA420 2.5 97.3 1.0
O C:THR373 2.5 87.4 1.0
OD1 C:ASN378 2.6 72.6 1.0
OG1 C:THR373 2.6 74.1 1.0
O C:ALA376 2.6 68.7 1.0
N C:ASN378 2.9 71.3 1.0
C C:SER377 3.3 70.2 1.0
CA C:ASN378 3.4 69.7 1.0
CG C:ASN378 3.5 74.7 1.0
C C:ALA420 3.5 91.8 1.0
C C:THR373 3.5 82.4 1.0
C C:ALA376 3.7 72.0 1.0
O C:SER377 3.7 71.5 1.0
CB C:ALA414 3.7 75.0 1.0
CB C:THR373 3.7 77.4 1.0
OG1 C:THR421 3.8 83.9 1.0
CA C:SER377 3.9 69.4 1.0
CA C:THR373 3.9 82.1 1.0
O C:ALA411 4.0 66.0 1.0
CB C:ASN378 4.0 74.6 1.0
CA C:ALA420 4.1 90.8 1.0
N C:SER377 4.2 67.9 1.0
ND2 C:ASN378 4.5 74.4 1.0
CB C:ALA420 4.5 82.5 1.0
N C:THR421 4.5 88.4 1.0
CG2 C:THR373 4.5 74.2 1.0
N C:GLU374 4.7 77.7 1.0
C C:ASN378 4.7 66.0 1.0
CA C:THR421 4.8 84.7 1.0
CB C:THR421 4.9 82.9 1.0
O1 C:SIN503 4.9 82.6 1.0
CA C:ALA376 5.0 75.4 1.0
OG C:SER381 5.0 68.0 1.0
CA C:ALA414 5.0 80.8 1.0

Sodium binding site 7 out of 8 in 5ul7

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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:79.8
occ:1.00
 OG D:SER146 2.3 70.7 1.0
OD1 D:ASN151 2.5 87.2 1.0
O D:SER146 2.5 72.2 1.0
O D:GLY199 2.7 80.4 1.0
O D:SER150 2.9 88.5 1.0
CA D:GLY193 3.2 62.7 1.0
C D:SER150 3.3 80.4 1.0
C D:SER146 3.3 74.5 1.0
C D:GLY199 3.5 72.3 1.0
CB D:SER146 3.5 74.0 1.0
CG D:ASN151 3.6 89.3 1.0
N D:GLY193 3.7 61.8 1.0
CA D:SER146 3.7 73.8 1.0
N D:ASN151 3.8 78.7 1.0
CA D:GLY199 3.8 72.7 1.0
O D:ALA189 3.9 83.7 1.0
CA D:SER150 3.9 77.6 1.0
N D:SER150 4.0 76.0 1.0
CA D:ASN151 4.1 78.5 1.0
C D:GLY192 4.1 62.2 1.0
O D:GLY192 4.2 61.6 1.0
N D:MET147 4.3 72.9 1.0
CB D:ASN151 4.5 84.2 1.0
C D:GLY193 4.5 66.4 1.0
ND2 D:ASN151 4.5 97.6 1.0
N D:SER200 4.6 67.7 1.0
CA D:MET147 4.8 72.2 1.0
O D:GLY193 4.8 67.7 1.0
CB D:SER200 5.0 72.6 1.0
C D:MET147 5.0 70.3 1.0
OG1 D:THR154 5.0 74.4 1.0

Sodium binding site 8 out of 8 in 5ul7

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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:79.1
occ:1.00
 O D:THR373 2.5 68.2 1.0
O D:ALA420 2.5 86.4 1.0
OD1 D:ASN378 2.6 62.9 1.0
OG1 D:THR373 2.6 62.1 1.0
O D:ALA376 2.6 66.0 1.0
N D:ASN378 3.0 63.5 1.0
C D:SER377 3.3 65.1 1.0
CA D:ASN378 3.4 65.9 1.0
CG D:ASN378 3.5 68.1 1.0
C D:THR373 3.5 68.9 1.0
C D:ALA420 3.5 81.4 1.0
C D:ALA376 3.7 68.3 1.0
CB D:THR373 3.7 64.0 1.0
CB D:ALA414 3.7 70.1 1.0
OG1 D:THR421 3.8 82.2 1.0
O D:SER377 3.8 64.9 1.0
CA D:THR373 3.9 65.8 1.0
CA D:SER377 3.9 66.9 1.0
O D:ALA411 3.9 63.6 1.0
CB D:ASN378 4.0 69.6 1.0
CA D:ALA420 4.1 81.9 1.0
N D:SER377 4.2 68.2 1.0
CB D:ALA420 4.5 79.9 1.0
CG2 D:THR373 4.5 66.2 1.0
ND2 D:ASN378 4.5 70.1 1.0
N D:THR421 4.5 80.6 1.0
N D:GLU374 4.7 72.2 1.0
C D:ASN378 4.8 63.2 1.0
CA D:THR421 4.8 76.7 1.0
CB D:THR421 4.9 74.6 1.0
O2 D:SIN503 4.9 99.2 1.0
CA D:ALA376 5.0 70.3 1.0
CA D:ALA414 5.0 73.2 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 Dec 15 11:42:33 2020

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