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Sodium in PDB 5ule: 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: 5ule 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 (°) 107.143, 102.283, 170.860, 90.00, 98.31, 90.00
R / Rfree (%) 24.7 / 26.6

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

Sodium binding site 1 out of 8 in 5ule

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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:65.0
occ:1.00
 O A:SER146 2.4 78.0 1.0
OG A:SER146 2.4 57.5 1.0
OD1 A:ASN151 2.6 84.6 1.0
O A:GLY199 2.7 0.4 1.0
O A:SER150 3.0 80.4 1.0
C A:SER150 3.0 79.3 1.0
C A:SER146 3.3 79.1 1.0
C A:GLY199 3.5 0.6 1.0
N A:ASN151 3.5 74.6 1.0
CG A:ASN151 3.5 86.0 1.0
CA A:SER150 3.6 79.9 1.0
CB A:SER146 3.6 73.5 1.0
CA A:GLY193 3.6 84.7 1.0
N A:SER150 3.6 85.1 1.0
CA A:SER146 3.7 76.0 1.0
CA A:GLY199 3.8 97.3 1.0
N A:GLY193 4.0 83.3 1.0
CA A:ASN151 4.0 78.0 1.0
O A:ALA189 4.1 0.7 1.0
ND2 A:ASN151 4.3 90.0 1.0
CB A:ASN151 4.4 82.0 1.0
N A:MET147 4.4 81.2 1.0
C A:GLY192 4.4 82.8 1.0
N A:THR200 4.5 93.4 1.0
O A:GLY192 4.6 82.6 1.0
OG1 A:THR154 4.7 76.0 1.0
C A:ILE149 4.8 93.2 1.0
CA A:MET147 4.9 85.7 1.0
C A:GLY193 4.9 88.8 1.0
CB A:THR200 5.0 89.6 1.0
C A:MET147 5.0 84.7 1.0

Sodium binding site 2 out of 8 in 5ule

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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:70.9
occ:1.00
 O A:THR373 2.4 67.9 1.0
O A:ALA420 2.5 90.7 1.0
O A:THR376 2.5 81.4 1.0
OD1 A:ASN378 2.7 69.5 1.0
OG1 A:THR373 2.7 59.1 1.0
N A:ASN378 3.1 80.5 1.0
C A:SER377 3.3 89.5 1.0
C A:ALA420 3.4 87.0 1.0
C A:THR373 3.5 70.9 1.0
CG A:ASN378 3.5 78.8 1.0
C A:THR376 3.5 91.7 1.0
CA A:ASN378 3.6 78.5 1.0
CA A:SER377 3.7 90.2 1.0
OG1 A:THR421 3.8 93.5 1.0
CB A:THR373 3.9 64.6 1.0
O A:SER377 3.9 99.6 1.0
CA A:THR373 3.9 68.6 1.0
CB A:ALA414 4.0 84.0 1.0
N A:SER377 4.0 92.1 1.0
CA A:ALA420 4.1 85.4 1.0
CB A:ASN378 4.2 78.8 1.0
O A:ALA411 4.4 90.1 1.0
ND2 A:ASN378 4.4 83.1 1.0
CB A:ALA420 4.4 71.4 1.0
N A:THR421 4.5 87.8 1.0
N A:GLU374 4.6 73.5 1.0
CG2 A:THR373 4.7 64.4 1.0
CA A:THR376 4.8 99.3 1.0
CA A:THR421 4.8 84.5 1.0
N A:THR376 4.9 90.2 1.0
CB A:THR421 5.0 83.8 1.0
O1 A:SIN503 5.0 88.4 1.0

Sodium binding site 3 out of 8 in 5ule

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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:0.8
occ:1.00
 O B:SER146 2.4 0.8 1.0
OG B:SER146 2.5 0.1 1.0
OD1 B:ASN151 2.6 0.8 1.0
O B:GLY199 2.7 0.8 1.0
O B:SER150 2.9 0.8 1.0
C B:SER150 3.0 97.9 1.0
C B:SER146 3.3 0.2 1.0
C B:GLY199 3.4 96.8 1.0
N B:ASN151 3.5 96.8 1.0
CA B:SER150 3.5 91.3 1.0
CG B:ASN151 3.5 99.7 1.0
N B:SER150 3.6 98.3 1.0
CA B:GLY193 3.6 0.3 1.0
CB B:SER146 3.6 0.3 1.0
CA B:SER146 3.7 0.2 1.0
CA B:GLY199 3.7 93.1 1.0
CA B:ASN151 4.0 96.7 1.0
N B:GLY193 4.0 0.8 1.0
O B:ALA189 4.1 0.7 1.0
ND2 B:ASN151 4.4 99.8 1.0
CB B:ASN151 4.4 98.2 1.0
N B:MET147 4.4 0.3 1.0
C B:GLY192 4.5 0.2 1.0
N B:THR200 4.5 92.9 1.0
O B:GLY192 4.6 0.3 1.0
OG1 B:THR154 4.8 0.1 1.0
C B:ILE149 4.8 0.8 1.0
CA B:MET147 4.9 0.3 1.0
C B:GLY193 5.0 0.3 1.0
CB B:THR200 5.0 0.4 1.0
C B:MET147 5.0 0.5 1.0

Sodium binding site 4 out of 8 in 5ule

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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:0.4
occ:1.00
 O B:THR373 2.4 0.5 1.0
O B:ALA420 2.5 0.9 1.0
O B:THR376 2.6 89.3 1.0
OD1 B:ASN378 2.6 97.9 1.0
OG1 B:THR373 2.7 0.7 1.0
N B:ASN378 3.2 92.6 1.0
C B:ALA420 3.4 0.1 1.0
C B:SER377 3.4 95.9 1.0
C B:THR373 3.5 0.5 1.0
CG B:ASN378 3.5 99.0 1.0
C B:THR376 3.7 96.4 1.0
CA B:ASN378 3.7 94.3 1.0
OG1 B:THR421 3.7 0.7 1.0
CA B:SER377 3.8 95.0 1.0
CB B:THR373 3.8 0.5 1.0
CB B:ALA414 3.9 0.7 1.0
CA B:THR373 3.9 0.4 1.0
O B:SER377 4.0 0.8 1.0
CA B:ALA420 4.0 0.3 1.0
N B:SER377 4.2 93.2 1.0
CB B:ASN378 4.2 99.1 1.0
ND2 B:ASN378 4.3 0.4 1.0
O B:ALA411 4.3 0.2 1.0
CB B:ALA420 4.4 0.5 1.0
N B:THR421 4.4 1.0 1.0
CG2 B:THR373 4.6 97.9 1.0
N B:GLU374 4.6 0.2 1.0
CA B:THR421 4.8 0.7 1.0
CB B:THR421 4.9 0.8 1.0
O1 B:SIN503 4.9 97.2 1.0
CA B:THR376 5.0 0.1 1.0

Sodium binding site 5 out of 8 in 5ule

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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:83.0
occ:1.00
 O C:SER146 2.4 94.8 1.0
OG C:SER146 2.5 97.3 1.0
OD1 C:ASN151 2.6 0.4 1.0
O C:GLY199 2.7 97.3 1.0
O C:SER150 2.9 0.5 1.0
C C:SER150 3.0 88.8 1.0
C C:SER146 3.3 90.7 1.0
C C:GLY199 3.4 86.6 1.0
N C:ASN151 3.4 91.1 1.0
CG C:ASN151 3.5 0.8 1.0
CA C:SER150 3.5 74.4 1.0
N C:SER150 3.6 73.0 1.0
CA C:GLY193 3.6 0.2 1.0
CB C:SER146 3.6 95.5 1.0
CA C:GLY199 3.7 85.3 1.0
CA C:SER146 3.7 91.8 1.0
CA C:ASN151 3.9 97.6 1.0
N C:GLY193 4.0 0.5 1.0
O C:ALA189 4.1 0.8 1.0
ND2 C:ASN151 4.3 0.2 1.0
CB C:ASN151 4.3 0.1 1.0
N C:MET147 4.4 92.0 1.0
N C:THR200 4.5 83.8 1.0
C C:GLY192 4.5 96.5 1.0
O C:GLY192 4.6 0.2 1.0
OG1 C:THR154 4.8 0.7 1.0
C C:ILE149 4.8 86.3 1.0
CA C:MET147 4.9 95.7 1.0
CB C:THR200 5.0 83.5 1.0
C C:GLY193 5.0 0.7 1.0
O3 C:SIN503 5.0 0.3 1.0

Sodium binding site 6 out of 8 in 5ule

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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:92.3
occ:1.00
 O C:THR373 2.5 0.5 1.0
O C:ALA420 2.5 95.6 1.0
O C:THR376 2.6 69.4 1.0
OD1 C:ASN378 2.6 83.4 1.0
OG1 C:THR373 2.7 76.4 1.0
N C:ASN378 3.1 75.2 1.0
C C:SER377 3.4 73.5 1.0
C C:ALA420 3.4 93.2 1.0
CG C:ASN378 3.4 85.7 1.0
C C:THR373 3.5 0.3 1.0
C C:THR376 3.6 79.7 1.0
CA C:ASN378 3.6 75.8 1.0
CA C:SER377 3.8 73.1 1.0
OG1 C:THR421 3.8 89.2 1.0
CB C:THR373 3.9 82.1 1.0
CB C:ALA414 3.9 71.1 1.0
O C:SER377 3.9 70.6 1.0
CA C:THR373 4.0 92.8 1.0
CA C:ALA420 4.1 94.7 1.0
N C:SER377 4.1 74.9 1.0
CB C:ASN378 4.1 81.6 1.0
ND2 C:ASN378 4.3 89.1 1.0
O C:ALA411 4.4 81.7 1.0
CB C:ALA420 4.4 94.2 1.0
N C:THR421 4.4 88.3 1.0
CG2 C:THR373 4.6 74.7 1.0
N C:GLU374 4.7 97.1 1.0
CA C:THR421 4.8 85.7 1.0
CB C:THR421 4.9 86.6 1.0
O1 C:SIN503 4.9 87.4 1.0
CA C:THR376 4.9 89.4 1.0

Sodium binding site 7 out of 8 in 5ule

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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:88.7
occ:1.00
 OG D:SER146 2.4 59.9 1.0
O D:SER146 2.4 61.8 1.0
OD1 D:ASN151 2.5 84.9 1.0
O D:GLY199 2.7 96.8 1.0
O D:SER150 3.0 87.1 1.0
C D:SER150 3.0 79.1 1.0
C D:SER146 3.3 64.7 1.0
C D:GLY199 3.4 85.3 1.0
N D:ASN151 3.4 80.0 1.0
CG D:ASN151 3.5 83.8 1.0
CA D:SER150 3.6 73.2 1.0
CA D:GLY193 3.6 77.7 1.0
CB D:SER146 3.6 66.3 1.0
N D:SER150 3.6 73.0 1.0
CA D:SER146 3.7 64.2 1.0
CA D:GLY199 3.8 82.5 1.0
CA D:ASN151 3.9 80.6 1.0
N D:GLY193 4.0 79.4 1.0
O D:ALA189 4.1 0.5 1.0
ND2 D:ASN151 4.3 84.2 1.0
CB D:ASN151 4.3 82.6 1.0
N D:MET147 4.4 64.5 1.0
C D:GLY192 4.5 81.3 1.0
N D:THR200 4.5 79.8 1.0
O D:GLY192 4.6 75.8 1.0
OG1 D:THR154 4.8 71.0 1.0
C D:ILE149 4.8 81.5 1.0
CA D:MET147 4.9 73.4 1.0
C D:GLY193 4.9 84.4 1.0
CB D:THR200 4.9 86.5 1.0
O4 D:SIN503 5.0 99.1 1.0

Sodium binding site 8 out of 8 in 5ule

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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:82.4
occ:1.00
 O D:THR373 2.5 76.3 1.0
O D:ALA420 2.5 0.5 1.0
OD1 D:ASN378 2.5 68.1 1.0
O D:THR376 2.6 84.9 1.0
OG1 D:THR373 2.7 62.0 1.0
N D:ASN378 3.1 82.4 1.0
CG D:ASN378 3.4 74.5 1.0
C D:SER377 3.4 90.7 1.0
C D:ALA420 3.5 0.9 1.0
C D:THR373 3.5 75.1 1.0
CA D:ASN378 3.6 80.5 1.0
OG1 D:THR421 3.7 95.8 1.0
C D:THR376 3.7 93.8 1.0
CA D:SER377 3.8 89.6 1.0
CB D:THR373 3.9 66.3 1.0
CB D:ALA414 3.9 88.0 1.0
CA D:THR373 4.0 71.8 1.0
O D:SER377 4.0 0.3 1.0
CB D:ASN378 4.1 77.1 1.0
CA D:ALA420 4.1 0.2 1.0
N D:SER377 4.2 92.8 1.0
ND2 D:ASN378 4.3 80.1 1.0
O D:ALA411 4.3 73.3 1.0
CB D:ALA420 4.4 99.6 1.0
N D:THR421 4.4 98.7 1.0
CG2 D:THR373 4.6 64.7 1.0
N D:GLU374 4.7 79.5 1.0
CA D:THR421 4.8 92.2 1.0
CB D:THR421 4.8 86.7 1.0
O2 D:SIN503 4.9 96.4 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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