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Sodium in PDB 3usk: Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles

Protein crystallography data

The structure of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles, PDB code: 3usk was solved by H.Wang, J.Elferich, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 4.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 70.160, 112.483, 165.320, 90.00, 97.57, 90.00
R / Rfree (%) 26.5 / 27.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles (pdb code 3usk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles, PDB code: 3usk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3usk

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Sodium binding site 1 out of 8 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na751

b:81.4
occ:1.00
 O A:VAL23 2.0 74.4 1.0
O A:GLY20 2.2 67.6 1.0
OG1 A:THR354 2.4 78.7 1.0
OG A:SER355 2.4 84.5 1.0
O A:ALA351 2.4 79.4 1.0
C A:VAL23 3.1 81.2 1.0
N A:SER355 3.2 78.8 1.0
C A:GLY20 3.4 82.8 1.0
CB A:THR354 3.4 81.7 1.0
CB A:SER355 3.4 79.8 1.0
C A:ALA351 3.5 78.9 1.0
CA A:GLY24 3.5 75.5 1.0
C A:THR354 3.6 75.6 1.0
CA A:SER355 3.7 76.7 1.0
N A:GLY24 3.7 89.4 1.0
CA A:THR354 3.9 78.4 1.0
CA A:ALA351 4.0 82.4 1.0
O A:ASN21 4.1 78.3 1.0
CA A:GLY20 4.1 78.2 1.0
O A:THR354 4.2 75.8 1.0
CA A:VAL23 4.2 80.2 1.0
N A:VAL23 4.3 81.6 1.0
N A:THR354 4.3 69.0 1.0
C A:ASN21 4.3 79.5 1.0
N A:ASN21 4.4 74.4 1.0
C A:ALA22 4.6 72.3 1.0
CA A:ASN21 4.6 80.5 1.0
N A:GLY352 4.6 73.2 1.0
CG2 A:THR354 4.7 67.8 1.0
O A:ALA22 4.7 71.5 1.0
CB A:ALA351 4.7 70.9 1.0
O A:PHE350 4.8 74.6 1.0
CB A:VAL23 4.8 76.8 1.0
O A:ALA19 4.8 82.2 1.0
N A:ALA22 4.9 71.3 1.0
CA A:GLY352 5.0 77.6 1.0
C A:GLY24 5.0 79.0 1.0

Sodium binding site 2 out of 8 in 3usk

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Sodium binding site 2 out of 8 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na752

b:77.8
occ:1.00
 OD1 A:ASN27 2.4 85.1 1.0
O A:THR254 2.4 71.0 1.0
O A:ALA22 2.4 71.5 1.0
OG1 A:THR254 2.4 81.2 1.0
OD1 A:ASN286 2.4 74.2 1.0
O A:LEU601 2.6 74.8 1.0
C A:ALA22 3.1 72.3 1.0
C A:THR254 3.1 74.8 1.0
CA A:THR254 3.2 74.4 1.0
CG A:ASN27 3.3 82.4 1.0
CG A:ASN286 3.3 79.6 1.0
CB A:THR254 3.4 84.8 1.0
ND2 A:ASN27 3.5 81.7 1.0
ND2 A:ASN286 3.6 74.7 1.0
C A:LEU601 3.7 75.9 1.0
N A:VAL23 3.7 81.6 1.0
CA A:VAL23 3.7 80.2 1.0
N A:LEU601 3.8 69.0 1.0
N A:GLY24 4.0 89.4 1.0
CA A:ALA22 4.1 71.0 1.0
OE2 A:GLU290 4.3 83.7 1.0
C A:VAL23 4.3 81.2 1.0
CA A:LEU601 4.3 73.2 1.0
CG2 A:THR254 4.3 84.1 1.0
CB A:ALA22 4.4 63.0 1.0
N A:LEU255 4.4 73.8 1.0
OXT A:LEU601 4.6 77.0 1.0
N A:ASN27 4.6 70.3 1.0
N A:THR254 4.7 75.4 1.0
CB A:ASN27 4.7 74.0 1.0
CB A:ASN286 4.8 78.5 1.0
O A:PHE253 5.0 74.3 1.0
C A:GLY26 5.0 84.9 1.0

Sodium binding site 3 out of 8 in 3usk

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Sodium binding site 3 out of 8 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na751

b:81.4
occ:1.00
 O B:VAL23 2.0 74.4 1.0
O B:GLY20 2.2 67.6 1.0
OG B:SER355 2.4 84.5 1.0
OG1 B:THR354 2.4 78.7 1.0
O B:ALA351 2.4 79.4 1.0
C B:VAL23 3.1 81.2 1.0
N B:SER355 3.2 78.8 1.0
CB B:THR354 3.4 81.7 1.0
C B:GLY20 3.4 82.8 1.0
CB B:SER355 3.4 79.8 1.0
C B:ALA351 3.5 78.9 1.0
CA B:GLY24 3.5 75.5 1.0
C B:THR354 3.6 75.6 1.0
CA B:SER355 3.7 76.7 1.0
N B:GLY24 3.7 89.4 1.0
CA B:THR354 3.9 78.4 1.0
CA B:ALA351 4.0 82.4 1.0
O B:ASN21 4.1 78.3 1.0
CA B:GLY20 4.1 78.2 1.0
O B:THR354 4.2 75.8 1.0
CA B:VAL23 4.2 80.2 1.0
N B:VAL23 4.3 81.6 1.0
N B:THR354 4.3 69.0 1.0
C B:ASN21 4.3 79.5 1.0
N B:ASN21 4.4 74.4 1.0
C B:ALA22 4.6 72.3 1.0
CA B:ASN21 4.6 80.5 1.0
N B:GLY352 4.6 73.2 1.0
CG2 B:THR354 4.7 67.8 1.0
O B:ALA22 4.7 71.5 1.0
CB B:ALA351 4.7 70.9 1.0
O B:PHE350 4.8 74.6 1.0
CB B:VAL23 4.8 76.8 1.0
O B:ALA19 4.8 82.2 1.0
N B:ALA22 4.9 71.3 1.0
CA B:GLY352 5.0 77.6 1.0
C B:GLY24 5.0 79.0 1.0

Sodium binding site 4 out of 8 in 3usk

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Sodium binding site 4 out of 8 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na752

b:77.8
occ:1.00
 OD1 B:ASN27 2.4 85.1 1.0
O B:THR254 2.4 71.0 1.0
O B:ALA22 2.4 71.5 1.0
OG1 B:THR254 2.4 81.2 1.0
OD1 B:ASN286 2.4 74.2 1.0
O B:LEU601 2.6 74.8 1.0
C B:ALA22 3.1 72.3 1.0
C B:THR254 3.1 74.8 1.0
CA B:THR254 3.2 74.4 1.0
CG B:ASN27 3.3 82.4 1.0
CG B:ASN286 3.3 79.6 1.0
CB B:THR254 3.4 84.8 1.0
ND2 B:ASN27 3.5 81.7 1.0
ND2 B:ASN286 3.6 74.7 1.0
C B:LEU601 3.7 75.9 1.0
N B:VAL23 3.7 81.6 1.0
CA B:VAL23 3.7 80.2 1.0
N B:LEU601 3.8 69.0 1.0
N B:GLY24 4.0 89.4 1.0
CA B:ALA22 4.1 71.0 1.0
OE2 B:GLU290 4.3 83.7 1.0
C B:VAL23 4.3 81.2 1.0
CA B:LEU601 4.3 73.2 1.0
CG2 B:THR254 4.3 84.1 1.0
CB B:ALA22 4.4 63.0 1.0
N B:LEU255 4.4 73.8 1.0
OXT B:LEU601 4.6 77.0 1.0
N B:ASN27 4.6 70.3 1.0
N B:THR254 4.7 75.4 1.0
CB B:ASN27 4.7 74.0 1.0
CB B:ASN286 4.8 78.5 1.0
O B:PHE253 5.0 74.3 1.0
C B:GLY26 5.0 84.9 1.0

Sodium binding site 5 out of 8 in 3usk

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Sodium binding site 5 out of 8 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na751

b:81.4
occ:1.00
 O C:VAL23 2.0 74.4 1.0
O C:GLY20 2.2 67.6 1.0
OG1 C:THR354 2.4 78.7 1.0
OG C:SER355 2.4 84.5 1.0
O C:ALA351 2.4 79.4 1.0
C C:VAL23 3.1 81.2 1.0
N C:SER355 3.2 78.8 1.0
CB C:THR354 3.4 81.7 1.0
C C:GLY20 3.4 82.8 1.0
CB C:SER355 3.4 79.8 1.0
C C:ALA351 3.5 78.9 1.0
CA C:GLY24 3.5 75.5 1.0
C C:THR354 3.6 75.6 1.0
CA C:SER355 3.7 76.7 1.0
N C:GLY24 3.7 89.4 1.0
CA C:THR354 3.9 78.4 1.0
CA C:ALA351 4.0 82.4 1.0
O C:ASN21 4.1 78.3 1.0
CA C:GLY20 4.1 78.2 1.0
O C:THR354 4.2 75.8 1.0
CA C:VAL23 4.2 80.2 1.0
N C:VAL23 4.3 81.6 1.0
N C:THR354 4.3 69.0 1.0
C C:ASN21 4.3 79.5 1.0
N C:ASN21 4.4 74.4 1.0
C C:ALA22 4.6 72.3 1.0
CA C:ASN21 4.6 80.5 1.0
N C:GLY352 4.6 73.2 1.0
CG2 C:THR354 4.7 67.8 1.0
O C:ALA22 4.7 71.5 1.0
CB C:ALA351 4.7 70.9 1.0
O C:PHE350 4.8 74.6 1.0
CB C:VAL23 4.8 76.8 1.0
O C:ALA19 4.8 82.2 1.0
N C:ALA22 4.9 71.3 1.0
CA C:GLY352 5.0 77.6 1.0
C C:GLY24 5.0 79.0 1.0

Sodium binding site 6 out of 8 in 3usk

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Sodium binding site 6 out of 8 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na752

b:77.8
occ:1.00
 OD1 C:ASN27 2.4 85.1 1.0
O C:THR254 2.4 71.0 1.0
O C:ALA22 2.4 71.5 1.0
OG1 C:THR254 2.4 81.2 1.0
OD1 C:ASN286 2.4 74.2 1.0
O C:LEU601 2.6 74.8 1.0
C C:ALA22 3.1 72.3 1.0
C C:THR254 3.1 74.8 1.0
CA C:THR254 3.2 74.4 1.0
CG C:ASN27 3.3 82.4 1.0
CG C:ASN286 3.3 79.6 1.0
CB C:THR254 3.4 84.8 1.0
ND2 C:ASN27 3.5 81.7 1.0
ND2 C:ASN286 3.6 74.7 1.0
C C:LEU601 3.7 75.9 1.0
N C:VAL23 3.7 81.6 1.0
CA C:VAL23 3.7 80.2 1.0
N C:LEU601 3.8 69.0 1.0
N C:GLY24 4.0 89.4 1.0
CA C:ALA22 4.1 71.0 1.0
OE2 C:GLU290 4.3 83.7 1.0
C C:VAL23 4.3 81.2 1.0
CA C:LEU601 4.3 73.2 1.0
CG2 C:THR254 4.3 84.1 1.0
CB C:ALA22 4.4 63.0 1.0
N C:LEU255 4.4 73.8 1.0
OXT C:LEU601 4.6 77.0 1.0
N C:ASN27 4.6 70.3 1.0
N C:THR254 4.7 75.4 1.0
CB C:ASN27 4.7 74.0 1.0
CB C:ASN286 4.8 78.5 1.0
O C:PHE253 5.0 74.3 1.0
C C:GLY26 5.0 84.9 1.0

Sodium binding site 7 out of 8 in 3usk

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Sodium binding site 7 out of 8 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na751

b:81.4
occ:1.00
 O D:VAL23 2.0 74.4 1.0
O D:GLY20 2.2 67.6 1.0
OG D:SER355 2.4 84.5 1.0
OG1 D:THR354 2.4 78.7 1.0
O D:ALA351 2.4 79.4 1.0
C D:VAL23 3.1 81.2 1.0
N D:SER355 3.2 78.8 1.0
CB D:THR354 3.4 81.7 1.0
C D:GLY20 3.4 82.8 1.0
CB D:SER355 3.4 79.8 1.0
C D:ALA351 3.5 78.9 1.0
CA D:GLY24 3.5 75.5 1.0
C D:THR354 3.6 75.6 1.0
CA D:SER355 3.7 76.7 1.0
N D:GLY24 3.7 89.4 1.0
CA D:THR354 3.9 78.4 1.0
CA D:ALA351 4.0 82.4 1.0
O D:ASN21 4.1 78.3 1.0
CA D:GLY20 4.1 78.2 1.0
O D:THR354 4.2 75.8 1.0
CA D:VAL23 4.2 80.2 1.0
N D:VAL23 4.3 81.6 1.0
N D:THR354 4.3 69.0 1.0
C D:ASN21 4.3 79.5 1.0
N D:ASN21 4.4 74.4 1.0
C D:ALA22 4.6 72.3 1.0
CA D:ASN21 4.6 80.5 1.0
N D:GLY352 4.6 73.2 1.0
CG2 D:THR354 4.7 67.8 1.0
O D:ALA22 4.7 71.5 1.0
CB D:ALA351 4.7 70.9 1.0
O D:PHE350 4.8 74.6 1.0
CB D:VAL23 4.8 76.8 1.0
O D:ALA19 4.8 82.2 1.0
N D:ALA22 4.9 71.3 1.0
CA D:GLY352 5.0 77.6 1.0

Sodium binding site 8 out of 8 in 3usk

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Sodium binding site 8 out of 8 in the Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Leut Bound to L-Leucine in Space Group P21 From Lipid Bicelles within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na752

b:77.8
occ:1.00
 OD1 D:ASN27 2.4 85.1 1.0
O D:THR254 2.4 71.0 1.0
O D:ALA22 2.4 71.5 1.0
OG1 D:THR254 2.4 81.2 1.0
OD1 D:ASN286 2.4 74.2 1.0
O D:LEU601 2.6 74.8 1.0
C D:ALA22 3.1 72.3 1.0
C D:THR254 3.1 74.8 1.0
CA D:THR254 3.2 74.4 1.0
CG D:ASN27 3.3 82.4 1.0
CG D:ASN286 3.3 79.6 1.0
CB D:THR254 3.4 84.8 1.0
ND2 D:ASN27 3.5 81.7 1.0
ND2 D:ASN286 3.6 74.7 1.0
C D:LEU601 3.7 75.9 1.0
N D:VAL23 3.7 81.6 1.0
CA D:VAL23 3.7 80.2 1.0
N D:LEU601 3.8 69.0 1.0
N D:GLY24 4.0 89.4 1.0
CA D:ALA22 4.1 71.0 1.0
OE2 D:GLU290 4.3 83.7 1.0
C D:VAL23 4.3 81.2 1.0
CA D:LEU601 4.3 73.2 1.0
CG2 D:THR254 4.3 84.1 1.0
CB D:ALA22 4.4 63.0 1.0
N D:LEU255 4.4 73.8 1.0
OXT D:LEU601 4.6 77.0 1.0
N D:ASN27 4.6 70.3 1.0
N D:THR254 4.7 75.4 1.0
CB D:ASN27 4.7 74.0 1.0
CB D:ASN286 4.8 78.5 1.0
O D:PHE253 5.0 74.3 1.0
C D:GLY26 5.0 84.9 1.0

Reference:

H.Wang, J.Elferich, E.Gouaux. Structures of Leut in Bicelles Define Conformation and Substrate Binding in A Membrane-Like Context. Nat.Struct.Mol.Biol. V. 19 212 2012.
ISSN: ISSN 1545-9993
PubMed: 22245965
DOI: 10.1038/NSMB.2215
Page generated: Mon Oct 7 13:32:02 2024

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