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Sodium in PDB 3usj: 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: 3usj 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) 48.33 / 3.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.307, 179.880, 57.207, 90.00, 89.96, 90.00
R / Rfree (%) 26.4 / 30.9

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 3usj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 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: 3usj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3usj

Go back to Sodium Binding Sites List in 3usj
Sodium binding site 1 out of 4 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:0.7
occ:1.00
 O A:VAL23 2.1 58.5 1.0
O A:GLY20 2.2 41.4 1.0
O A:ALA351 2.3 0.7 1.0
OG1 A:THR354 2.4 97.0 1.0
OG A:SER355 2.4 98.8 1.0
C A:VAL23 3.1 65.6 1.0
N A:SER355 3.2 92.4 1.0
CB A:THR354 3.3 99.7 1.0
C A:GLY20 3.4 56.6 1.0
C A:ALA351 3.4 0.4 1.0
CB A:SER355 3.5 93.8 1.0
CA A:GLY24 3.5 90.8 1.0
C A:THR354 3.5 93.4 1.0
CA A:SER355 3.7 90.3 1.0
N A:GLY24 3.7 1.0 1.0
CA A:THR354 3.9 96.2 1.0
CA A:ALA351 3.9 0.2 1.0
O A:ASN21 4.0 61.6 1.0
O A:THR354 4.1 93.6 1.0
CA A:GLY20 4.1 52.2 1.0
CA A:VAL23 4.3 65.1 1.0
N A:THR354 4.3 86.8 1.0
N A:VAL23 4.3 66.3 1.0
C A:ASN21 4.3 62.8 1.0
N A:ASN21 4.4 57.5 1.0
N A:GLY352 4.5 0.2 1.0
C A:ALA22 4.6 86.2 1.0
CB A:ALA351 4.6 0.2 1.0
CG2 A:THR354 4.6 85.9 1.0
CA A:ASN21 4.6 63.5 1.0
O A:ALA22 4.7 85.4 1.0
O A:PHE350 4.7 60.5 1.0
CB A:VAL23 4.8 61.9 1.0
O A:ALA19 4.9 0.5 1.0
CA A:GLY352 4.9 0.4 1.0
C A:GLY24 4.9 94.7 1.0
C A:GLY352 5.0 0.7 1.0

Sodium binding site 2 out of 4 in 3usj

Go back to Sodium Binding Sites List in 3usj
Sodium binding site 2 out of 4 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:63.5
occ:1.00
 OD1 A:ASN27 2.3 0.3 1.0
O A:ALA22 2.3 85.4 1.0
O A:THR254 2.4 74.0 1.0
OG1 A:THR254 2.4 85.4 1.0
OD1 A:ASN286 2.4 52.4 1.0
O A:LEU601 2.6 62.0 1.0
C A:ALA22 3.0 86.2 1.0
C A:THR254 3.1 78.2 1.0
CG A:ASN27 3.2 0.8 1.0
CA A:THR254 3.2 78.1 1.0
CG A:ASN286 3.3 58.5 1.0
CB A:THR254 3.4 89.2 1.0
ND2 A:ASN27 3.5 0.2 1.0
ND2 A:ASN286 3.5 54.1 1.0
N A:VAL23 3.6 66.3 1.0
CA A:VAL23 3.6 65.1 1.0
C A:LEU601 3.7 62.6 1.0
N A:LEU601 3.7 55.6 1.0
CA A:ALA22 3.9 84.9 1.0
N A:GLY24 3.9 1.0 1.0
CB A:ALA22 4.2 77.5 1.0
C A:VAL23 4.2 65.6 1.0
CA A:LEU601 4.3 59.6 1.0
CG2 A:THR254 4.3 89.1 1.0
OE2 A:GLU290 4.4 82.9 1.0
N A:LEU255 4.4 79.5 1.0
N A:ASN27 4.5 94.8 1.0
OXT A:LEU601 4.6 63.7 1.0
CB A:ASN27 4.6 98.8 1.0
N A:THR254 4.7 79.2 1.0
CB A:ASN286 4.7 57.6 1.0
C A:GLY26 4.8 71.3 1.0
CB A:VAL23 4.9 61.9 1.0
CA A:GLY26 5.0 58.8 1.0
O A:PHE253 5.0 79.9 1.0
CA A:GLY24 5.0 90.8 1.0
CA A:ASN27 5.0 0.9 1.0

Sodium binding site 3 out of 4 in 3usj

Go back to Sodium Binding Sites List in 3usj
Sodium binding site 3 out of 4 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:76.5
occ:1.00
 O B:VAL23 2.1 96.3 1.0
O B:GLY20 2.2 78.7 1.0
O B:ALA351 2.3 76.5 1.0
OG1 B:THR354 2.4 60.9 1.0
OG B:SER355 2.4 99.9 1.0
C B:VAL23 3.1 0.4 1.0
N B:SER355 3.2 93.6 1.0
CB B:THR354 3.3 63.5 1.0
C B:GLY20 3.4 93.7 1.0
C B:ALA351 3.4 76.2 1.0
CB B:SER355 3.5 95.2 1.0
CA B:GLY24 3.5 59.8 1.0
C B:THR354 3.5 57.7 1.0
CA B:SER355 3.7 91.6 1.0
N B:GLY24 3.7 73.6 1.0
CA B:THR354 3.9 60.3 1.0
CA B:ALA351 3.9 79.7 1.0
O B:ASN21 4.0 0.2 1.0
O B:THR354 4.1 57.7 1.0
CA B:GLY20 4.1 89.0 1.0
CA B:VAL23 4.3 0.4 1.0
N B:THR354 4.3 51.1 1.0
N B:VAL23 4.3 0.6 1.0
C B:ASN21 4.3 0.1 1.0
N B:ASN21 4.4 0.6 1.0
N B:GLY352 4.5 79.9 1.0
C B:ALA22 4.6 82.5 1.0
CB B:ALA351 4.6 68.7 1.0
CA B:ASN21 4.6 0.8 1.0
CG2 B:THR354 4.6 49.5 1.0
O B:ALA22 4.7 82.0 1.0
O B:PHE350 4.7 0.2 1.0
CB B:VAL23 4.8 98.8 1.0
O B:ALA19 4.9 0.1 1.0
CA B:GLY352 4.9 84.4 1.0
C B:GLY24 4.9 63.9 1.0
C B:GLY352 5.0 84.6 1.0

Sodium binding site 4 out of 4 in 3usj

Go back to Sodium Binding Sites List in 3usj
Sodium binding site 4 out of 4 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:0.8
occ:1.00
 OD1 B:ASN27 2.3 74.1 1.0
O B:ALA22 2.3 82.0 1.0
O B:THR254 2.4 57.1 1.0
OG1 B:THR254 2.4 68.2 1.0
OD1 B:ASN286 2.4 76.9 1.0
O B:LEU601 2.6 83.5 1.0
C B:ALA22 3.0 82.5 1.0
C B:THR254 3.1 61.3 1.0
CG B:ASN27 3.2 71.4 1.0
CA B:THR254 3.2 61.4 1.0
CG B:ASN286 3.3 82.5 1.0
CB B:THR254 3.4 72.1 1.0
ND2 B:ASN286 3.5 78.0 1.0
ND2 B:ASN27 3.5 70.3 1.0
N B:VAL23 3.6 0.6 1.0
CA B:VAL23 3.6 0.4 1.0
C B:LEU601 3.7 84.4 1.0
N B:LEU601 3.7 77.2 1.0
CA B:ALA22 3.9 81.1 1.0
N B:GLY24 3.9 73.6 1.0
CB B:ALA22 4.2 73.2 1.0
C B:VAL23 4.2 0.4 1.0
CA B:LEU601 4.3 81.4 1.0
CG2 B:THR254 4.3 71.5 1.0
OE2 B:GLU290 4.4 0.2 1.0
N B:LEU255 4.4 68.7 1.0
N B:ASN27 4.5 60.2 1.0
OXT B:LEU601 4.6 85.8 1.0
CB B:ASN27 4.6 63.5 1.0
N B:THR254 4.7 62.7 1.0
CB B:ASN286 4.7 81.2 1.0
C B:GLY26 4.8 74.0 1.0
CB B:VAL23 4.9 98.8 1.0
CA B:GLY26 5.0 61.9 1.0
O B:PHE253 5.0 74.6 1.0
CA B:ASN27 5.0 75.9 1.0
CA B:GLY24 5.0 59.8 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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