Atomistry » Sodium » PDB 3uq0-3v3r » 3usk
Atomistry »
  Sodium »
    PDB 3uq0-3v3r »
      3usk »

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

Go back to Sodium Binding Sites List in 3usk
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

Go back to Sodium Binding Sites List in 3usk
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

Go back to Sodium Binding Sites List in 3usk
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

Go back to Sodium Binding Sites List in 3usk
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

Go back to Sodium Binding Sites List in 3usk
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

Go back to Sodium Binding Sites List in 3usk
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

Go back to Sodium Binding Sites List in 3usk
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

Go back to Sodium Binding Sites List in 3usk
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy