Sodium in PDB 3usm: Crystal Structure of Leut Bound to L-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A)

The structure of Crystal Structure of Leut Bound to L-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A), PDB code: 3usm 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)	37.48 / 3.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	122.254, 90.396, 82.164, 90.00, 103.62, 90.00
R / Rfree (%)	20.8 / 21.9

The structure of Crystal Structure of Leut Bound to L-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A) also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A) (pdb code 3usm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Leut Bound to L-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A), PDB code: 3usm:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to L-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A)


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-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na751 b:60.4 occ:1.00 O A:VAL23 2.0 57.0 1.0 O A:GLY20 2.2 60.3 1.0 O A:ALA351 2.3 61.6 1.0 OG1 A:THR354 2.4 61.4 1.0 OG A:SER355 2.4 55.6 1.0 N A:SER355 3.0 60.8 1.0 C A:VAL23 3.2 59.2 1.0 CB A:THR354 3.3 59.2 1.0 CB A:SER355 3.4 61.3 1.0 C A:GLY20 3.4 61.2 1.0 C A:ALA351 3.4 60.6 1.0 C A:THR354 3.5 61.3 1.0 CA A:GLY24 3.6 51.2 1.0 CA A:SER355 3.6 61.1 1.0 N A:GLY24 3.8 58.0 1.0 CA A:THR354 3.8 57.6 1.0 O A:ASN21 4.0 58.9 1.0 CA A:ALA351 4.1 56.5 1.0 N A:THR354 4.2 54.7 1.0 CA A:GLY20 4.2 60.4 1.0 O A:THR354 4.2 68.5 1.0 CA A:VAL23 4.4 60.0 1.0 C A:ASN21 4.4 59.7 1.0 N A:ASN21 4.5 63.0 1.0 N A:VAL23 4.5 59.7 1.0 N A:GLY352 4.5 56.6 1.0 O A:GLY352 4.6 70.3 1.0 O A:PHE350 4.6 61.7 1.0 CA A:ASN21 4.6 62.1 1.0 CG2 A:THR354 4.6 59.5 1.0 C A:ALA22 4.7 56.3 1.0 O A:ALA22 4.7 57.3 1.0 C A:GLY352 4.7 63.0 1.0 CA A:GLY352 4.8 56.9 1.0 CB A:ALA351 4.9 48.9 1.0 CB A:VAL23 4.9 58.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to L-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A)


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-Selenomethionine in Space Group C2 From Lipid Bicelles (Collected at 1.2 A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na752 b:62.3 occ:1.00 O A:THR254 2.4 56.3 1.0 OD1 A:ASN27 2.4 61.9 1.0 OG1 A:THR254 2.4 63.6 1.0 O A:ALA22 2.4 57.3 1.0 OD1 A:ASN286 2.4 66.0 1.0 OXT A:MSE601 2.6 62.1 1.0 C A:THR254 3.1 61.3 1.0 C A:ALA22 3.1 56.3 1.0 CA A:THR254 3.2 60.6 1.0 CG A:ASN27 3.3 58.0 1.0 CB A:THR254 3.4 61.2 1.0 CG A:ASN286 3.4 63.1 1.0 ND2 A:ASN27 3.5 55.4 1.0 ND2 A:ASN286 3.6 63.2 1.0 N A:VAL23 3.7 59.7 1.0 CA A:VAL23 3.7 60.0 1.0 C A:MSE601 3.8 63.1 1.0 N A:MSE601 3.9 61.4 1.0 N A:GLY24 4.0 58.0 1.0 CA A:ALA22 4.1 52.5 1.0 C A:VAL23 4.2 59.2 1.0 OE2 A:GLU290 4.3 57.4 1.0 N A:LEU255 4.3 58.7 1.0 CB A:ALA22 4.4 60.5 1.0 CG2 A:THR254 4.4 59.5 1.0 CA A:MSE601 4.5 56.6 1.0 N A:THR254 4.6 60.4 1.0 N A:ASN27 4.7 57.5 1.0 O A:MSE601 4.7 62.8 1.0 CB A:ASN27 4.7 63.8 1.0 CB A:ASN286 4.8 62.7 1.0 O A:PHE253 5.0 57.1 1.0 CB A:VAL23 5.0 58.9 1.0

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