Sodium in PDB 3tt1: Crystal Structure of Leut in the Outward-Open Conformation in Complex with Fab

The structure of Crystal Structure of Leut in the Outward-Open Conformation in Complex with Fab, PDB code: 3tt1 was solved by H.Krishnamurthy, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.17 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	102.859, 162.761, 210.081, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 24

The binding sites of Sodium atom in the Crystal Structure of Leut in the Outward-Open Conformation in Complex with Fab (pdb code 3tt1). 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 in the Outward-Open Conformation in Complex with Fab, PDB code: 3tt1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Leut in the Outward-Open Conformation in Complex with Fab


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 in the Outward-Open Conformation in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:78.0 occ:1.00 O A:THR254 2.4 79.1 1.0 OG1 A:THR254 2.4 81.5 1.0 O A:ALA22 2.4 82.9 1.0 OD1 A:ASN286 2.4 76.5 1.0 OD1 A:ASN27 2.4 80.2 1.0 C A:THR254 3.1 68.0 1.0 CA A:THR254 3.2 72.3 1.0 CG A:ASN286 3.3 71.3 1.0 C A:ALA22 3.3 73.5 1.0 CG A:ASN27 3.3 77.5 1.0 CB A:THR254 3.3 79.9 1.0 ND2 A:ASN286 3.5 70.9 1.0 ND2 A:ASN27 3.5 75.1 1.0 N A:VAL23 4.0 71.4 1.0 OE2 A:GLU290 4.0 68.9 1.0 CA A:VAL23 4.1 66.6 1.0 N A:GLY24 4.2 71.3 1.0 CA A:ALA22 4.2 68.2 1.0 N A:LEU255 4.3 63.1 1.0 O A:HOH612 4.4 93.0 1.0 CB A:ALA22 4.4 79.1 1.0 C A:VAL23 4.4 65.1 1.0 CG2 A:THR254 4.5 84.3 1.0 N A:THR254 4.6 74.5 1.0 CB A:ASN286 4.7 65.7 1.0 CB A:ASN27 4.8 74.1 1.0 O A:PHE253 4.9 72.6 1.0 N A:ASN27 5.0 76.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Leut in the Outward-Open Conformation in Complex with Fab


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 in the Outward-Open Conformation in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:82.5 occ:1.00 O A:ALA351 2.0 82.3 1.0 O A:VAL23 2.1 60.3 1.0 OG1 A:THR354 2.4 50.3 1.0 OG A:SER355 2.4 54.3 1.0 O A:GLY20 2.4 66.6 1.0 C A:ALA351 3.2 77.2 1.0 C A:VAL23 3.3 65.1 1.0 CB A:SER355 3.5 56.5 1.0 N A:SER355 3.6 63.8 1.0 C A:GLY20 3.7 62.3 1.0 CB A:THR354 3.7 55.0 1.0 CA A:ALA351 3.8 69.7 1.0 C A:THR354 3.9 66.5 1.0 CA A:SER355 4.0 60.4 1.0 CA A:GLY24 4.0 75.4 1.0 N A:GLY24 4.1 71.3 1.0 O A:ASN21 4.1 67.8 1.0 CA A:THR354 4.2 62.0 1.0 N A:GLY352 4.3 68.6 1.0 CA A:VAL23 4.3 66.6 1.0 O A:PHE350 4.3 53.8 1.0 N A:THR354 4.4 55.7 1.0 CB A:VAL23 4.4 61.0 1.0 C A:ASN21 4.5 61.6 1.0 N A:ASN21 4.6 59.5 1.0 N A:VAL23 4.6 71.4 1.0 CA A:ASN21 4.6 55.5 1.0 CA A:GLY20 4.6 56.9 1.0 CA A:GLY352 4.6 59.2 1.0 O A:THR354 4.6 69.7 1.0 CG1 A:VAL23 4.6 50.1 1.0 CB A:ALA351 4.6 72.1 1.0 CG2 A:THR354 4.7 46.5 1.0 C A:GLY352 4.8 61.0 1.0 O A:GLY352 4.9 63.0 1.0 N A:ALA351 4.9 57.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Leut in the Outward-Open Conformation in Complex with Fab


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 in the Outward-Open Conformation in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:89.5 occ:1.00 O B:THR254 2.4 81.2 1.0 O B:ALA22 2.4 83.5 1.0 OG1 B:THR254 2.4 83.5 1.0 OD1 B:ASN27 2.4 79.2 1.0 OD1 B:ASN286 2.5 80.0 1.0 C B:THR254 3.1 71.3 1.0 CA B:THR254 3.2 72.4 1.0 C B:ALA22 3.3 75.4 1.0 CG B:ASN286 3.3 71.7 1.0 CG B:ASN27 3.3 77.5 1.0 CB B:THR254 3.4 80.1 1.0 ND2 B:ASN27 3.5 75.6 1.0 ND2 B:ASN286 3.5 71.0 1.0 N B:VAL23 4.0 70.9 1.0 OE2 B:GLU290 4.0 73.2 1.0 CA B:VAL23 4.1 67.2 1.0 N B:GLY24 4.1 71.0 1.0 CA B:ALA22 4.2 71.0 1.0 N B:LEU255 4.4 63.4 1.0 C B:VAL23 4.4 66.7 1.0 CB B:ALA22 4.4 81.5 1.0 CG2 B:THR254 4.5 84.4 1.0 N B:THR254 4.6 73.0 1.0 CB B:ASN286 4.7 65.2 1.0 CB B:ASN27 4.8 74.2 1.0 O B:PHE253 4.9 74.7 1.0 N B:ASN27 4.9 76.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Leut in the Outward-Open Conformation in Complex with Fab


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 in the Outward-Open Conformation in Complex with Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:0.5 occ:1.00 O B:ALA351 2.0 81.5 1.0 O B:VAL23 2.1 61.4 1.0 OG1 B:THR354 2.4 53.5 1.0 OG B:SER355 2.4 57.9 1.0 O B:GLY20 2.5 69.3 1.0 C B:ALA351 3.1 78.1 1.0 C B:VAL23 3.3 66.7 1.0 CB B:SER355 3.5 57.5 1.0 N B:SER355 3.6 63.7 1.0 C B:GLY20 3.7 62.9 1.0 CB B:THR354 3.7 56.3 1.0 CA B:ALA351 3.8 70.9 1.0 C B:THR354 4.0 66.6 1.0 CA B:GLY24 4.0 74.7 1.0 CA B:SER355 4.1 60.7 1.0 N B:GLY24 4.1 71.0 1.0 O B:ASN21 4.1 64.8 1.0 CA B:THR354 4.2 62.2 1.0 N B:GLY352 4.3 71.2 1.0 O B:PHE350 4.3 55.5 1.0 CA B:VAL23 4.3 67.2 1.0 N B:THR354 4.4 56.0 1.0 CB B:VAL23 4.4 64.3 1.0 C B:ASN21 4.5 61.0 1.0 N B:VAL23 4.6 70.9 1.0 N B:ASN21 4.6 60.3 1.0 CA B:GLY352 4.6 60.3 1.0 CA B:GLY20 4.6 58.7 1.0 CA B:ASN21 4.6 57.1 1.0 CB B:ALA351 4.6 71.9 1.0 CG1 B:VAL23 4.6 53.4 1.0 O B:THR354 4.6 70.1 1.0 CG2 B:THR354 4.8 48.4 1.0 C B:GLY352 4.8 62.0 1.0 O B:GLY352 4.9 61.3 1.0 N B:ALA351 4.9 61.1 1.0

H.Krishnamurthy, E.Gouaux. X-Ray Structures of Leut in Substrate-Free Outward-Open and Apo Inward-Open States. Nature V. 481 469 2012.
ISSN: ISSN 0028-0836
PubMed: 22230955
DOI: 10.1038/NATURE10737