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Sodium in PDB 3f48: Crystal Structure of Leut Bound to L-Alanine and Sodium

Protein crystallography data

The structure of Crystal Structure of Leut Bound to L-Alanine and Sodium, PDB code: 3f48 was solved by S.K.Singh, C.L.Piscitelli, A.Yamashita, E.Gouaux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.68 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.400, 87.200, 81.200, 90.00, 95.90, 90.00
R / Rfree (%) 21.1 / 22.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Alanine and Sodium (pdb code 3f48). 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-Alanine and Sodium, PDB code: 3f48:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3f48

Go back to Sodium Binding Sites List in 3f48
Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to L-Alanine and Sodium


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-Alanine and Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na751

b:26.2
occ:1.00
O A:VAL23 2.1 26.8 1.0
O A:GLY20 2.2 29.5 1.0
OG1 A:THR354 2.3 28.1 1.0
O A:ALA351 2.3 25.3 1.0
OG A:SER355 2.4 27.1 1.0
N A:SER355 3.0 27.1 1.0
C A:VAL23 3.2 27.2 1.0
CB A:SER355 3.3 27.0 1.0
C A:GLY20 3.3 30.6 1.0
CB A:THR354 3.4 28.1 1.0
C A:THR354 3.4 27.1 1.0
C A:ALA351 3.4 25.3 1.0
CA A:SER355 3.5 25.9 1.0
CA A:GLY24 3.7 26.9 1.0
CA A:THR354 3.8 27.4 1.0
N A:GLY24 3.8 26.2 1.0
CA A:GLY20 4.0 30.2 1.0
CA A:ALA351 4.0 25.5 1.0
O A:THR354 4.1 27.0 1.0
N A:THR354 4.1 25.5 1.0
CA A:VAL23 4.2 27.6 1.0
O A:ASN21 4.3 28.7 1.0
N A:VAL23 4.3 26.5 1.0
N A:ASN21 4.5 29.4 1.0
O A:PHE350 4.5 26.6 1.0
C A:ASN21 4.5 30.8 1.0
N A:GLY352 4.6 24.5 1.0
O A:GLY352 4.7 23.4 1.0
CG2 A:THR354 4.7 28.5 1.0
CB A:VAL23 4.7 30.1 1.0
C A:GLY352 4.8 24.4 1.0
C A:ALA22 4.8 28.1 1.0
CA A:ASN21 4.8 30.2 1.0
CB A:ALA351 4.8 25.6 1.0
CA A:GLY352 4.9 23.2 1.0
C A:SER355 5.0 26.2 1.0

Sodium binding site 2 out of 2 in 3f48

Go back to Sodium Binding Sites List in 3f48
Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to L-Alanine and Sodium


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-Alanine and Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na752

b:28.3
occ:1.00
O A:ALA22 2.2 27.8 1.0
OD1 A:ASN27 2.2 29.5 1.0
O A:THR254 2.2 27.3 1.0
OG1 A:THR254 2.5 30.9 1.0
OD1 A:ASN286 2.5 27.8 1.0
OXT A:ALA601 2.7 28.1 1.0
C A:THR254 3.0 28.4 1.0
C A:ALA22 3.1 28.1 1.0
CG A:ASN27 3.2 30.3 1.0
CA A:THR254 3.2 29.2 1.0
CG A:ASN286 3.4 31.1 1.0
CB A:THR254 3.4 30.1 1.0
ND2 A:ASN286 3.5 30.2 1.0
ND2 A:ASN27 3.6 32.4 1.0
N A:ALA601 3.7 25.0 1.0
C A:ALA601 3.7 26.9 1.0
CA A:VAL23 3.8 27.6 1.0
N A:VAL23 3.8 26.5 1.0
N A:GLY24 3.9 26.2 1.0
CA A:ALA22 4.1 28.4 1.0
OE2 A:GLU290 4.1 32.9 1.0
CA A:ALA601 4.2 27.7 1.0
N A:LEU255 4.3 26.9 1.0
N A:ASN27 4.3 29.0 1.0
C A:VAL23 4.3 27.2 1.0
CB A:ALA22 4.4 29.1 1.0
CG2 A:THR254 4.4 29.4 1.0
CB A:ASN27 4.5 29.4 1.0
N A:THR254 4.6 27.6 1.0
O A:ALA601 4.6 27.1 1.0
O A:PHE253 4.8 27.1 1.0
CB A:ASN286 4.8 29.9 1.0
CA A:ASN27 4.8 29.2 1.0
C A:GLY26 4.8 28.9 1.0
CA A:GLY26 4.9 28.5 1.0
CA A:LEU255 4.9 29.5 1.0
CA A:GLY24 5.0 26.9 1.0

Reference:

S.K.Singh, C.L.Piscitelli, A.Yamashita, E.Gouaux. A Competitive Inhibitor Traps Leut in An Open-to-Out Conformation. Science V. 322 1655 2008.
ISSN: ISSN 0036-8075
PubMed: 19074341
DOI: 10.1126/SCIENCE.1166777
Page generated: Tue Dec 15 06:10:18 2020

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