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Sodium in PDB 3f3e: Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium

Protein crystallography data

The structure of Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium, PDB code: 3f3e 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) 44.44 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 89.361, 86.664, 81.382, 90.00, 95.94, 90.00
R / Rfree (%) 18 / 20.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Leucine (30 Mm) and Sodium (pdb code 3f3e). 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-Leucine (30 Mm) and Sodium, PDB code: 3f3e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3f3e

Go back to Sodium Binding Sites List in 3f3e
Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to L-Leucine (30 Mm) 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-Leucine (30 Mm) and Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na751

b:22.5
occ:1.00
O A:VAL23 2.2 21.4 1.0
O A:GLY20 2.3 22.8 1.0
O A:ALA351 2.4 19.8 1.0
OG1 A:THR354 2.4 24.8 1.0
OG A:SER355 2.5 19.7 1.0
N A:SER355 2.9 21.5 1.0
C A:VAL23 3.2 21.2 1.0
CB A:SER355 3.3 20.4 1.0
C A:THR354 3.3 21.5 1.0
C A:GLY20 3.4 21.5 1.0
CB A:THR354 3.4 24.8 1.0
C A:ALA351 3.4 22.8 1.0
CA A:SER355 3.5 20.1 1.0
CA A:GLY24 3.6 20.9 1.0
CA A:THR354 3.7 19.5 1.0
N A:GLY24 3.9 21.8 1.0
CA A:ALA351 4.0 20.4 1.0
O A:THR354 4.0 21.9 1.0
CA A:GLY20 4.0 28.5 1.0
N A:THR354 4.1 19.7 1.0
O A:ASN21 4.3 20.9 1.0
CA A:VAL23 4.3 18.7 1.0
N A:VAL23 4.3 19.6 1.0
O A:PHE350 4.4 21.9 1.0
N A:ASN21 4.5 19.8 1.0
C A:ASN21 4.6 27.2 1.0
N A:GLY352 4.6 19.1 1.0
O A:GLY352 4.6 20.5 1.0
C A:GLY352 4.7 18.4 1.0
CG2 A:THR354 4.8 20.2 1.0
C A:ALA22 4.8 22.8 1.0
CB A:VAL23 4.8 20.4 1.0
CA A:ASN21 4.8 21.2 1.0
CB A:ALA351 4.8 19.9 1.0
CA A:GLY352 4.8 18.4 1.0
C A:SER355 5.0 22.8 1.0
O A:ALA22 5.0 20.6 1.0

Sodium binding site 2 out of 2 in 3f3e

Go back to Sodium Binding Sites List in 3f3e
Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to L-Leucine (30 Mm) 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-Leucine (30 Mm) and Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na752

b:22.8
occ:1.00
O A:ALA22 2.3 20.6 1.0
OD1 A:ASN27 2.3 21.6 1.0
O A:THR254 2.4 20.5 1.0
OG1 A:THR254 2.5 22.6 1.0
OD1 A:ASN286 2.6 21.8 1.0
OXT A:LEU601 2.6 20.9 1.0
C A:THR254 3.2 25.5 1.0
C A:ALA22 3.2 22.8 1.0
CG A:ASN27 3.2 24.2 1.0
CA A:THR254 3.2 24.0 1.0
CG A:ASN286 3.4 23.6 1.0
CB A:THR254 3.4 24.5 1.0
ND2 A:ASN27 3.6 23.7 1.0
C A:LEU601 3.6 21.1 1.0
ND2 A:ASN286 3.6 26.9 1.0
N A:LEU601 3.6 21.0 1.0
CA A:VAL23 3.8 18.7 1.0
N A:GLY24 3.9 21.8 1.0
N A:VAL23 3.9 19.6 1.0
CA A:ALA22 4.1 19.8 1.0
CA A:LEU601 4.2 24.0 1.0
OE2 A:GLU290 4.2 26.1 1.0
N A:ASN27 4.3 22.1 1.0
C A:VAL23 4.3 21.2 1.0
N A:LEU255 4.4 21.6 1.0
CB A:ALA22 4.4 23.7 1.0
CB A:ASN27 4.5 23.5 1.0
CG2 A:THR254 4.5 22.7 1.0
O A:LEU601 4.5 21.9 1.0
N A:THR254 4.6 20.7 1.0
O A:PHE253 4.7 21.4 1.0
C A:GLY26 4.8 23.9 1.0
CA A:ASN27 4.8 24.8 1.0
CB A:ASN286 4.8 20.8 1.0
CA A:GLY26 4.9 22.8 1.0
CA A:GLY24 4.9 20.9 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 06:10:17 2020

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