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Sodium in PDB 3f3c: Crystal Structure of Leut Bound to 4-Fluoro-L-Phenylalanine and Sodium

Protein crystallography data

The structure of Crystal Structure of Leut Bound to 4-Fluoro-L-Phenylalanine and Sodium, PDB code: 3f3c 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) 47.95 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.120, 86.322, 81.579, 90.00, 95.19, 90.00
R / Rfree (%) 19.6 / 23.7

Other elements in 3f3c:

The structure of Crystal Structure of Leut Bound to 4-Fluoro-L-Phenylalanine and Sodium also contains other interesting chemical elements:

Fluorine (F) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to 4-Fluoro-L-Phenylalanine and Sodium (pdb code 3f3c). 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 4-Fluoro-L-Phenylalanine and Sodium, PDB code: 3f3c:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3f3c

Go back to Sodium Binding Sites List in 3f3c
Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to 4-Fluoro-L-Phenylalanine 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 4-Fluoro-L-Phenylalanine and Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na751

b:22.1
occ:1.00
O A:VAL23 2.2 27.3 1.0
O A:ALA351 2.3 29.1 1.0
OG1 A:THR354 2.3 26.8 1.0
O A:GLY20 2.3 31.1 1.0
OG A:SER355 2.4 26.4 1.0
N A:SER355 2.9 29.3 1.0
CB A:SER355 3.2 27.2 1.0
C A:VAL23 3.3 26.2 1.0
C A:ALA351 3.4 27.6 1.0
C A:THR354 3.4 28.7 1.0
CB A:THR354 3.4 28.2 1.0
CA A:SER355 3.4 27.3 1.0
C A:GLY20 3.5 29.9 1.0
CA A:GLY24 3.7 26.4 1.0
CA A:THR354 3.8 27.3 1.0
CA A:ALA351 3.9 28.9 1.0
N A:GLY24 4.0 27.4 1.0
N A:THR354 4.0 25.8 1.0
CA A:GLY20 4.1 28.7 1.0
O A:THR354 4.1 28.8 1.0
O A:PHE350 4.2 28.3 1.0
O A:ASN21 4.3 26.2 1.0
CA A:VAL23 4.4 27.1 1.0
N A:GLY352 4.5 28.8 1.0
O A:GLY352 4.6 28.0 1.0
N A:VAL23 4.6 27.1 1.0
N A:ASN21 4.6 28.4 1.0
C A:ASN21 4.7 26.2 1.0
CG2 A:THR354 4.7 26.0 1.0
C A:GLY352 4.7 29.1 1.0
CB A:ALA351 4.8 27.4 1.0
CA A:GLY352 4.8 28.1 1.0
CB A:VAL23 4.8 28.1 1.0
C A:SER355 4.9 27.2 1.0
CA A:ASN21 4.9 28.6 1.0
C A:LEU353 5.0 25.6 1.0
N A:ALA351 5.0 28.5 1.0

Sodium binding site 2 out of 2 in 3f3c

Go back to Sodium Binding Sites List in 3f3c
Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to 4-Fluoro-L-Phenylalanine 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 4-Fluoro-L-Phenylalanine and Sodium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na752

b:33.0
occ:1.00
O A:ALA22 2.1 25.8 1.0
OD1 A:ASN27 2.3 27.0 1.0
O A:THR254 2.5 27.6 1.0
OD1 A:ASN286 2.5 30.1 1.0
OXT A:PFF601 2.7 21.4 1.0
OG1 A:THR254 2.8 30.1 1.0
C A:ALA22 3.1 26.6 1.0
CG A:ASN27 3.2 27.6 1.0
C A:THR254 3.3 27.1 1.0
CA A:THR254 3.4 27.8 1.0
ND2 A:ASN27 3.5 27.7 1.0
CG A:ASN286 3.5 28.6 1.0
N A:PFF601 3.6 25.0 1.0
C A:PFF601 3.6 25.4 1.0
CB A:THR254 3.7 27.3 1.0
N A:GLY24 3.7 27.4 1.0
CA A:VAL23 3.7 27.1 1.0
N A:VAL23 3.8 27.1 1.0
ND2 A:ASN286 3.8 27.7 1.0
CA A:ALA22 4.1 25.7 1.0
CA A:PFF601 4.1 26.8 1.0
C A:VAL23 4.2 26.2 1.0
N A:ASN27 4.3 29.3 1.0
OE2 A:GLU290 4.4 30.3 1.0
CB A:ALA22 4.5 25.5 1.0
O A:PFF601 4.5 26.4 1.0
CB A:ASN27 4.5 27.3 1.0
N A:LEU255 4.6 28.1 1.0
N A:THR254 4.7 26.5 1.0
O A:PHE253 4.7 26.0 1.0
CG2 A:THR254 4.8 27.4 1.0
CA A:GLY24 4.8 26.4 1.0
C A:GLY26 4.8 29.6 1.0
CB A:ASN286 4.8 29.5 1.0
CA A:ASN27 4.8 28.4 1.0
CA A:GLY26 4.9 29.3 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 06:10:15 2020

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