Sodium in PDB 7lqj: Crystal Structure of Leut Bound to L-Alanine

Protein crystallography data

The structure of Crystal Structure of Leut Bound to L-Alanine, PDB code: 7lqj was solved by J.Font, J.Aguilar, A.Galli, R.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.99 / 2.14
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 88.484, 86.866, 81.145, 90, 96.09, 90
R / Rfree (%) 16.7 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Leut Bound to L-Alanine (pdb code 7lqj). 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, PDB code: 7lqj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7lqj

Go back to Sodium Binding Sites List in 7lqj
Sodium binding site 1 out of 2 in the Crystal Structure of Leut Bound to L-Alanine


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:33.1
occ:1.00
OD1 A:ASN27 2.2 31.3 1.0
O A:THR254 2.3 31.4 1.0
OG1 A:THR254 2.5 32.3 1.0
OD1 A:ASN286 2.5 30.6 1.0
O A:ALA22 2.6 30.7 1.0
O A:ALA801 2.7 31.0 1.0
C A:THR254 3.0 31.2 1.0
CA A:THR254 3.1 33.5 1.0
CG A:ASN27 3.1 33.8 1.0
C A:ALA22 3.3 31.8 1.0
CB A:THR254 3.3 31.9 1.0
CG A:ASN286 3.4 32.2 1.0
ND2 A:ASN27 3.5 33.4 1.0
ND2 A:ASN286 3.6 31.9 1.0
N A:ALA801 3.7 30.9 1.0
C A:ALA801 3.7 30.8 1.0
CA A:VAL23 3.9 36.4 1.0
N A:VAL23 3.9 34.5 1.0
N A:GLY24 4.0 31.2 1.0
OE2 A:GLU290 4.1 36.5 1.0
CA A:ALA22 4.2 30.9 1.0
CA A:ALA801 4.2 30.8 1.0
N A:ASN27 4.3 30.5 1.0
N A:LEU255 4.3 29.7 1.0
CG2 A:THR254 4.4 31.2 1.0
C A:VAL23 4.4 33.1 1.0
CB A:ASN27 4.5 32.8 1.0
N A:THR254 4.5 32.5 1.0
CB A:ALA22 4.6 31.2 1.0
OXT A:ALA801 4.6 29.6 1.0
C A:GLY26 4.7 32.7 1.0
CA A:ASN27 4.8 34.0 1.0
CB A:ASN286 4.8 31.9 1.0
O A:PHE253 4.8 30.8 1.0
CA A:GLY26 4.9 30.8 1.0

Sodium binding site 2 out of 2 in 7lqj

Go back to Sodium Binding Sites List in 7lqj
Sodium binding site 2 out of 2 in the Crystal Structure of Leut Bound to L-Alanine


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na803

b:32.8
occ:1.00
O A:VAL23 2.2 33.7 1.0
OG1 A:THR354 2.3 31.0 1.0
O A:GLY20 2.3 33.5 1.0
O A:ALA351 2.3 29.3 1.0
OG A:SER355 2.5 30.1 1.0
N A:SER355 2.8 29.7 1.0
C A:THR354 3.2 30.9 1.0
CB A:SER355 3.2 29.6 1.0
C A:VAL23 3.2 33.1 1.0
CB A:THR354 3.3 31.3 1.0
CA A:SER355 3.4 28.6 1.0
C A:ALA351 3.4 30.1 1.0
C A:GLY20 3.4 34.3 1.0
CA A:THR354 3.6 31.0 1.0
CA A:GLY24 3.6 29.7 1.0
N A:GLY24 3.8 31.2 1.0
O A:THR354 3.9 30.8 1.0
N A:THR354 4.0 29.0 1.0
CA A:ALA351 4.0 29.6 1.0
CA A:GLY20 4.0 35.6 1.0
CA A:VAL23 4.4 36.4 1.0
N A:VAL23 4.4 34.5 1.0
O A:PHE350 4.4 32.8 1.0
O A:ASN21 4.4 28.7 1.0
N A:GLY352 4.5 31.4 1.0
N A:ASN21 4.5 34.5 1.0
O A:GLY352 4.6 31.5 1.0
C A:ASN21 4.6 29.9 1.0
CG2 A:THR354 4.6 33.6 1.0
C A:GLY352 4.7 31.3 1.0
CA A:ASN21 4.8 32.9 1.0
CA A:GLY352 4.8 31.0 1.0
C A:SER355 4.9 30.9 1.0
C A:ALA22 4.9 31.8 1.0
CB A:ALA351 4.9 28.7 1.0
CB A:VAL23 4.9 35.6 1.0
O A:ALA22 5.0 30.7 1.0
C A:LEU353 5.0 31.2 1.0

Reference:

J.Aguilar, M.Cheng, J.Font, A.Schwartz, K.Ledwitch, A.Duran, S.Mabry, A.Belovich, Y.Zhu, A.M.Carter, L.Shei, M.Kurian, C.Fenollar Ferrer, J.Meiler, R.Ryan, H.Mchaourab, I.Bahar, H.Matthies, A.Galli. Psychomotor Impairments and Therapeutic Implications Revealed By A Mutation Associated with Infantile Parkinsonism-Dystonia Elife 2021.
ISSN: ESSN 2050-084X
DOI: 10.7554/ELIFE.68039
Page generated: Mon Jul 12 15:59:30 2021

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