Sodium in PDB 7lql: Crystal Structure of the R375D Mutant of Leut

Protein crystallography data

The structure of Crystal Structure of the R375D Mutant of Leut, PDB code: 7lql 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) 43.53 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 86.629, 87.059, 80.589, 90, 95.32, 90
R / Rfree (%) 19.3 / 23.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the R375D Mutant of Leut (pdb code 7lql). 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 the R375D Mutant of Leut, PDB code: 7lql:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7lql

Go back to Sodium Binding Sites List in 7lql
Sodium binding site 1 out of 2 in the Crystal Structure of the R375D Mutant of Leut


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 the R375D Mutant of Leut within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na601

b:38.0
occ:1.00
OG1 A:THR354 2.2 38.7 1.0
O A:GLY20 2.2 40.8 1.0
O A:ALA351 2.2 38.5 1.0
O A:VAL23 2.3 40.2 1.0
OG A:SER355 2.4 41.2 1.0
N A:SER355 2.7 40.0 1.0
CB A:SER355 3.1 36.4 1.0
C A:THR354 3.1 39.5 1.0
CA A:SER355 3.2 38.5 1.0
C A:VAL23 3.3 41.0 1.0
CB A:THR354 3.3 35.1 1.0
C A:ALA351 3.4 38.3 1.0
C A:GLY20 3.4 42.0 1.0
CA A:GLY24 3.6 40.4 1.0
CA A:THR354 3.6 39.6 1.0
N A:GLY24 3.8 39.7 1.0
O A:THR354 3.8 36.8 1.0
N A:THR354 4.0 37.6 1.0
CA A:ALA351 4.1 39.8 1.0
CA A:GLY20 4.1 43.0 1.0
O A:ASN21 4.1 40.9 1.0
C A:ASN21 4.4 42.5 1.0
CA A:VAL23 4.4 42.3 1.0
N A:ASN21 4.5 42.4 1.0
N A:GLY352 4.5 35.0 1.0
O A:PHE350 4.5 38.2 1.0
N A:VAL23 4.5 40.0 1.0
O A:GLY352 4.5 38.3 1.0
CG2 A:THR354 4.5 40.5 1.0
C A:GLY352 4.6 38.8 1.0
CA A:ASN21 4.7 41.0 1.0
CA A:GLY352 4.7 39.5 1.0
C A:SER355 4.7 42.0 1.0
C A:ALA22 4.8 40.2 1.0
C A:LEU353 4.9 36.2 1.0
CB A:ALA351 4.9 38.1 1.0
O A:ALA22 4.9 44.8 1.0
CB A:VAL23 4.9 45.2 1.0
C A:GLY24 5.0 41.1 1.0
N A:ALA22 5.0 41.2 1.0
OH A:TYR108 5.0 42.8 1.0

Sodium binding site 2 out of 2 in 7lql

Go back to Sodium Binding Sites List in 7lql
Sodium binding site 2 out of 2 in the Crystal Structure of the R375D Mutant of Leut


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 the R375D Mutant of Leut within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:39.1
occ:1.00
OD1 A:ASN27 2.2 42.5 1.0
O A:THR254 2.2 45.2 1.0
O A:ALA22 2.3 44.8 1.0
OG1 A:THR254 2.4 46.9 1.0
OD1 A:ASN286 2.4 44.3 1.0
O A:ALA603 2.7 43.5 1.0
C A:THR254 3.0 46.2 1.0
CA A:THR254 3.0 43.7 1.0
C A:ALA22 3.2 40.2 1.0
CG A:ASN27 3.2 42.8 1.0
CB A:THR254 3.2 48.6 1.0
CG A:ASN286 3.3 41.2 1.0
ND2 A:ASN286 3.5 44.9 1.0
N A:ALA603 3.5 40.4 1.0
ND2 A:ASN27 3.5 40.4 1.0
C A:ALA603 3.6 42.0 1.0
N A:VAL23 3.9 40.0 1.0
N A:GLY24 3.9 39.7 1.0
CA A:VAL23 3.9 42.3 1.0
OE2 A:GLU290 3.9 49.8 1.0
CA A:ALA22 4.1 40.9 1.0
CA A:ALA603 4.1 42.2 1.0
CG2 A:THR254 4.2 41.1 1.0
N A:LEU255 4.2 45.9 1.0
N A:ASN27 4.3 40.9 1.0
CB A:ALA22 4.3 42.1 1.0
C A:VAL23 4.4 41.0 1.0
N A:THR254 4.4 41.2 1.0
CB A:ASN27 4.5 42.3 1.0
OXT A:ALA603 4.5 39.7 1.0
CB A:ASN286 4.7 41.3 1.0
O A:PHE253 4.7 40.1 1.0
C A:GLY26 4.7 39.8 1.0
CA A:ASN27 4.7 41.9 1.0
CA A:GLY26 4.8 39.5 1.0
CA A:LEU255 4.9 42.9 1.0
CA A:GLY24 5.0 40.4 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 15:59:19 2021

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