Sodium in PDB 7k89: Crystal Structure of Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate

Enzymatic activity of Crystal Structure of Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate

All present enzymatic activity of Crystal Structure of Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate:
3.1.1.64; 5.3.3.22;

Protein crystallography data

The structure of Crystal Structure of Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate, PDB code: 7k89 was solved by P.D.Kiser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.84 / 2.15
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 175.695, 175.695, 86.214, 90, 90, 120
R / Rfree (%) 18.9 / 21.7

Other elements in 7k89:

The structure of Crystal Structure of Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate also contains other interesting chemical elements:

Iron (Fe) 2 atoms
Fluorine (F) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate (pdb code 7k89). 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 Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate, PDB code: 7k89:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7k89

Go back to Sodium Binding Sites List in 7k89
Sodium binding site 1 out of 2 in the Crystal Structure of Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate


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 Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:74.2
occ:1.00
O5 A:PG4603 2.6 59.4 1.0
O1 A:PG4603 2.7 70.6 1.0
O3 A:PG4603 3.0 63.1 1.0
O2 A:PG4603 3.1 68.8 1.0
O A:GLN461 3.2 45.6 1.0
O4 A:PG4603 3.3 61.0 1.0
C6 A:PG4603 3.7 62.0 1.0
C1 A:PG4603 3.8 69.9 1.0
C3 A:PG4603 3.8 66.8 1.0
C8 A:PG4603 3.8 60.0 1.0
C2 A:PG4603 3.8 69.8 1.0
C7 A:PG4603 3.9 60.1 1.0
C5 A:PG4603 4.0 62.4 1.0
C4 A:PG4603 4.0 65.1 1.0
C A:GLN461 4.4 44.8 1.0

Sodium binding site 2 out of 2 in 7k89

Go back to Sodium Binding Sites List in 7k89
Sodium binding site 2 out of 2 in the Crystal Structure of Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate


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 Bovine RPE65 in Complex with 4-Fluoro-Emixustat and Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na604

b:60.5
occ:1.00
O B:GLN461 2.4 41.4 1.0
O B:HOH1000 2.4 55.5 1.0
O5 B:PG4603 2.5 54.6 1.0
O1 B:PG4603 2.6 62.4 1.0
O2 B:PG4603 2.9 63.5 1.0
O3 B:PG4603 2.9 58.8 1.0
O4 B:PG4603 2.9 55.8 1.0
C8 B:PG4603 3.5 55.9 1.0
C B:GLN461 3.6 41.6 1.0
C1 B:PG4603 3.6 63.6 1.0
C7 B:PG4603 3.7 55.6 1.0
C6 B:PG4603 3.7 56.9 1.0
C2 B:PG4603 3.7 64.0 1.0
C3 B:PG4603 3.7 62.0 1.0
C5 B:PG4603 3.8 58.0 1.0
C4 B:PG4603 3.8 60.6 1.0
N B:GLU462 4.5 42.7 1.0
CA B:GLN461 4.5 41.1 1.0
CA B:GLU462 4.6 43.8 1.0
N B:GLN461 4.6 38.7 1.0
CG B:GLU462 4.7 46.5 1.0
CB B:GLN461 4.8 41.6 1.0

Reference:

P.D.Kiser, P.D.Kiser. N/A N/A.
Page generated: Mon Jul 12 15:58:09 2021

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