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Sodium in PDB 5ul5: Crystal Structure of RPE65 in Complex with Mb-004 and Palmitate

Enzymatic activity of Crystal Structure of RPE65 in Complex with Mb-004 and Palmitate

All present enzymatic activity of Crystal Structure of RPE65 in Complex with Mb-004 and Palmitate:
3.1.1.64;

Protein crystallography data

The structure of Crystal Structure of RPE65 in Complex with Mb-004 and Palmitate, PDB code: 5ul5 was solved by P.D.Kiser, K.Palczewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.88 / 2.20
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 175.730, 175.730, 86.370, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 20.9

Other elements in 5ul5:

The structure of Crystal Structure of RPE65 in Complex with Mb-004 and Palmitate also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of RPE65 in Complex with Mb-004 and Palmitate (pdb code 5ul5). 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 RPE65 in Complex with Mb-004 and Palmitate, PDB code: 5ul5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ul5

Go back to Sodium Binding Sites List in 5ul5
Sodium binding site 1 out of 2 in the Crystal Structure of RPE65 in Complex with Mb-004 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 RPE65 in Complex with Mb-004 and Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:58.3
occ:1.00
O A:GLN461 2.3 44.4 1.0
O2 A:PG6605 2.5 71.7 1.0
O6 A:PG6605 2.6 63.8 1.0
O4 A:PG6605 2.7 55.6 1.0
O5 A:PG6605 2.7 54.9 1.0
O3 A:PG6605 2.8 70.0 1.0
C4 A:PG6605 3.3 69.6 1.0
C6 A:PG6605 3.4 66.3 1.0
C9 A:PG6605 3.4 52.2 1.0
C7 A:PG6605 3.5 59.6 1.0
C8 A:PG6605 3.5 52.4 1.0
C A:GLN461 3.5 42.3 1.0
C5 A:PG6605 3.5 67.8 1.0
C11 A:PG6605 3.6 61.1 1.0
C10 A:PG6605 3.6 59.6 1.0
C3 A:PG6605 3.7 72.7 1.0
C2 A:PG6605 3.9 76.7 1.0
CA A:GLN461 4.4 44.1 1.0
N A:GLN461 4.4 40.3 1.0
N A:GLU462 4.5 44.5 1.0
CA A:GLU462 4.6 45.4 1.0
CB A:GLN461 4.7 43.2 1.0
CG A:GLN461 4.9 46.4 1.0
CG A:GLU462 4.9 51.7 1.0

Sodium binding site 2 out of 2 in 5ul5

Go back to Sodium Binding Sites List in 5ul5
Sodium binding site 2 out of 2 in the Crystal Structure of RPE65 in Complex with Mb-004 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 RPE65 in Complex with Mb-004 and Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na605

b:54.0
occ:1.00
O B:GLN461 2.3 42.6 1.0
O5 B:PG6604 2.4 52.5 1.0
O B:HOH885 2.5 54.6 1.0
O2 B:PG6604 2.6 65.1 1.0
O4 B:PG6604 2.7 46.7 1.0
O3 B:PG6604 2.7 50.4 1.0
O1 B:PG6604 2.8 64.1 1.0
C9 B:PG6604 3.3 53.6 1.0
C8 B:PG6604 3.5 48.1 1.0
C B:GLN461 3.5 42.7 1.0
C4 B:PG6604 3.5 57.4 1.0
C2 B:PG6604 3.6 62.9 1.0
C3 B:PG6604 3.6 64.9 1.0
C7 B:PG6604 3.6 48.1 1.0
C5 B:PG6604 3.6 54.7 1.0
C6 B:PG6604 3.7 48.6 1.0
N B:GLU462 4.4 40.9 1.0
CA B:GLN461 4.4 41.7 1.0
N B:GLN461 4.4 37.4 1.0
CA B:GLU462 4.5 42.4 1.0
CB B:GLN461 4.8 40.4 1.0
CG B:GLU462 4.8 46.8 1.0

Reference:

P.D.Kiser, J.Zhang, M.Badiee, J.Kinoshita, N.S.Peachey, G.P.Tochtrop, K.Palczewski. Rational Tuning of Visual Cycle Modulator Pharmacodynamics. J. Pharmacol. Exp. Ther. V. 362 131 2017.
ISSN: ESSN 1521-0103
PubMed: 28476927
DOI: 10.1124/JPET.117.240721
Page generated: Tue Dec 15 11:42:27 2020

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