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Sodium in PDB 5ulg: Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate

Enzymatic activity of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate

All present enzymatic activity of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate:
3.1.1.64;

Protein crystallography data

The structure of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate, PDB code: 5ulg 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) 47.85 / 2.10
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 175.319, 175.319, 86.653, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 20.7

Other elements in 5ulg:

The structure of Crystal Structure of RPE65 in Complex with Mb-008 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-008 and Palmitate (pdb code 5ulg). 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-008 and Palmitate, PDB code: 5ulg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5ulg

Go back to Sodium Binding Sites List in 5ulg
Sodium binding site 1 out of 2 in the Crystal Structure of RPE65 in Complex with Mb-008 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-008 and Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:52.3
occ:1.00
O A:GLN461 2.4 40.4 1.0
O A:HOH842 2.4 57.1 1.0
O1 A:PG4604 2.5 59.3 1.0
O5 A:PG4604 2.5 54.2 1.0
O3 A:PG4604 2.7 51.0 1.0
O4 A:PG4604 2.7 51.3 1.0
O2 A:PG4604 2.9 64.2 1.0
C1 A:PG4604 3.3 61.7 1.0
C3 A:PG4604 3.5 62.9 1.0
C6 A:PG4604 3.6 50.4 1.0
C8 A:PG4604 3.6 54.0 1.0
C4 A:PG4604 3.6 57.0 1.0
C A:GLN461 3.6 39.1 1.0
C2 A:PG4604 3.6 61.3 1.0
C7 A:PG4604 3.6 53.6 1.0
C5 A:PG4604 3.7 49.3 1.0
N A:GLN461 4.4 35.4 1.0
CA A:GLN461 4.5 37.5 1.0
N A:GLU462 4.5 41.5 1.0
CA A:GLU462 4.6 41.7 1.0
CG A:GLU462 4.7 49.1 1.0
CB A:GLN461 4.8 36.7 1.0

Sodium binding site 2 out of 2 in 5ulg

Go back to Sodium Binding Sites List in 5ulg
Sodium binding site 2 out of 2 in the Crystal Structure of RPE65 in Complex with Mb-008 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-008 and Palmitate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na605

b:47.1
occ:1.00
O B:GLN461 2.2 38.1 1.0
O B:HOH925 2.4 51.0 1.0
O5 B:PG4604 2.4 44.4 1.0
O1 B:PG4604 2.6 62.6 1.0
O4 B:PG4604 2.6 41.5 1.0
O3 B:PG4604 2.7 46.6 1.0
O2 B:PG4604 2.8 59.0 1.0
C8 B:PG4604 3.3 46.2 1.0
C7 B:PG4604 3.4 42.7 1.0
C6 B:PG4604 3.4 42.5 1.0
C B:GLN461 3.5 35.7 1.0
C1 B:PG4604 3.5 59.2 1.0
C5 B:PG4604 3.6 41.5 1.0
C3 B:PG4604 3.6 52.9 1.0
C4 B:PG4604 3.6 49.4 1.0
C2 B:PG4604 3.6 57.1 1.0
N B:GLN461 4.3 32.4 1.0
CA B:GLN461 4.3 37.2 1.0
N B:GLU462 4.4 38.5 1.0
CA B:GLU462 4.5 40.3 1.0
CG B:GLU462 4.6 44.1 1.0
CB B:GLN461 4.7 37.4 1.0
CG B:GLN461 5.0 40.8 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 11:42:42 2020

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