Iron in PDB 5ulg: 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;

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

The structure of Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of RPE65 in Complex with Mb-008 and Palmitate, PDB code: 5ulg:
Jump to Iron binding site number: 1; 2;

Iron 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 Iron with other atoms in the Fe 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:Fe601 b:33.2 occ:1.00 O2 A:PLM602 1.9 58.6 1.0 NE2 A:HIS180 2.2 32.9 1.0 NE2 A:HIS527 2.2 32.0 1.0 NE2 A:HIS313 2.3 29.9 1.0 NE2 A:HIS241 2.4 29.7 1.0 C1 A:PLM602 2.8 53.2 1.0 CE1 A:HIS180 3.0 31.3 1.0 CE1 A:HIS527 3.1 32.9 1.0 C2 A:PLM602 3.1 51.8 1.0 CD2 A:HIS313 3.1 31.7 1.0 CD2 A:HIS527 3.2 31.9 1.0 CD2 A:HIS180 3.2 33.7 1.0 CE1 A:HIS241 3.3 28.7 1.0 CE1 A:HIS313 3.3 29.7 1.0 CD2 A:HIS241 3.4 26.8 1.0 O1 A:PLM602 4.0 56.3 1.0 ND1 A:HIS527 4.2 33.0 1.0 ND1 A:HIS180 4.2 34.0 1.0 CG A:HIS527 4.2 32.6 1.0 CG A:HIS313 4.3 30.8 1.0 CG A:HIS180 4.3 33.3 1.0 C3 A:PLM602 4.3 58.4 1.0 ND1 A:HIS313 4.4 31.6 1.0 C4 A:PLM602 4.4 58.5 1.0 ND1 A:HIS241 4.4 31.0 1.0 CG A:HIS241 4.5 26.9 1.0 CG1 A:VAL134 4.8 35.5 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe601 b:30.2 occ:1.00 O1 B:PLM602 1.9 50.1 1.0 NE2 B:HIS527 2.2 32.0 1.0 NE2 B:HIS180 2.2 35.0 1.0 NE2 B:HIS313 2.2 28.8 1.0 NE2 B:HIS241 2.3 29.0 1.0 C1 B:PLM602 2.9 49.9 1.0 CE1 B:HIS527 3.1 30.1 1.0 CE1 B:HIS180 3.1 34.5 1.0 CD2 B:HIS313 3.1 29.0 1.0 CD2 B:HIS527 3.2 33.3 1.0 C2 B:PLM602 3.2 50.5 1.0 CE1 B:HIS241 3.2 28.8 1.0 CE1 B:HIS313 3.3 29.5 1.0 CD2 B:HIS180 3.3 31.8 1.0 CD2 B:HIS241 3.3 29.2 1.0 O2 B:PLM602 4.1 49.4 1.0 ND1 B:HIS527 4.2 31.2 1.0 CG B:HIS527 4.3 32.7 1.0 ND1 B:HIS180 4.3 34.9 1.0 C4 B:PLM602 4.3 52.3 1.0 CG B:HIS313 4.3 27.5 1.0 C3 B:PLM602 4.3 54.6 1.0 ND1 B:HIS313 4.3 28.6 1.0 ND1 B:HIS241 4.4 32.4 1.0 CG B:HIS180 4.4 35.5 1.0 CG B:HIS241 4.4 29.2 1.0 CG1 B:VAL134 4.9 35.1 1.0

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