Iron in PDB 5ul5: 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;

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

The structure of Crystal Structure of RPE65 in Complex with Mb-004 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-004 and Palmitate (pdb code 5ul5). 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-004 and Palmitate, PDB code: 5ul5:
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-004 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-004 and Palmitate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:36.1 occ:1.00 O2 A:PLM602 1.9 56.9 1.0 NE2 A:HIS180 2.2 33.8 1.0 NE2 A:HIS313 2.2 33.3 1.0 NE2 A:HIS527 2.3 33.0 1.0 NE2 A:HIS241 2.3 34.5 1.0 C1 A:PLM602 2.8 53.8 1.0 C2 A:PLM602 3.0 52.9 1.0 CE1 A:HIS180 3.1 30.8 1.0 CD2 A:HIS313 3.1 36.0 1.0 CE1 A:HIS527 3.1 33.5 1.0 CD2 A:HIS527 3.2 34.8 1.0 CE1 A:HIS313 3.2 33.7 1.0 CE1 A:HIS241 3.3 31.1 1.0 CD2 A:HIS180 3.3 33.7 1.0 CD2 A:HIS241 3.3 33.1 1.0 O1 A:PLM602 4.0 53.9 1.0 ND1 A:HIS527 4.2 35.0 1.0 ND1 A:HIS180 4.2 33.8 1.0 CG A:HIS527 4.3 33.9 1.0 CG A:HIS313 4.3 35.6 1.0 C3 A:PLM602 4.3 59.3 1.0 ND1 A:HIS313 4.3 35.7 1.0 CG A:HIS180 4.4 33.5 1.0 C4 A:PLM602 4.4 58.0 1.0 ND1 A:HIS241 4.4 33.2 1.0 CG A:HIS241 4.5 32.0 1.0 CG1 A:VAL134 4.8 40.3 1.0 O A:HOH786 4.9 28.0 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe601 b:33.5 occ:1.00 O1 B:PLM602 1.8 49.4 1.0 NE2 B:HIS313 2.2 31.9 1.0 NE2 B:HIS180 2.3 36.6 1.0 NE2 B:HIS241 2.3 32.1 1.0 NE2 B:HIS527 2.3 33.7 1.0 C1 B:PLM602 2.8 48.2 1.0 CD2 B:HIS313 3.1 32.4 1.0 CE1 B:HIS180 3.1 35.7 1.0 CE1 B:HIS527 3.2 31.6 1.0 C2 B:PLM602 3.2 48.7 1.0 CE1 B:HIS241 3.2 30.0 1.0 CE1 B:HIS313 3.2 31.4 1.0 CD2 B:HIS527 3.3 33.0 1.0 CD2 B:HIS241 3.3 31.0 1.0 CD2 B:HIS180 3.3 33.5 1.0 O2 B:PLM602 3.9 49.7 1.0 ND1 B:HIS527 4.3 32.5 1.0 C4 B:PLM602 4.3 52.2 1.0 CG B:HIS313 4.3 31.3 1.0 ND1 B:HIS313 4.3 33.4 1.0 ND1 B:HIS180 4.3 36.1 1.0 CG B:HIS527 4.3 31.8 1.0 ND1 B:HIS241 4.3 34.4 1.0 C3 B:PLM602 4.4 51.4 1.0 CG B:HIS180 4.4 36.0 1.0 CG B:HIS241 4.4 31.5 1.0 CG1 B:VAL134 4.8 38.2 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