Iron in PDB 6c7k: Crystal Structure of An Aco/RPE65 Chimera

All present enzymatic activity of Crystal Structure of An Aco/RPE65 Chimera:
1.13.11.75;

The structure of Crystal Structure of An Aco/RPE65 Chimera, PDB code: 6c7k was solved by P.D.Kiser, W.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.84 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	119.346, 125.663, 204.412, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.7

The structure of Crystal Structure of An Aco/RPE65 Chimera also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Crystal Structure of An Aco/RPE65 Chimera (pdb code 6c7k). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of An Aco/RPE65 Chimera, PDB code: 6c7k:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of An Aco/RPE65 Chimera


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 An Aco/RPE65 Chimera within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:54.1 occ:1.00 NE2 A:HIS238 2.1 63.2 1.0 NE2 A:HIS304 2.3 51.8 1.0 NE2 A:HIS183 2.3 49.9 1.0 NE2 A:HIS484 2.3 44.1 1.0 CE1 A:HIS238 3.0 54.2 1.0 CD2 A:HIS484 3.1 44.6 1.0 CE1 A:HIS304 3.1 52.4 1.0 CE1 A:HIS183 3.1 51.4 1.0 CD2 A:HIS238 3.2 66.4 1.0 CD2 A:HIS183 3.3 47.8 1.0 CD2 A:HIS304 3.4 50.3 1.0 CE1 A:HIS484 3.4 44.7 1.0 ND1 A:HIS238 4.1 64.0 1.0 CG A:HIS484 4.3 43.9 1.0 ND1 A:HIS304 4.3 44.5 1.0 CG A:HIS238 4.3 60.1 1.0 ND1 A:HIS183 4.3 45.2 1.0 ND1 A:HIS484 4.4 43.0 1.0 CG A:HIS304 4.4 47.4 1.0 CG A:HIS183 4.4 46.1 1.0 CG2 A:THR136 4.5 41.9 1.0 CE1 A:PHE303 4.8 0.5 1.0

Iron binding site 2 out of 4 in the Crystal Structure of An Aco/RPE65 Chimera


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 An Aco/RPE65 Chimera within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:48.2 occ:1.00 NE2 B:HIS304 2.2 46.8 1.0 NE2 B:HIS238 2.2 49.3 1.0 NE2 B:HIS484 2.3 38.4 1.0 NE2 B:HIS183 2.3 48.2 1.0 CE1 B:HIS304 3.0 49.1 1.0 CE1 B:HIS238 3.1 51.6 1.0 CD2 B:HIS484 3.1 37.4 1.0 CE1 B:HIS183 3.1 57.1 1.0 CD2 B:HIS238 3.3 46.2 1.0 CD2 B:HIS304 3.3 52.7 1.0 CE1 B:HIS484 3.3 42.9 1.0 CD2 B:HIS183 3.4 51.3 1.0 ND1 B:HIS304 4.2 52.1 1.0 ND1 B:HIS238 4.2 52.7 1.0 CG B:HIS484 4.3 40.1 1.0 ND1 B:HIS484 4.3 39.3 1.0 ND1 B:HIS183 4.3 46.2 1.0 CG B:HIS304 4.4 51.9 1.0 CG B:HIS238 4.4 48.4 1.0 CG B:HIS183 4.5 45.2 1.0 CG2 B:THR136 4.5 47.3 1.0 CE1 B:PHE303 4.7 99.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of An Aco/RPE65 Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of An Aco/RPE65 Chimera within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:54.2 occ:0.98 NE2 C:HIS304 2.2 59.6 1.0 NE2 C:HIS238 2.2 59.3 1.0 NE2 C:HIS484 2.3 48.9 1.0 NE2 C:HIS183 2.3 51.5 1.0 CE1 C:HIS304 3.0 58.1 1.0 CE1 C:HIS238 3.1 59.6 1.0 CD2 C:HIS484 3.1 51.3 1.0 CE1 C:HIS183 3.1 56.6 1.0 CD2 C:HIS238 3.3 53.9 1.0 CD2 C:HIS304 3.3 57.9 1.0 CE1 C:HIS484 3.3 48.3 1.0 CD2 C:HIS183 3.4 55.7 1.0 ND1 C:HIS304 4.2 57.1 1.0 ND1 C:HIS238 4.2 58.7 1.0 CG C:HIS484 4.3 49.6 1.0 ND1 C:HIS183 4.3 50.6 1.0 ND1 C:HIS484 4.3 44.7 1.0 CG C:HIS304 4.4 54.4 1.0 CG C:HIS238 4.4 56.5 1.0 CG C:HIS183 4.5 52.4 1.0 CG2 C:THR136 4.6 49.0 1.0 CE1 C:PHE303 4.8 87.7 1.0

Iron binding site 4 out of 4 in the Crystal Structure of An Aco/RPE65 Chimera


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of An Aco/RPE65 Chimera within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:56.1 occ:1.00 NE2 D:HIS238 2.2 52.7 1.0 NE2 D:HIS304 2.3 56.2 1.0 NE2 D:HIS484 2.3 48.2 1.0 NE2 D:HIS183 2.4 47.1 1.0 CE1 D:HIS238 3.0 52.2 1.0 CE1 D:HIS304 3.1 50.6 1.0 CD2 D:HIS484 3.1 43.3 1.0 CE1 D:HIS183 3.2 54.5 1.0 CD2 D:HIS238 3.3 51.3 1.0 CE1 D:HIS484 3.4 48.6 1.0 CD2 D:HIS304 3.4 62.2 1.0 CD2 D:HIS183 3.5 48.0 1.0 ND1 D:HIS238 4.2 52.6 1.0 ND1 D:HIS304 4.3 44.5 1.0 CG D:HIS484 4.3 46.3 1.0 CG D:HIS238 4.4 52.4 1.0 ND1 D:HIS484 4.4 42.4 1.0 ND1 D:HIS183 4.4 48.4 1.0 CG D:HIS304 4.4 50.0 1.0 CG2 D:THR136 4.5 50.5 1.0 CG D:HIS183 4.5 46.0 1.0 CE1 D:PHE303 4.8 97.8 1.0

E.H.Choi, S.Suh, C.L.Sander, C.J.O.Hernandez, E.R.Bulman, N.Khadka, Z.Dong, W.Shi, K.Palczewski, P.D.Kiser. Insights Into the Pathogenesis of Dominant Retinitis Pigmentosa Associated with A D477G Mutation in RPE65. Hum.Mol.Genet. V. 27 2225 2018.
ISSN: ESSN 1460-2083
PubMed: 29659842
DOI: 10.1093/HMG/DDY128