Calcium in PDB 1x8l: Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap

The structure of Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap, PDB code: 1x8l was solved by S.Pakhomova, J.Buck, M.E.Newcomer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.506, 67.192, 85.066, 90.00, 111.85, 90.00
R / Rfree (%)	19.6 / 23.1

The structure of Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap also contains other interesting chemical elements:

Mercury

(Hg)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap (pdb code 1x8l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap, PDB code: 1x8l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1104 b:59.7 occ:1.00 O A:GLU118 2.5 19.3 1.0 OD1 A:ASP122 2.5 33.2 1.0 O A:HOH1243 2.8 45.6 1.0 OD1 A:ASN121 3.1 33.2 1.0 C A:GLU118 3.5 20.8 1.0 CG A:ASP122 3.6 34.4 1.0 CG A:ASN121 3.7 30.6 1.0 ND2 A:ASN121 3.9 29.8 1.0 CA A:GLU118 3.9 21.3 1.0 OD2 A:ASP122 4.1 35.7 1.0 N A:ASP122 4.2 32.7 1.0 CB A:GLU118 4.2 21.0 1.0 C A:ASN121 4.5 31.0 1.0 N A:GLU119 4.7 21.1 1.0 CG A:GLU118 4.8 21.4 1.0 CB A:ASP122 4.8 33.9 1.0 N A:ASN121 4.8 27.9 1.0 CA A:ASP122 4.8 33.9 1.0 CB A:ASN121 4.9 30.2 1.0 CA A:ASN121 4.9 29.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Retinol Dehydratase in Complex with All-Trans-4-Oxoretinol and Inactive Cofactor Pap within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2204 b:45.5 occ:1.00 OD1 B:ASN121 2.3 39.9 1.0 O B:GLU118 2.4 18.3 1.0 OD1 B:ASP122 2.5 31.6 1.0 CG B:ASN121 3.3 31.4 1.0 C B:GLU118 3.4 19.9 1.0 CG B:ASP122 3.5 33.9 1.0 ND2 B:ASN121 3.7 30.6 1.0 OD2 B:ASP122 3.7 36.1 1.0 CA B:GLU118 4.0 20.3 1.0 CB B:GLU118 4.4 20.0 1.0 N B:ASP122 4.4 32.0 1.0 N B:GLU119 4.6 20.5 1.0 CB B:ASN121 4.7 29.1 1.0 CB B:ASP122 4.7 33.6 1.0 N B:ASN121 5.0 27.3 1.0 CA B:ASP122 5.0 33.6 1.0 CA B:GLU119 5.0 21.8 1.0

S.Pakhomova, J.Buck, M.E.Newcomer. The Structures of the Unique Sulfotransferase Retinol Dehydratase with Product and Inhibitors Provide Insight Into Enzyme Mechanism and Inhibition. Protein Sci. V. 14 176 2005.
ISSN: ISSN 0961-8368
PubMed: 15608121
DOI: 10.1110/PS.041061105