Arsenic in PDB 7cyz: The Structure of Human ORP3 Osbp-Related Domain

The structure of The Structure of Human ORP3 Osbp-Related Domain, PDB code: 7cyz was solved by X.Dong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.28 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.336, 95.336, 185.251, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 21.9

The binding sites of Arsenic atom in the The Structure of Human ORP3 Osbp-Related Domain (pdb code 7cyz). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 6 binding sites of Arsenic where determined in the The Structure of Human ORP3 Osbp-Related Domain, PDB code: 7cyz:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6;

Arsenic binding site 1 out of 6 in the The Structure of Human ORP3 Osbp-Related Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of The Structure of Human ORP3 Osbp-Related Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:As515 b:0.4 occ:1.00 AS A:CAF515 0.0 0.4 1.0 O1 A:CAF515 1.7 58.6 1.0 CE1 A:CAF515 2.0 43.6 1.0 CE2 A:CAF515 2.0 0.6 1.0 SG A:CAF515 2.2 40.9 1.0 O A:CAF515 3.4 25.2 1.0 CB A:CAF515 3.6 22.7 1.0 C A:CAF515 3.6 30.3 1.0 C A:LEU516 3.9 28.1 1.0 O A:LEU516 4.0 31.9 1.0 N A:LEU516 4.1 30.6 1.0 CA A:CAF515 4.2 28.3 1.0 CA A:LEU516 4.2 24.2 1.0 N A:PRO517 4.3 28.2 1.0 N A:CAF515 4.5 27.0 1.0 O A:HOH1056 4.6 44.5 1.0 O A:HOH934 4.6 37.0 1.0 CA A:PRO517 4.7 26.6 1.0 CD A:PRO517 4.8 31.3 1.0 CB A:ARG513 4.9 26.3 1.0

Arsenic binding site 2 out of 6 in the The Structure of Human ORP3 Osbp-Related Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of The Structure of Human ORP3 Osbp-Related Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:As689 b:64.8 occ:1.00 AS A:CAF689 0.0 64.8 1.0 O1 A:CAF689 1.7 0.1 1.0 CE1 A:CAF689 1.9 0.7 1.0 CE2 A:CAF689 2.0 27.9 1.0 SG A:CAF689 2.2 53.7 1.0 CB A:CAF689 3.2 24.6 1.0 OH A:TYR703 3.8 46.1 1.0 CA A:CAF689 4.1 27.5 1.0 CB A:GLU663 4.3 31.9 1.0 CA A:GLU663 4.3 31.8 1.0 O A:MET662 4.4 31.9 1.0 N A:GLU663 4.5 27.5 1.0 OE2 A:GLU663 4.5 45.0 1.0 C A:MET662 4.5 38.4 1.0 O A:HOH908 4.7 58.0 1.0 CE1 A:HIS691 4.7 47.7 1.0 CB A:SER661 4.8 40.8 1.0 CG A:GLU663 4.8 39.1 1.0 C A:CAF689 5.0 24.7 1.0 CD1 A:TRP658 5.0 52.4 1.0 CZ A:TYR703 5.0 43.2 1.0

Arsenic binding site 3 out of 6 in the The Structure of Human ORP3 Osbp-Related Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of The Structure of Human ORP3 Osbp-Related Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:As760 b:72.2 occ:1.00 AS A:CAF760 0.0 72.2 1.0 O1 A:CAF760 1.7 72.5 1.0 CE2 A:CAF760 2.0 56.9 1.0 CE1 A:CAF760 2.0 63.1 1.0 SG A:CAF760 2.2 54.9 1.0 CB A:CAF760 3.0 21.2 1.0 O A:CAF760 3.9 41.0 1.0 C A:CAF760 4.0 32.6 1.0 CA A:CAF760 4.1 27.5 1.0 ND1 A:HIS748 4.3 42.6 1.0 N A:GLY761 4.4 40.5 1.0 CE1 A:HIS748 4.4 31.6 1.0 CG A:HIS748 4.7 33.9 1.0 C A:GLY761 4.8 64.6 1.0 CA A:GLY761 4.8 54.8 1.0 NE2 A:HIS748 4.9 37.2 1.0 N A:GLY762 5.0 77.9 1.0

Arsenic binding site 4 out of 6 in the The Structure of Human ORP3 Osbp-Related Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of The Structure of Human ORP3 Osbp-Related Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:As515 b:20.0 occ:1.00 AS B:CAF515 0.0 20.0 1.0 O1 B:CAF515 1.7 20.0 1.0 CE1 B:CAF515 2.0 20.0 1.0 CE2 B:CAF515 2.0 20.0 1.0 SG B:CAF515 2.2 20.0 1.0 CB B:CAF515 3.1 20.0 1.0 CA B:CAF515 3.7 20.0 1.0 N B:CAF515 3.7 20.0 1.0 O B:CAF515 3.7 20.0 1.0 C B:CAF515 3.7 20.0 1.0 N B:LEU516 4.4 51.6 1.0 C B:THR514 4.6 53.3 1.0 OG1 B:THR514 4.7 46.3 1.0 N B:THR514 4.8 36.2 1.0

Arsenic binding site 5 out of 6 in the The Structure of Human ORP3 Osbp-Related Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of The Structure of Human ORP3 Osbp-Related Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:As689 b:38.0 occ:1.00 AS B:CAF689 0.0 38.0 1.0 O1 B:CAF689 1.7 0.9 1.0 CE1 B:CAF689 2.0 41.6 1.0 CE2 B:CAF689 2.0 40.0 1.0 SG B:CAF689 2.2 29.7 1.0 CB B:CAF689 3.1 23.5 1.0 O B:HOH937 3.6 41.9 1.0 OH B:TYR703 3.7 53.5 1.0 CZ B:TYR703 4.1 44.6 1.0 CE1 B:HIS691 4.2 40.3 1.0 CE1 B:TYR703 4.2 41.2 1.0 CB B:SER661 4.4 25.3 1.0 O B:HOH944 4.4 32.1 1.0 OG B:SER661 4.5 29.3 1.0 CA B:CAF689 4.5 22.2 1.0 ND1 B:HIS691 4.7 38.5 1.0 CE2 B:TYR703 4.9 39.6 1.0 NE2 B:HIS691 5.0 39.2 1.0

Arsenic binding site 6 out of 6 in the The Structure of Human ORP3 Osbp-Related Domain


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of The Structure of Human ORP3 Osbp-Related Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:As760 b:52.7 occ:1.00 AS B:CAF760 0.0 52.7 1.0 O1 B:CAF760 1.7 0.2 1.0 CE2 B:CAF760 2.0 67.8 1.0 CE1 B:CAF760 2.0 38.0 1.0 SG B:CAF760 2.2 53.6 1.0 CB B:CAF760 3.1 27.3 1.0 O B:CAF760 3.5 29.9 1.0 C B:CAF760 3.6 29.1 1.0 CA B:CAF760 4.0 26.1 1.0 N B:GLY761 4.0 37.2 1.0 CD2 B:HIS748 4.4 42.6 1.0 CA B:GLY761 4.5 50.0 1.0 C B:GLY761 4.6 57.8 1.0 NE2 B:HIS748 4.6 47.1 1.0 CG B:HIS748 4.6 45.9 1.0 N B:GLY762 4.6 78.4 1.0 CE1 B:HIS748 4.9 46.7 1.0 ND1 B:HIS748 4.9 47.4 1.0 N B:CAF760 4.9 21.1 1.0 O B:SER765 5.0 97.2 1.0

X.Dong, Z.Wang, S.Ye, R.Zhang. The Crystal Structure of ORP3 Reveals the Conservative PI4P Binding Pattern. Biochem.Biophys.Res.Commun. V. 529 1005 2020.
ISSN: ESSN 1090-2104
PubMed: 32819557
DOI: 10.1016/J.BBRC.2020.06.090