Zinc in PDB 7d7p: Crystal Structure of the Phosphodiesterase Domain of Salpingoeca Rosetta Rhodopsin Phosphodiesterase

The structure of Crystal Structure of the Phosphodiesterase Domain of Salpingoeca Rosetta Rhodopsin Phosphodiesterase, PDB code: 7d7p was solved by T.Ikuta, W.Shihoya, K.Yamashita, O.Nureki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.52 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	117.200, 67.540, 56.890, 90.00, 110.82, 90.00
R / Rfree (%)	18.8 / 24

The structure of Crystal Structure of the Phosphodiesterase Domain of Salpingoeca Rosetta Rhodopsin Phosphodiesterase also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Crystal Structure of the Phosphodiesterase Domain of Salpingoeca Rosetta Rhodopsin Phosphodiesterase (pdb code 7d7p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Phosphodiesterase Domain of Salpingoeca Rosetta Rhodopsin Phosphodiesterase, PDB code: 7d7p:

Zinc binding site 1 out of 1 in the Crystal Structure of the Phosphodiesterase Domain of Salpingoeca Rosetta Rhodopsin Phosphodiesterase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Phosphodiesterase Domain of Salpingoeca Rosetta Rhodopsin Phosphodiesterase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn806 b:22.9 occ:1.00 OD2 A:ASP492 2.2 17.1 1.0 NE2 A:HIS491 2.2 16.5 1.0 NE2 A:HIS456 2.3 16.1 1.0 OD1 A:ASP605 2.3 17.0 1.0 O A:HOH974 2.4 18.6 1.0 O A:HOH916 2.5 18.1 1.0 CD2 A:HIS491 3.0 15.8 1.0 CG A:ASP605 3.1 22.9 1.0 CD2 A:HIS456 3.2 17.2 1.0 CG A:ASP492 3.2 16.7 1.0 CE1 A:HIS456 3.3 14.7 1.0 CE1 A:HIS491 3.3 18.1 1.0 OD2 A:ASP605 3.3 28.1 1.0 O A:HOH1022 3.7 25.0 1.0 OD1 A:ASP492 3.8 14.9 1.0 O A:HOH953 3.9 16.9 1.0 MG A:MG807 3.9 21.8 1.0 CG A:HIS491 4.2 21.1 1.0 CD2 A:HIS452 4.2 18.0 1.0 CB A:ASP492 4.3 14.7 1.0 ND1 A:HIS491 4.3 19.4 1.0 CG A:HIS456 4.3 14.8 1.0 ND1 A:HIS456 4.4 16.8 1.0 O A:HOH994 4.5 22.9 1.0 CB A:ASP605 4.5 20.9 1.0 NE2 A:HIS452 4.6 17.1 1.0 CG2 A:VAL460 4.7 13.1 1.0 O A:ASP605 4.9 20.2 1.0 O A:HOH917 4.9 17.3 1.0 CA A:ASP605 4.9 15.2 1.0

T.Ikuta, W.Shihoya, M.Sugiura, K.Yoshida, M.Watari, T.Tokano, K.Yamashita, K.Katayama, S.P.Tsunoda, T.Uchihashi, H.Kandori, O.Nureki. Structural Insights Into the Mechanism of Rhodopsin Phosphodiesterase. Nat Commun V. 11 5605 2020.
ISSN: ESSN 2041-1723
PubMed: 33154353
DOI: 10.1038/S41467-020-19376-7