Magnesium 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:

Zinc

(Zn)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of the Phosphodiesterase Domain of Salpingoeca Rosetta Rhodopsin Phosphodiesterase, PDB code: 7d7p:

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg807 b:21.8 occ:1.00 O A:HOH1003 2.0 13.9 1.0 O A:HOH916 2.0 18.1 1.0 O A:HOH954 2.2 15.6 1.0 OD1 A:ASP492 2.2 14.9 1.0 O A:HOH917 2.2 17.3 1.0 O A:HOH953 2.3 16.9 1.0 CG A:ASP492 3.1 16.7 1.0 OD2 A:ASP492 3.4 17.1 1.0 ZN A:ZN806 3.9 22.9 1.0 NE2 A:HIS524 4.1 14.6 1.0 OE2 A:GLU521 4.1 22.9 1.0 CD2 A:HIS524 4.2 10.2 1.0 O A:HIS491 4.2 19.3 1.0 O A:HOH974 4.2 18.6 1.0 O A:HOH996 4.2 22.8 1.0 CD2 A:HIS491 4.3 15.8 1.0 OG1 A:THR562 4.3 20.1 1.0 CD2 A:HIS495 4.4 16.6 1.0 CB A:ASP492 4.5 14.7 1.0 OD2 A:ASP605 4.5 28.1 1.0 NE2 A:HIS495 4.7 20.8 1.0 CA A:ASP492 4.8 14.8 1.0 CD2 A:HIS452 4.8 18.0 1.0 NE2 A:HIS491 4.8 16.5 1.0 O A:THR562 4.8 22.5 1.0 NE2 A:HIS452 4.9 17.1 1.0 CB A:THR562 4.9 12.8 1.0 CG A:GLU521 4.9 16.6 1.0 CD A:GLU521 4.9 24.1 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