Magnesium in PDB 5vyd: Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta

The structure of Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta, PDB code: 5vyd was solved by R.Prem Kumar, L.B.Lamarche, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.649, 96.400, 108.639, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 24.6

The structure of Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta (pdb code 5vyd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta, PDB code: 5vyd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta


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 Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:27.6 occ:1.00 O A:HOH535 2.0 24.4 1.0 O A:HOH540 2.2 26.1 1.0 O A:HOH614 2.2 24.4 1.0 OD1 A:ASP123 2.2 27.8 1.0 O A:HOH524 2.2 24.8 1.0 O A:HOH543 2.3 25.9 1.0 CG A:ASP123 3.1 26.2 1.0 OD2 A:ASP123 3.3 22.7 1.0 ZN A:ZN401 3.7 33.2 1.0 O A:HOH541 3.8 35.1 1.0 OE2 A:GLU152 3.9 30.0 1.0 O A:HOH637 4.1 48.4 1.0 O A:HOH597 4.2 32.7 1.0 OG1 A:THR193 4.3 25.4 1.0 O A:HIS122 4.3 27.0 1.0 NE2 A:HIS155 4.3 28.3 1.0 CD2 A:HIS122 4.3 24.4 1.0 OD2 A:ASP236 4.3 26.3 1.0 CD2 A:HIS155 4.4 25.9 1.0 NE2 A:HIS83 4.4 27.8 1.0 CD2 A:HIS126 4.5 27.6 1.0 CD2 A:HIS83 4.5 32.0 1.0 CB A:ASP123 4.5 30.8 1.0 O A:HOH517 4.7 36.1 1.0 NE2 A:HIS126 4.7 32.7 1.0 CB A:THR193 4.8 24.2 1.0 NE2 A:HIS122 4.8 28.8 1.0 CD A:GLU152 4.8 33.1 1.0 O A:THR193 4.8 29.9 1.0 CA A:ASP123 4.9 26.9 1.0 CG A:GLU152 5.0 27.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:28.0 occ:1.00 O B:HOH516 2.0 31.4 1.0 O B:HOH540 2.0 25.1 1.0 O B:HOH560 2.1 28.0 1.0 O B:HOH531 2.2 32.5 1.0 O B:HOH530 2.3 26.2 1.0 OD1 B:ASP123 2.3 27.8 1.0 CG B:ASP123 3.2 34.9 1.0 OD2 B:ASP123 3.4 31.2 1.0 ZN B:ZN401 3.7 35.3 1.0 OE2 B:GLU152 4.0 35.5 1.0 O B:HOH512 4.1 38.7 1.0 OG1 B:THR193 4.2 21.1 1.0 OD2 B:ASP236 4.3 31.6 1.0 CD2 B:HIS122 4.4 31.5 1.0 CD2 B:HIS126 4.4 34.7 1.0 NE2 B:HIS155 4.4 28.2 1.0 O B:HOH605 4.4 34.1 1.0 O B:HIS122 4.5 29.2 1.0 CD2 B:HIS83 4.5 39.4 1.0 CD2 B:HIS155 4.5 30.8 1.0 NE2 B:HIS83 4.6 38.0 1.0 CB B:ASP123 4.6 26.9 1.0 O B:THR193 4.6 32.9 1.0 NE2 B:HIS126 4.6 32.9 1.0 O B:HOH564 4.8 44.7 1.0 CB B:THR193 4.8 27.3 1.0 NE2 B:HIS122 4.8 31.3 1.0 CD B:GLU152 4.9 31.9 1.0

L.B.Lamarche, R.P.Kumar, M.M.Trieu, E.L.Devine, L.E.Cohen-Abeles, D.L.Theobald, D.D.Oprian. Purification and Characterization of Rhopde, A Retinylidene/Phosphodiesterase Fusion Protein and Potential Optogenetic Tool From the Choanoflagellate Salpingoeca Rosetta. Biochemistry V. 56 5812 2017.
ISSN: ISSN 1520-4995
PubMed: 28976747
DOI: 10.1021/ACS.BIOCHEM.7B00519