Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Phosphodiesterase Domain of Rhopde Fusion Protein From the Choanoflagellate Salpingoeca Rosetta, PDB code: 5vyd:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn401 b:33.2 occ:1.00 O A:HOH535 2.1 24.4 1.0 OD2 A:ASP123 2.1 22.7 1.0 OD1 A:ASP236 2.2 26.6 1.0 NE2 A:HIS122 2.2 28.8 1.0 NE2 A:HIS87 2.2 26.6 1.0 O A:HOH541 2.6 35.1 1.0 CD2 A:HIS122 3.0 24.4 1.0 CG A:ASP236 3.0 30.2 1.0 CG A:ASP123 3.1 26.2 1.0 OD2 A:ASP236 3.1 26.3 1.0 CD2 A:HIS87 3.1 27.4 1.0 CE1 A:HIS87 3.2 28.4 1.0 CE1 A:HIS122 3.3 27.8 1.0 OD1 A:ASP123 3.6 27.8 1.0 MG A:MG402 3.7 27.6 1.0 O A:HOH540 4.0 26.1 1.0 CD2 A:HIS83 4.2 32.0 1.0 CG A:HIS122 4.2 33.6 1.0 O A:HOH634 4.3 33.5 1.0 CB A:ASP123 4.3 30.8 1.0 ND1 A:HIS122 4.3 31.7 1.0 CG A:HIS87 4.3 27.6 1.0 ND1 A:HIS87 4.3 29.9 1.0 CB A:ASP236 4.4 26.3 1.0 NE2 A:HIS83 4.5 27.8 1.0 O A:HOH637 4.7 48.4 1.0 CG2 A:VAL91 4.7 28.4 1.0 O A:HOH543 4.7 25.9 1.0 CA A:ASP236 4.9 26.4 1.0 O A:ASP236 4.9 29.1 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn401 b:35.3 occ:1.00 O B:HOH516 2.2 31.4 1.0 OD2 B:ASP123 2.2 31.2 1.0 OD1 B:ASP236 2.2 35.7 1.0 NE2 B:HIS87 2.3 35.1 1.0 NE2 B:HIS122 2.3 31.3 1.0 O B:HOH605 2.8 34.1 1.0 CG B:ASP236 3.0 29.9 1.0 CD2 B:HIS122 3.0 31.5 1.0 OD2 B:ASP236 3.1 31.6 1.0 CD2 B:HIS87 3.1 32.5 1.0 CG B:ASP123 3.2 34.9 1.0 CE1 B:HIS87 3.3 30.8 1.0 CE1 B:HIS122 3.5 35.5 1.0 MG B:MG402 3.7 28.0 1.0 OD1 B:ASP123 3.8 27.8 1.0 O B:HOH531 3.9 32.5 1.0 CD2 B:HIS83 4.2 39.4 1.0 CG B:HIS122 4.2 30.0 1.0 CG B:HIS87 4.3 35.8 1.0 CB B:ASP236 4.4 26.7 1.0 ND1 B:HIS87 4.4 38.4 1.0 CB B:ASP123 4.4 26.9 1.0 ND1 B:HIS122 4.4 32.9 1.0 NE2 B:HIS83 4.5 38.0 1.0 CG2 B:VAL91 4.7 29.1 1.0 O B:ASP236 4.8 34.6 1.0 O B:HOH530 4.8 26.2 1.0 CA B:ASP236 4.9 27.0 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