Calcium in PDB 6pfz: Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus

The structure of Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus, PDB code: 6pfz was solved by M.H.Sazinsky, S.Shabdar, A.Garcia-Constineiras, E.J.Crane Iii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.48 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.976, 100.355, 136.196, 90.00, 91.89, 90.00
R / Rfree (%)	20.2 / 22.9

The binding sites of Calcium atom in the Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus (pdb code 6pfz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus, PDB code: 6pfz:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:0.1 occ:1.00 O A:THR332 2.2 46.9 1.0 OD2 A:ASP306 2.4 61.7 1.0 O B:LEU428 2.4 51.5 1.0 OD1 B:ASP427 2.6 30.8 1.0 CG A:ASP306 3.4 43.9 1.0 C A:THR332 3.4 39.3 1.0 C B:LEU428 3.6 34.1 1.0 CG B:ASP427 3.8 25.9 1.0 OD1 A:ASP306 4.0 42.2 1.0 N B:TYR430 4.1 22.7 1.0 CA B:ALA429 4.2 32.1 1.0 OD2 B:ASP427 4.3 22.5 1.0 CB A:THR332 4.3 31.4 1.0 CA A:THR332 4.3 31.9 1.0 N B:ALA429 4.4 34.5 1.0 N B:LEU428 4.4 25.3 1.0 N A:ALA333 4.4 34.8 1.0 CA A:ALA333 4.5 40.0 1.0 CB A:ASP306 4.6 24.7 1.0 N A:THR332 4.6 30.3 1.0 C B:ALA429 4.6 48.1 1.0 CA B:LEU428 4.7 18.9 1.0 C B:ASP427 4.9 30.4 1.0 CG2 A:THR332 4.9 33.8 1.0 CB B:TYR430 5.0 47.6 1.0

Calcium binding site 2 out of 4 in the Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca903 b:69.4 occ:1.00 O A:LEU428 2.4 36.4 1.0 OD2 B:ASP306 2.5 38.9 1.0 O B:THR332 2.6 40.3 1.0 OD1 A:ASP427 2.8 32.1 1.0 CG B:ASP306 3.1 31.5 1.0 OD1 B:ASP306 3.1 50.7 1.0 C A:LEU428 3.7 30.4 1.0 C B:THR332 3.8 33.5 1.0 CG A:ASP427 3.9 31.2 1.0 OD2 A:ASP427 4.2 44.3 1.0 N A:TYR430 4.2 33.5 1.0 N A:LEU428 4.3 32.6 1.0 CB B:ASP306 4.5 27.1 1.0 N A:ALA429 4.6 38.3 1.0 CA A:ALA429 4.6 32.6 1.0 CA A:LEU428 4.6 23.0 1.0 CA B:ALA333 4.7 34.8 1.0 N B:ALA333 4.7 42.1 1.0 CA B:THR332 4.7 31.6 1.0 CB A:TYR430 4.8 41.8 1.0 CB B:THR332 4.8 32.1 1.0 N B:THR332 4.8 31.8 1.0 C A:ALA429 4.9 37.0 1.0 C A:ASP427 4.9 32.8 1.0

Calcium binding site 3 out of 4 in the Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca903 b:62.7 occ:1.00 OD1 C:ASP427 2.3 64.9 1.0 O C:LEU428 2.4 65.4 1.0 O D:THR332 2.5 30.4 1.0 OD2 D:ASP306 2.5 60.6 1.0 CG C:ASP427 3.3 60.7 1.0 CG D:ASP306 3.4 50.8 1.0 OD1 D:ASP306 3.5 49.2 1.0 C C:LEU428 3.6 51.7 1.0 C D:THR332 3.6 33.7 1.0 OD2 C:ASP427 3.7 57.9 1.0 N C:LEU428 4.0 43.7 1.0 CB D:THR332 4.0 45.6 1.0 CA D:THR332 4.2 47.3 1.0 N D:THR332 4.3 25.5 1.0 C C:ASP427 4.4 47.4 1.0 CA C:LEU428 4.4 45.6 1.0 CB C:ASP427 4.5 53.2 1.0 N C:ALA429 4.5 45.6 1.0 CG2 D:THR332 4.6 41.3 1.0 CA C:ASP427 4.6 41.3 1.0 CA C:ALA429 4.6 48.0 1.0 CB D:ASP306 4.7 48.3 1.0 N D:ALA333 4.7 38.6 1.0 N C:TYR430 4.7 43.8 1.0 CA D:ALA333 5.0 38.3 1.0

Calcium binding site 4 out of 4 in the Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A Nad-Dependent Persulfide Reductase From A. Fulgidus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca904 b:0.0 occ:1.00 OD1 D:ASP427 2.2 54.0 1.0 OD2 C:ASP306 2.4 47.4 1.0 O C:THR332 2.7 62.3 1.0 O D:LEU428 3.0 38.0 1.0 CG D:ASP427 3.2 51.7 1.0 CG C:ASP306 3.2 53.2 1.0 OD1 C:ASP306 3.4 69.3 1.0 OG1 C:THR332 3.5 57.3 1.0 OD2 D:ASP427 3.5 58.1 1.0 C C:THR332 3.8 47.0 1.0 C D:LEU428 4.2 32.2 1.0 N C:THR332 4.4 51.4 1.0 N D:LEU428 4.4 33.2 1.0 CD2 C:PHE304 4.4 54.0 1.0 CA C:THR332 4.5 47.5 1.0 CB C:THR332 4.5 46.0 1.0 CB D:ASP427 4.6 50.2 1.0 CG2 C:VAL307 4.6 62.1 1.0 CB C:ASP306 4.7 39.3 1.0 C D:ASP427 4.7 37.9 1.0 N C:ALA333 4.8 40.2 1.0 CA D:ASP427 4.8 43.2 1.0 CG C:PHE304 4.8 48.3 1.0 CB C:PHE304 4.9 51.5 1.0 CA D:LEU428 4.9 25.5 1.0 CA C:ALA333 4.9 42.6 1.0 NZ C:LYS310 5.0 38.8 1.0

S.Shabdar, B.Anklet, A.Garcia-Costineiras, N.Desir, N.Choe, E.J.Crane Iii, M.H.Sazinsky. Structural and Kinetic Characterization of Hyperthermophilic Nadh-Dependent Persulfide Reductase From Archaeoglobus Fulgidus To Be Published.