Calcium in PDB 8tff: Porx with BEF3 Phosphate Analog

The structure of Porx with BEF3 Phosphate Analog, PDB code: 8tff was solved by A.Saran, N.Zeytuni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.81 / 2.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.32, 97.518, 131.258, 90, 90, 90
R / Rfree (%)	16.5 / 23.1

The structure of Porx with BEF3 Phosphate Analog also contains other interesting chemical elements:

Fluorine

(F)

12 atoms

The binding sites of Calcium atom in the Porx with BEF3 Phosphate Analog (pdb code 8tff). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Porx with BEF3 Phosphate Analog, PDB code: 8tff:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Porx with BEF3 Phosphate Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:21.9 occ:1.00 OD1 A:ASN238 2.1 21.2 1.0 OD2 A:ASP414 2.2 16.1 1.0 OG1 A:THR271 2.2 16.9 1.0 OD1 A:ASP237 2.2 24.5 1.0 NE2 A:HIS415 2.4 15.4 1.0 CG A:ASP414 2.9 20.3 1.0 OD1 A:ASP414 3.1 21.3 1.0 CG A:ASP237 3.1 23.6 1.0 CB A:THR271 3.2 19.8 1.0 CE1 A:HIS415 3.2 17.9 1.0 CD2 A:HIS415 3.2 16.0 1.0 O A:HOH703 3.3 32.2 1.0 CG A:ASN238 3.3 23.8 1.0 OD2 A:ASP237 3.6 25.9 1.0 CA A:THR271 3.6 20.9 1.0 CG2 A:THR271 3.6 21.2 1.0 N A:THR271 3.7 22.2 1.0 N A:ASN238 3.8 19.5 1.0 ND2 A:ASN238 4.2 23.3 1.0 ND1 A:HIS415 4.2 16.0 1.0 CG A:HIS415 4.2 16.1 1.0 CA A:ASN238 4.3 21.1 1.0 CB A:ASP237 4.3 22.5 1.0 CB A:ASN238 4.4 22.0 1.0 CB A:ASP414 4.4 20.5 1.0 CA A:ASP237 4.4 22.2 1.0 C A:ASP237 4.5 22.0 1.0 O A:HOH851 4.6 29.4 1.0 C A:ALA270 4.7 21.3 1.0 NH1 A:ARG275 4.7 24.1 1.0

Calcium binding site 2 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Porx with BEF3 Phosphate Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:35.2 occ:1.00 O A:MET467 2.3 28.6 1.0 O A:HOH876 2.3 38.1 1.0 O A:LYS455 2.3 34.1 1.0 O A:HOH748 2.4 29.2 1.0 OXT A:ACT604 2.6 34.6 1.0 O A:ACT604 2.9 36.3 1.0 C A:ACT604 3.1 44.2 1.0 C A:MET467 3.3 30.0 1.0 C A:LYS455 3.5 27.1 1.0 O A:SER469 4.0 29.4 1.0 CA A:MET467 4.1 36.1 1.0 CA A:LYS455 4.2 27.7 1.0 CB A:LYS455 4.2 35.2 1.0 OE2 A:GLU456 4.2 37.9 1.0 N A:SER468 4.3 29.3 1.0 CA A:SER468 4.4 30.8 1.0 N A:GLU456 4.5 25.8 1.0 C A:SER468 4.5 26.5 1.0 O A:HOH921 4.5 12.3 1.0 CH3 A:ACT604 4.6 41.2 1.0 CB A:MET467 4.7 42.5 1.0 CA A:GLU456 4.7 30.7 1.0 N A:SER469 4.7 24.1 1.0 CG A:GLU456 4.8 35.1 1.0 C A:SER469 4.9 24.8 1.0 CD A:GLU456 4.9 36.6 1.0 O A:SER468 5.0 28.7 1.0

Calcium binding site 3 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Porx with BEF3 Phosphate Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:40.2 occ:1.00 F3 A:BEF605 2.1 50.3 1.0 OD2 A:ASP54 2.3 35.6 1.0 O A:ASN56 2.3 34.6 0.5 O A:ASN56 2.4 34.1 0.5 O A:HOH728 2.4 34.0 1.0 OD1 A:ASP11 2.5 39.6 1.0 O A:HOH800 2.5 37.1 1.0 CG A:ASP11 3.3 33.7 1.0 CG A:ASP54 3.4 36.1 1.0 OD2 A:ASP11 3.4 36.1 1.0 BE A:BEF605 3.4 42.1 1.0 C A:ASN56 3.6 32.1 0.5 C A:ASN56 3.6 31.4 0.5 OD1 A:ASP54 3.9 37.7 1.0 OD1 A:ASP10 4.1 36.5 1.0 OE1 A:GLU12 4.2 47.3 1.0 F1 A:BEF605 4.4 39.1 1.0 CB A:ASN56 4.4 35.2 0.5 CG A:MET57 4.4 35.7 1.0 CA A:ASN56 4.4 33.0 0.5 N A:MET57 4.5 31.5 1.0 CA A:ASN56 4.5 31.7 0.5 CD A:GLU12 4.5 50.6 1.0 CB A:ASN56 4.6 33.0 0.5 CA A:MET57 4.6 31.9 1.0 F2 A:BEF605 4.6 46.6 1.0 CB A:ASP54 4.7 34.5 1.0 CG A:GLU12 4.7 44.8 1.0 CB A:ASP11 4.7 29.6 1.0 N A:ASN56 4.7 32.7 0.5 N A:ASN56 4.8 32.1 0.5 N A:ASP11 4.8 32.4 1.0 CG A:ASP10 4.9 36.9 1.0 CG A:ASN56 5.0 32.1 0.5

Calcium binding site 4 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Porx with BEF3 Phosphate Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:40.5 occ:1.00 F3 B:BEF605 2.0 40.5 1.0 O B:ASN56 2.3 35.3 1.0 OD1 B:ASP11 2.4 40.4 1.0 OD2 B:ASP54 2.4 42.0 1.0 O B:HOH705 2.5 32.0 1.0 O B:HOH811 2.5 45.5 1.0 O B:HOH756 3.0 48.1 1.0 CG B:ASP11 3.2 40.5 1.0 OD2 B:ASP11 3.3 62.3 1.0 CG B:ASP54 3.4 39.4 1.0 BE B:BEF605 3.5 40.9 1.0 C B:ASN56 3.5 36.6 1.0 OD1 B:ASP54 3.9 32.1 1.0 ND2 B:ASN56 4.1 37.5 0.5 OD1 B:ASP10 4.2 47.8 1.0 NZ B:LYS83 4.2 63.2 1.0 OE1 B:GLU12 4.3 48.9 1.0 F2 B:BEF605 4.4 48.9 1.0 CB B:ASN56 4.4 36.9 0.5 CA B:ASN56 4.4 36.2 0.5 CA B:ASN56 4.4 36.2 0.5 CG B:MET57 4.5 39.1 1.0 CB B:ASN56 4.5 36.9 0.5 N B:MET57 4.5 38.7 1.0 CB B:ASP11 4.6 35.8 1.0 CD B:GLU12 4.6 55.4 1.0 CA B:MET57 4.6 37.8 1.0 CG B:GLU12 4.6 46.2 1.0 CE B:LYS83 4.7 58.4 1.0 N B:ASN56 4.7 38.1 1.0 CB B:ASP54 4.7 38.7 1.0 N B:ASP11 4.7 32.9 1.0 CG B:ASN56 4.8 36.8 0.5 F1 B:BEF605 4.8 42.4 1.0 CG B:ASP10 4.9 40.5 1.0

Calcium binding site 5 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Porx with BEF3 Phosphate Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:32.5 occ:1.00 OD2 B:ASP414 2.1 28.7 1.0 OG1 B:THR271 2.2 32.8 1.0 OD2 B:ASP237 2.3 29.9 1.0 OD1 B:ASP237 2.3 28.4 1.0 NE2 B:HIS415 2.4 26.8 1.0 O B:HOH729 2.6 36.7 1.0 CG B:ASP237 2.6 29.1 1.0 CG B:ASP414 3.0 25.7 1.0 CB B:THR271 3.2 33.0 1.0 CE1 B:HIS415 3.2 27.5 1.0 OD1 B:ASP414 3.2 23.7 1.0 CD2 B:HIS415 3.2 30.4 1.0 CA B:THR271 3.5 32.2 1.0 CG2 B:THR271 3.5 29.1 1.0 N B:THR271 3.7 30.8 1.0 CB B:ASP237 4.1 25.8 1.0 F3 B:BEF606 4.1 51.1 1.0 ND1 B:HIS415 4.2 29.3 1.0 CG B:HIS415 4.2 28.9 1.0 N B:ASN238 4.3 25.2 1.0 CB B:ASP414 4.4 24.8 1.0 OD1 B:ASP360 4.5 43.2 1.0 CA B:ASP237 4.6 25.2 1.0 C B:ALA270 4.6 28.6 1.0 F2 B:BEF606 4.6 49.4 1.0 NH1 B:ARG275 4.8 25.6 1.0 CB B:ASN238 4.8 30.8 1.0 CA B:ASN238 4.8 29.1 1.0 C B:ASP237 4.8 26.1 1.0 BE B:BEF606 4.8 47.2 1.0

Calcium binding site 6 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Porx with BEF3 Phosphate Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:97.6 occ:1.00 NE2 B:HIS364 2.0 49.3 0.5 OD1 B:ASP360 2.8 43.2 1.0 CD2 B:HIS364 2.8 46.8 0.5 F1 B:BEF606 2.9 52.8 1.0 NE2 B:HIS499 2.9 45.3 1.0 CE1 B:HIS364 3.1 48.6 0.5 BE B:BEF606 3.2 47.2 1.0 O B:HOH729 3.2 36.7 1.0 OD2 B:ASP360 3.3 50.6 1.0 CG B:ASP360 3.4 38.9 1.0 CE1 B:HIS499 3.8 46.7 1.0 CD2 B:HIS499 3.8 34.1 1.0 F2 B:BEF606 3.9 49.4 1.0 CG B:HIS364 4.0 43.5 0.5 ND1 B:HIS364 4.1 45.9 0.5 F3 B:BEF606 4.1 51.1 1.0 ND2 B:ASN238 4.4 36.9 1.0 O B:HOH787 4.6 41.5 1.0 O B:ASP360 4.8 31.6 1.0 ND1 B:HIS364 4.8 48.0 0.5 CB B:ASP360 4.8 36.0 1.0 ND1 B:HIS499 4.9 44.6 1.0 CG B:HIS499 5.0 34.9 1.0 OG B:SER363 5.0 34.7 1.0

Calcium binding site 7 out of 7 in the Porx with BEF3 Phosphate Analog


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Porx with BEF3 Phosphate Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:94.5 occ:1.00 F3 B:BEF607 2.4 61.7 1.0 BE B:BEF607 3.1 58.1 1.0 F1 B:BEF607 3.3 64.2 1.0 OE2 B:GLU68 3.9 46.9 1.0 OE1 B:GLU68 4.0 41.5 1.0 CD B:GLU68 4.3 38.5 1.0 F2 B:BEF607 4.7 60.8 1.0

A.Saran, N.Zeytuni. Porx with BEF3 Phosphate Analog To Be Published.