Calcium in PDB 4wbq: Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing.

The structure of Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing., PDB code: 4wbq was solved by A.Boland, T.Weinert, O.Weichenrieder, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.96 / 2.69
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	77.040, 77.040, 112.310, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 22.7

The binding sites of Calcium atom in the Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing. (pdb code 4wbq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing., PDB code: 4wbq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:43.2 occ:1.00 OD2 A:ASP451 2.4 47.2 1.0 O A:HOH716 2.5 48.6 1.0 O A:HIS446 2.5 35.1 1.0 O A:HOH705 2.5 48.3 1.0 OD1 A:ASP339 2.6 43.1 1.0 O A:HOH717 2.7 45.9 1.0 O A:HOH713 2.9 35.3 1.0 CG A:ASP451 3.2 46.3 1.0 OD1 A:ASP451 3.3 39.7 1.0 C A:HIS446 3.6 33.9 1.0 CG A:ASP339 3.7 43.8 1.0 CA A:CA602 4.1 61.2 1.0 CB A:HIS446 4.1 37.5 1.0 N A:HIS446 4.1 44.0 1.0 CA A:HIS446 4.2 35.6 1.0 CB A:ASP339 4.3 32.5 1.0 O A:HOH708 4.4 34.6 1.0 CA A:ASP339 4.5 36.8 1.0 OD2 A:ASP510 4.5 47.8 1.0 O A:ASP447 4.6 38.4 1.0 O A:ILE338 4.7 35.0 1.0 OD2 A:ASP339 4.7 53.6 1.0 CB A:ASP451 4.7 36.1 1.0 N A:ASP447 4.7 42.9 1.0 NE2 A:GLN450 4.7 42.6 1.0 CB A:ASP447 4.7 40.1 1.0 CD2 A:HIS446 4.9 40.1 1.0 CG A:HIS446 4.9 32.1 1.0 O A:HOH707 4.9 44.5 1.0 N A:LEU340 4.9 39.1 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:61.2 occ:1.00 O A:HOH707 2.4 44.5 1.0 OE2 A:GLU341 2.5 83.3 1.0 OD1 A:ASP339 2.6 43.1 1.0 O A:LEU340 2.7 46.1 1.0 O A:HOH717 2.8 45.9 1.0 OD2 A:ASP339 3.0 53.6 1.0 CD A:GLU341 3.0 72.6 1.0 CG A:ASP339 3.1 43.8 1.0 O A:HOH709 3.6 47.8 1.0 OE1 A:GLU341 3.7 70.5 1.0 C A:LEU340 3.7 43.0 1.0 CG A:GLU341 3.7 67.3 1.0 CA A:CA601 4.1 43.2 1.0 O A:HOH705 4.3 48.3 1.0 N A:LEU340 4.3 39.1 1.0 NE2 A:GLN450 4.3 42.6 1.0 CA A:GLU341 4.4 45.6 1.0 N A:GLU341 4.4 38.8 1.0 O A:HOH713 4.5 35.3 1.0 CA A:LEU340 4.6 37.5 1.0 CB A:ASP339 4.6 32.5 1.0 CB A:GLU341 4.6 35.0 1.0 OD1 A:ASP451 4.7 39.7 1.0 C A:ASP339 4.9 48.7 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:56.2 occ:1.00 O B:HOH716 2.5 52.7 1.0 OD1 B:ASP339 2.5 39.7 1.0 O B:HOH707 2.5 39.8 1.0 O B:LEU340 2.6 53.9 1.0 O B:HOH715 2.6 62.0 1.0 OE2 B:GLU341 2.6 67.9 1.0 OD2 B:ASP339 3.0 60.7 1.0 CG B:ASP339 3.1 41.8 1.0 CD B:GLU341 3.2 71.7 1.0 OE1 B:GLU341 3.5 62.5 1.0 C B:LEU340 3.5 47.8 1.0 CA B:CA602 3.9 58.2 1.0 CA B:GLU341 4.1 43.5 1.0 N B:LEU340 4.2 36.8 1.0 N B:GLU341 4.2 43.3 1.0 OE1 B:GLN450 4.3 51.0 1.0 O B:HOH706 4.4 49.3 1.0 CG B:GLU341 4.4 68.9 1.0 OD1 B:ASP451 4.4 51.7 1.0 CB B:GLU341 4.5 49.6 1.0 CA B:LEU340 4.5 43.6 1.0 CB B:ASP339 4.6 32.5 1.0 O B:HOH711 4.8 46.0 1.0 C B:ASP339 4.8 45.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Exonuclease Domain of Qip (Qde-2 Interacting Protein) Solved By Native-Sad Phasing. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:58.2 occ:1.00 OD2 B:ASP451 2.3 50.5 1.0 O B:HOH705 2.5 42.5 1.0 O B:HIS446 2.5 43.2 1.0 O B:HOH706 2.6 49.3 1.0 OD1 B:ASP339 2.7 39.7 1.0 O B:HOH707 3.0 39.8 1.0 CG B:ASP451 3.1 61.3 1.0 OD1 B:ASP451 3.2 51.7 1.0 C B:HIS446 3.6 36.5 1.0 CG B:ASP339 3.8 41.8 1.0 CA B:CA601 3.9 56.2 1.0 CB B:HIS446 4.3 37.1 1.0 O B:HOH715 4.3 62.0 1.0 CA B:HIS446 4.3 35.4 1.0 N B:HIS446 4.3 34.4 1.0 CB B:ASP339 4.4 32.5 1.0 O B:ASP447 4.4 37.8 1.0 OE1 B:GLN450 4.4 51.0 1.0 CA B:ASP339 4.5 36.0 1.0 CB B:ASP451 4.5 44.0 1.0 CB B:ASP447 4.6 44.0 1.0 OD1 B:ASP510 4.7 54.3 1.0 N B:ASP447 4.7 45.3 1.0 OD2 B:ASP339 4.7 60.7 1.0 O B:HOH703 4.8 30.1 1.0 O B:ILE338 4.8 42.9 1.0 O B:HOH716 4.9 52.7 1.0 N B:LEU340 4.9 36.8 1.0 CD2 B:HIS446 5.0 44.3 1.0 O B:LEU340 5.0 53.9 1.0

T.Weinert, A.Boland, O.Weichenrieder, M.Wang. Fast Native-Sad Phasing For Routine Macromolecular Structure Determination Nat.Methods 2014.
ISSN: ESSN 1548-7105