Calcium in PDB 4ic5: Crystal Structure of DEG5

The structure of Crystal Structure of DEG5, PDB code: 4ic5 was solved by W.Gong, W.Sun, H.Fan, F.Gao, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.88 / 2.61
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	109.090, 125.952, 83.325, 90.00, 102.91, 90.00
R / Rfree (%)	18.2 / 23.2

The binding sites of Calcium atom in the Crystal Structure of DEG5 (pdb code 4ic5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of DEG5, PDB code: 4ic5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of DEG5


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 DEG5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:33.9 occ:1.00 O A:LEU84 2.3 29.1 1.0 OE2 A:GLU89 2.6 39.9 1.0 O A:GLU82 2.7 35.2 1.0 C A:LEU84 3.5 28.9 1.0 CD A:GLU89 3.7 33.8 1.0 C A:GLU82 3.8 60.6 1.0 N A:LEU84 4.0 38.8 1.0 OE2 A:GLU86 4.1 44.3 1.0 C A:GLU83 4.3 65.1 1.0 CA A:LEU84 4.4 33.2 1.0 N A:GLU85 4.5 21.9 1.0 CG A:GLU89 4.5 31.8 1.0 CA A:GLU83 4.5 61.8 1.0 C A:GLU85 4.5 31.5 1.0 CA A:GLU85 4.5 19.9 1.0 N A:GLU83 4.6 70.0 1.0 OE1 A:GLU89 4.7 52.3 1.0 N A:GLU86 4.7 31.2 1.0 CA A:GLU82 4.8 63.3 1.0 N A:GLU82 4.8 59.8 1.0 O A:GLU85 4.9 28.7 1.0 O A:GLU83 4.9 77.7 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of DEG5


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 DEG5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:64.5 occ:1.00 OE1 B:GLU87 2.7 43.6 1.0 OE2 C:GLU87 2.7 54.0 1.0 OE2 A:GLU87 2.7 46.0 1.0 O C:HOH543 2.9 52.6 1.0 O B:HOH538 3.0 63.6 1.0 OE1 C:GLU87 3.1 0.3 1.0 OE1 A:GLU87 3.1 99.3 1.0 O C:HOH523 3.1 65.7 1.0 OE2 B:GLU87 3.2 95.9 1.0 CD C:GLU87 3.2 74.4 1.0 CD A:GLU87 3.3 73.9 1.0 CD B:GLU87 3.3 71.2 1.0 O C:HOH546 4.1 48.6 1.0 O A:HOH532 4.2 40.9 1.0 O B:HOH515 4.3 37.1 1.0 CG C:GLU87 4.7 49.6 1.0 CG A:GLU87 4.7 50.4 1.0 CG B:GLU87 4.8 34.8 1.0 O C:HOH547 4.8 61.4 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of DEG5


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 DEG5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:88.5 occ:1.00 O A:HOH522 2.9 62.8 1.0 O B:HOH520 2.9 57.4 1.0 O C:HOH501 3.0 33.0 1.0 O B:HOH519 3.0 29.9 1.0 O A:HOH521 3.0 36.0 1.0 OD1 A:ASP260 3.2 79.0 1.0 OD1 C:ASP260 3.2 73.7 1.0 OD1 B:ASP260 3.6 75.9 1.0 CG C:ASP260 4.0 65.8 1.0 CG A:ASP260 4.0 70.1 1.0 O B:HOH525 4.0 49.3 1.0 O C:HOH532 4.1 41.2 1.0 O B:HOH524 4.1 45.2 1.0 OD2 A:ASP260 4.2 67.9 1.0 OD2 C:ASP260 4.2 67.9 1.0 CG B:ASP260 4.4 71.3 1.0 OD2 B:ASP260 4.6 78.8 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of DEG5


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 DEG5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:36.7 occ:1.00 O B:LEU84 2.4 30.6 1.0 OE2 B:GLU89 2.5 49.0 1.0 O B:GLU82 2.7 32.2 1.0 C B:LEU84 3.6 24.0 1.0 CD B:GLU89 3.7 34.5 1.0 C B:GLU82 3.9 64.0 1.0 OE2 B:GLU86 4.1 40.6 1.0 N B:LEU84 4.1 43.9 1.0 C B:GLU83 4.3 60.7 1.0 CG B:GLU89 4.5 38.9 1.0 N B:GLU85 4.5 22.4 1.0 CA B:LEU84 4.5 33.7 1.0 CA B:GLU83 4.5 58.4 1.0 C B:GLU85 4.5 31.9 1.0 CA B:GLU85 4.5 20.5 1.0 N B:GLU83 4.6 79.4 1.0 OE1 B:GLU89 4.7 54.6 1.0 O B:GLU83 4.7 66.2 1.0 N B:GLU86 4.8 34.3 1.0 O B:GLU85 4.8 26.4 1.0 CA B:GLU82 4.9 66.7 1.0 N B:GLU82 4.9 65.2 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of DEG5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of DEG5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:33.5 occ:1.00 O C:LEU84 2.4 28.4 1.0 OE2 C:GLU89 2.5 34.2 1.0 O C:GLU82 2.7 33.2 1.0 C C:LEU84 3.6 24.8 1.0 CD C:GLU89 3.7 32.6 1.0 C C:GLU82 3.8 62.4 1.0 N C:LEU84 4.0 38.0 1.0 OE2 C:GLU86 4.2 43.4 1.0 C C:GLU83 4.2 57.5 1.0 CA C:GLU83 4.4 62.1 1.0 CA C:LEU84 4.4 34.6 1.0 CG C:GLU89 4.5 33.8 1.0 N C:GLU85 4.5 25.6 1.0 C C:GLU85 4.5 28.6 1.0 N C:GLU83 4.5 74.6 1.0 CA C:GLU85 4.5 17.6 1.0 OE1 C:GLU89 4.6 48.9 1.0 N C:GLU86 4.7 29.9 1.0 O C:GLU85 4.8 32.9 1.0 CA C:GLU82 4.8 58.7 1.0 N C:GLU82 4.8 52.8 1.0 O C:GLU83 4.8 65.8 1.0

W.Sun, F.Gao, H.Fan, X.Shan, R.Sun, L.Liu, W.Gong. The Structures of Arabidopsis DEG5 and DEG8 Reveal New Insights Into Htra Proteases Acta Crystallogr.,Sect.D V. 69 830 2013.
ISSN: ISSN 0907-4449
PubMed: 23633592
DOI: 10.1107/S0907444913002023