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Calcium in PDB 4ic5: Crystal Structure of DEG5

Protein crystallography data

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

Calcium Binding Sites:

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 4ic5

Go back to Calcium Binding Sites List in 4ic5
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 4ic5

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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 4ic5

Go back to Calcium Binding Sites List in 4ic5
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 4ic5

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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 4ic5

Go back to Calcium Binding Sites List in 4ic5
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

Reference:

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
Page generated: Sat Dec 12 04:51:40 2020

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