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Calcium in PDB 7dad: Epd in Complex with Tubulin

Protein crystallography data

The structure of Epd in Complex with Tubulin, PDB code: 7dad was solved by Y.Wang, C.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.91 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.163, 158.506, 181.605, 90, 90, 90
R / Rfree (%) 17.9 / 22.6

Other elements in 7dad:

The structure of Epd in Complex with Tubulin also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Magnesium (Mg) 5 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Epd in Complex with Tubulin (pdb code 7dad). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Epd in Complex with Tubulin, PDB code: 7dad:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7dad

Go back to Calcium Binding Sites List in 7dad
Calcium binding site 1 out of 4 in the Epd in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:71.5
occ:1.00
OD2 A:ASP39 2.2 59.6 1.0
OE2 A:GLU55 2.3 60.5 1.0
OG1 A:THR41 2.4 84.6 1.0
O A:THR41 2.4 72.0 1.0
O A:GLY44 2.4 51.8 1.0
OE1 A:GLU55 2.5 65.3 1.0
OD1 A:ASP39 2.6 61.8 1.0
CG A:ASP39 2.7 56.7 1.0
CD A:GLU55 2.7 63.0 1.0
C A:THR41 3.5 70.4 1.0
C A:GLY44 3.5 54.2 1.0
CB A:THR41 3.6 69.3 1.0
CA A:THR41 4.0 75.3 1.0
CB A:ASP39 4.2 52.5 1.0
CG A:GLU55 4.2 48.1 1.0
OD2 A:ASP47 4.3 65.1 1.0
N A:GLY44 4.3 57.8 1.0
N A:GLY45 4.3 46.7 1.0
CA A:GLY44 4.4 67.6 1.0
N A:THR41 4.4 65.4 1.0
CA A:GLY45 4.5 67.4 1.0
CZ A:PHE49 4.5 62.5 1.0
OD1 A:ASN50 4.6 58.3 1.0
N A:ILE42 4.6 50.5 1.0
NE2 A:HIS61 4.6 64.7 1.0
ND2 A:ASN50 4.7 53.2 1.0
CG2 A:THR41 4.7 64.4 1.0
CA A:ILE42 4.9 57.6 1.0

Calcium binding site 2 out of 4 in 7dad

Go back to Calcium Binding Sites List in 7dad
Calcium binding site 2 out of 4 in the Epd in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:88.9
occ:1.00
OD2 E:ASP44 4.0 105.4 1.0
O A:GLU196 4.1 52.2 1.0
OD1 E:ASP44 4.2 60.4 1.0
NZ A:LYS166 4.4 65.1 1.0
OG A:SER158 4.4 46.5 1.0
CG E:ASP44 4.5 82.3 1.0
OD1 A:ASP199 4.6 30.8 1.0
CB A:SER158 4.8 38.8 1.0
O A:GLY162 4.8 56.8 1.0
O A:HIS197 4.8 41.8 1.0
CA A:HIS197 4.9 36.0 1.0
C A:HIS197 5.0 38.3 1.0

Calcium binding site 3 out of 4 in 7dad

Go back to Calcium Binding Sites List in 7dad
Calcium binding site 3 out of 4 in the Epd in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:82.5
occ:1.00
OE2 B:GLU111 2.6 84.8 1.0
OE1 B:GLU111 3.1 72.5 1.0
CD B:GLU111 3.2 77.3 1.0
OE1 B:GLU108 4.4 36.1 1.0
CG B:GLU111 4.7 38.4 1.0

Calcium binding site 4 out of 4 in 7dad

Go back to Calcium Binding Sites List in 7dad
Calcium binding site 4 out of 4 in the Epd in Complex with Tubulin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Epd in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:47.9
occ:1.00
OG1 C:THR41 2.1 69.7 1.0
OD1 C:ASP39 2.4 38.7 1.0
OE2 C:GLU55 2.4 49.3 1.0
OD2 C:ASP39 2.4 44.1 1.0
O C:THR41 2.4 53.0 1.0
O C:GLY44 2.5 60.4 1.0
OE1 C:GLU55 2.6 40.6 1.0
CG C:ASP39 2.7 33.9 1.0
CD C:GLU55 2.8 49.2 1.0
CB C:THR41 3.3 59.0 1.0
C C:THR41 3.4 46.4 1.0
C C:GLY44 3.7 51.2 1.0
CA C:THR41 3.8 46.9 1.0
OD2 C:ASP47 4.1 66.9 1.0
N C:THR41 4.1 45.0 1.0
CB C:ASP39 4.2 43.4 1.0
OD1 C:ASN50 4.3 55.4 1.0
CG C:GLU55 4.3 28.6 1.0
CZ C:PHE49 4.4 35.9 1.0
CA C:GLY45 4.4 47.1 1.0
N C:GLY45 4.5 55.6 1.0
CG2 C:THR41 4.5 29.5 1.0
N C:GLY44 4.6 51.3 1.0
CA C:GLY44 4.6 48.6 1.0
NE2 C:HIS61 4.6 30.6 1.0
N C:ILE42 4.7 39.2 1.0
CE1 C:PHE49 4.8 23.9 1.0
CA C:ASP39 5.0 46.1 1.0

Reference:

Q.Xiao, T.Xue, W.Shuai, C.Wu, Z.Zhang, T.Zhang, S.Zeng, B.Sun, Y.Wang. High-Resolution X-Ray Structure of Three Microtubule-Stabilizing Agents in Complex with Tubulin Provide A Rationale For Drug Design. Biochem.Biophys.Res.Commun. V. 534 330 2021.
ISSN: ESSN 1090-2104
PubMed: 33272565
DOI: 10.1016/J.BBRC.2020.11.082
Page generated: Wed Jul 9 21:31:48 2025

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