Calcium in PDB 7dae: Epb in Complex with Tubulin

Protein crystallography data

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

Resolution Low / High (Å) 49.71 / 2.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.792, 157.21, 181.53, 90, 90, 90
R / Rfree (%) 17.4 / 22.2

Other elements in 7dae:

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

Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

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

Calcium binding site 1 out of 4 in 7dae

Go back to Calcium Binding Sites List in 7dae
Calcium binding site 1 out of 4 in the Epb 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 Epb in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:47.6
occ:1.00
O A:THR41 2.3 55.5 1.0
OD2 A:ASP39 2.3 48.6 1.0
OD1 A:ASP39 2.4 46.0 1.0
O A:GLY44 2.4 44.5 1.0
O A:HOH617 2.6 47.0 1.0
OE1 A:GLU55 2.6 42.9 1.0
OE2 A:GLU55 2.6 43.4 1.0
OG1 A:THR41 2.7 50.9 1.0
CG A:ASP39 2.7 47.9 1.0
CD A:GLU55 2.9 54.4 1.0
C A:THR41 3.3 53.3 1.0
CB A:THR41 3.6 49.4 1.0
C A:GLY44 3.6 54.1 1.0
CA A:THR41 3.9 52.9 1.0
N A:THR41 4.1 56.2 1.0
CB A:ASP39 4.2 41.4 1.0
O A:HOH616 4.3 40.9 1.0
CA A:GLY45 4.4 58.8 1.0
N A:GLY45 4.4 49.2 1.0
CZ A:PHE49 4.4 40.7 1.0
N A:GLY44 4.4 51.0 1.0
CG A:GLU55 4.5 49.0 1.0
OD2 A:ASP47 4.5 59.3 1.0
N A:ILE42 4.5 51.8 1.0
NE2 A:HIS61 4.6 56.6 1.0
CA A:GLY44 4.6 58.2 1.0
OD1 A:ASN50 4.8 49.7 1.0
ND2 A:ASN50 4.8 49.5 1.0
CA A:ILE42 4.9 53.5 1.0
CE1 A:PHE49 4.9 47.6 1.0
CG2 A:THR41 5.0 44.7 1.0

Calcium binding site 2 out of 4 in 7dae

Go back to Calcium Binding Sites List in 7dae
Calcium binding site 2 out of 4 in the Epb 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 Epb in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:83.7
occ:1.00
O B:HOH637 2.4 48.8 1.0
O B:HOH602 2.7 60.6 1.0
OE2 B:GLU111 2.7 66.3 1.0
OE1 B:GLU111 3.0 70.1 1.0
CD B:GLU111 3.2 62.4 1.0
CG B:GLU111 4.7 37.0 1.0

Calcium binding site 3 out of 4 in 7dae

Go back to Calcium Binding Sites List in 7dae
Calcium binding site 3 out of 4 in the Epb 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 Epb in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:39.5
occ:1.00
O C:THR41 2.4 43.3 1.0
OE1 C:GLU55 2.4 33.9 1.0
OD2 C:ASP39 2.5 42.2 1.0
OD1 C:ASP39 2.5 40.6 1.0
O C:HOH602 2.5 34.9 1.0
O C:GLY44 2.5 43.2 1.0
OG1 C:THR41 2.6 39.3 1.0
OE2 C:GLU55 2.6 40.2 1.0
CG C:ASP39 2.8 41.1 1.0
CD C:GLU55 2.9 38.4 1.0
C C:THR41 3.4 37.6 1.0
C C:GLY44 3.6 46.6 1.0
CB C:THR41 3.6 45.9 1.0
CA C:THR41 3.9 38.7 1.0
N C:THR41 4.1 37.5 1.0
CA C:GLY45 4.2 43.2 1.0
N C:GLY45 4.3 46.0 1.0
OD2 C:ASP47 4.3 52.3 1.0
CB C:ASP39 4.3 38.7 1.0
O C:HOH624 4.4 32.1 1.0
CG C:GLU55 4.4 32.2 1.0
N C:GLY44 4.5 38.2 1.0
CA C:GLY44 4.6 39.6 1.0
N C:ILE42 4.6 39.0 1.0
OD1 C:ASN50 4.7 34.1 1.0
CZ C:PHE49 4.7 34.1 1.0
NE2 C:HIS61 4.7 42.1 1.0
O C:HOH744 4.9 40.6 1.0
CE1 C:PHE49 4.9 36.4 1.0
CG2 C:THR41 4.9 34.5 1.0

Calcium binding site 4 out of 4 in 7dae

Go back to Calcium Binding Sites List in 7dae
Calcium binding site 4 out of 4 in the Epb 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 Epb in Complex with Tubulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:77.8
occ:1.00
O A:HOH694 2.9 54.4 1.0
O A:HOH719 3.0 44.0 1.0
OD2 E:ASP44 3.4 59.8 1.0
O A:HOH624 3.6 53.5 1.0
OG A:SER158 4.1 37.2 1.0
O A:GLU196 4.4 37.8 1.0
O A:GLY162 4.5 50.0 1.0
CG E:ASP44 4.5 58.6 1.0
OD1 A:ASP199 4.7 36.2 1.0
OD1 E:ASP44 4.8 61.9 1.0
CB A:SER158 4.8 25.9 1.0
O A:HIS197 4.9 31.6 1.0
O A:HOH728 5.0 56.5 1.0
CA A:HIS197 5.0 34.2 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: Sat Apr 17 14:08:25 2021

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