Calcium in PDB 5jh7: Tubulin-Eribulin Complex

The structure of Tubulin-Eribulin Complex, PDB code: 5jh7 was solved by H.Doodhi, A.E.Prota, R.Rodriguez-Garcia, H.Xiao, D.W.Custar, K.Bargsten, E.A.Katrukha, M.Hilbert, S.Hua, K.Jiang, I.Grigoriev, C.-P.H.Yang, D.Cox, S.Band Horwitz, L.C.Kapitein, A.Akhmanova, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.18 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.217, 157.134, 182.824, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22

The structure of Tubulin-Eribulin Complex also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Calcium atom in the Tubulin-Eribulin Complex (pdb code 5jh7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Tubulin-Eribulin Complex, PDB code: 5jh7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin-Eribulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.7 occ:1.00 OD1 A:ASP39 2.5 93.5 1.0 O A:GLY44 2.5 94.1 1.0 OE2 A:GLU55 2.5 0.5 1.0 O A:HOH604 2.5 77.6 1.0 OG1 A:THR41 2.6 86.2 1.0 OD2 A:ASP39 2.6 96.5 1.0 O A:THR41 2.7 94.0 1.0 OE1 A:GLU55 2.9 0.5 1.0 CG A:ASP39 2.9 86.4 1.0 CD A:GLU55 3.1 0.3 1.0 C A:GLY44 3.6 1.0 1.0 CB A:THR41 3.7 89.6 1.0 C A:THR41 3.8 93.3 1.0 CZ A:PHE49 4.1 87.1 1.0 CA A:THR41 4.2 99.0 1.0 CA A:GLY45 4.3 0.4 1.0 OD1 A:ASN50 4.4 88.6 1.0 N A:GLY45 4.4 0.6 1.0 CB A:ASP39 4.4 87.5 1.0 N A:THR41 4.4 0.4 1.0 OD2 A:ASP47 4.5 96.8 1.0 CG A:GLU55 4.5 95.7 1.0 N A:GLY44 4.6 0.4 1.0 CA A:GLY44 4.6 0.0 1.0 ND2 A:ASN50 4.6 84.1 1.0 CE1 A:PHE49 4.7 87.4 1.0 NE2 A:HIS61 4.7 96.6 1.0 O A:HOH723 4.7 84.2 1.0 N A:ILE42 4.9 0.7 1.0 CG A:ASN50 5.0 81.8 1.0 CG2 A:THR41 5.0 91.3 1.0

Calcium binding site 2 out of 5 in the Tubulin-Eribulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:96.0 occ:1.00 O B:HOH646 2.5 65.9 1.0 OE2 B:GLU113 2.7 99.1 1.0 CD B:GLU113 3.4 83.1 1.0 OE1 B:GLU113 3.4 87.1 1.0 OE1 B:GLU110 4.5 64.6 1.0 O B:HOH686 4.8 58.4 1.0 CG B:GLU113 4.9 66.3 1.0

Calcium binding site 3 out of 5 in the Tubulin-Eribulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:69.7 occ:1.00 O C:THR41 2.4 77.6 1.0 OG1 C:THR41 2.4 74.0 1.0 OD2 C:ASP39 2.4 70.5 1.0 OE2 C:GLU55 2.5 78.6 1.0 O C:HOH639 2.6 60.1 1.0 OE1 C:GLU55 2.6 60.1 1.0 OD1 C:ASP39 2.6 70.0 1.0 O C:GLY44 2.6 87.9 1.0 CG C:ASP39 2.9 71.7 1.0 CD C:GLU55 2.9 73.9 1.0 C C:THR41 3.4 80.4 1.0 CB C:THR41 3.4 80.5 1.0 C C:GLY44 3.5 88.9 1.0 CA C:THR41 3.9 79.8 1.0 N C:GLY45 4.1 88.2 1.0 CA C:GLY45 4.1 82.5 1.0 N C:THR41 4.3 75.0 1.0 O C:HOH717 4.4 65.8 1.0 CA C:GLY44 4.4 84.3 1.0 CB C:ASP39 4.4 64.9 1.0 CG C:GLU55 4.4 68.0 1.0 N C:GLY44 4.4 82.5 1.0 CZ C:PHE49 4.5 56.1 1.0 OD2 C:ASP47 4.5 83.9 1.0 N C:ILE42 4.5 87.2 1.0 NE2 C:HIS61 4.6 62.8 1.0 OD1 C:ASN50 4.7 66.1 1.0 CG2 C:THR41 4.8 80.5 1.0 CE1 C:PHE49 4.8 58.1 1.0 ND2 C:ASN50 4.9 61.0 1.0 CA C:ILE42 5.0 74.8 1.0

Calcium binding site 4 out of 5 in the Tubulin-Eribulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:0.2 occ:1.00 O C:HOH797 2.5 90.0 1.0 O C:HOH796 2.6 0.4 1.0 O C:HOH785 3.5 90.8 1.0 OD2 C:ASP218 3.6 0.5 1.0 OE2 C:GLU220 3.8 0.8 1.0 OD1 C:ASP218 3.8 0.2 1.0 CG C:ASP218 4.0 0.4 1.0 CG C:GLU220 4.3 89.2 1.0 CD C:GLU220 4.5 0.2 1.0

Calcium binding site 5 out of 5 in the Tubulin-Eribulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-Eribulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca200 b:98.9 occ:1.00 O A:HOH737 2.7 89.4 1.0 OD2 E:ASP44 3.1 0.6 1.0 O A:HOH703 3.6 70.1 1.0 CG E:ASP44 3.9 0.3 1.0 O A:GLU196 3.9 66.7 1.0 OD1 E:ASP44 4.0 0.3 1.0 OG A:SER158 4.0 66.8 1.0 CB A:SER158 4.5 61.3 1.0 NZ A:LYS166 4.5 65.8 1.0 CA A:HIS197 4.6 66.0 1.0 O A:HIS197 4.7 72.3 1.0 OD1 A:ASP199 4.9 80.2 1.0 C A:HIS197 4.9 64.0 1.0 O A:GLY162 5.0 0.4 1.0 O A:HOH607 5.0 63.3 1.0

H.Doodhi, A.E.Prota, R.Rodriguez-Garcia, H.Xiao, D.W.Custar, K.Bargsten, E.A.Katrukha, M.Hilbert, S.Hua, K.Jiang, I.Grigoriev, C.P.Yang, D.Cox, S.B.Horwitz, L.C.Kapitein, A.Akhmanova, M.O.Steinmetz. Termination of Protofilament Elongation By Eribulin Induces Lattice Defects That Promote Microtubule Catastrophes. Curr.Biol. V. 26 1713 2016.
ISSN: ISSN 0960-9822
PubMed: 27321995
DOI: 10.1016/J.CUB.2016.04.053