Calcium in PDB 5fnv: A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone

The structure of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone, PDB code: 5fnv was solved by Y.Wang, J.Naismith, X.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.88 / 2.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.160, 157.200, 181.680, 90.00, 90.00, 90.00
R / Rfree (%)	18.575 / 22.555

The structure of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone (pdb code 5fnv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone, PDB code: 5fnv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1440 b:97.2 occ:1.00 OD2 A:ASP39 2.3 0.3 1.0 O A:THR41 2.3 0.7 1.0 O A:GLY44 2.3 0.5 1.0 OD1 A:ASP39 2.3 0.5 1.0 OE2 A:GLU55 2.3 0.8 1.0 OG1 A:THR41 2.3 0.9 1.0 CG A:ASP39 2.7 0.7 1.0 OE1 A:GLU55 2.9 0.5 1.0 CD A:GLU55 3.0 0.5 1.0 C A:THR41 3.4 0.0 1.0 C A:GLY44 3.4 1.0 1.0 CB A:THR41 3.5 0.9 1.0 CA A:THR41 3.8 0.2 1.0 CA A:GLY45 3.9 0.7 1.0 N A:GLY45 4.1 0.1 1.0 OD2 A:ASP47 4.1 0.3 1.0 N A:THR41 4.1 0.3 1.0 CB A:ASP39 4.2 0.9 1.0 CG A:GLU55 4.5 0.2 1.0 CZ A:PHE49 4.5 0.1 1.0 OD1 A:ASN50 4.5 0.3 1.0 CA A:GLY44 4.6 0.5 1.0 N A:ILE42 4.6 0.7 1.0 NE2 A:HIS61 4.6 99.6 1.0 CG2 A:THR41 4.7 0.7 1.0 CE1 A:PHE49 4.8 97.5 1.0 N A:GLY44 4.8 0.3 1.0

Calcium binding site 2 out of 3 in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1431 b:97.5 occ:1.00 OE1 B:GLU111 2.3 0.5 1.0 CD B:GLU111 3.4 0.4 1.0 OE2 B:GLU111 3.9 0.6 1.0 OE1 B:GLU108 4.1 73.4 1.0 CG B:GLU111 4.7 99.2 1.0 CD B:GLU108 4.9 73.0 1.0

Calcium binding site 3 out of 3 in the A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A New Complex Structure of Tubulin with An Alpha-Beta Unsaturated Lactone within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1442 b:83.7 occ:1.00 OG1 C:THR41 2.3 0.7 1.0 O C:GLY44 2.3 1.0 1.0 OD1 C:ASP39 2.3 97.8 1.0 OE2 C:GLU55 2.3 90.8 1.0 OD2 C:ASP39 2.3 93.9 1.0 O C:THR41 2.3 0.7 1.0 CG C:ASP39 2.7 90.6 1.0 OE1 C:GLU55 2.9 84.7 1.0 CD C:GLU55 3.0 83.6 1.0 C C:THR41 3.4 0.3 1.0 C C:GLY44 3.4 0.3 1.0 CB C:THR41 3.5 1.0 1.0 CA C:THR41 3.8 0.2 1.0 CA C:GLY45 3.9 0.6 1.0 OD2 C:ASP47 4.1 86.5 1.0 N C:GLY45 4.1 0.2 1.0 N C:THR41 4.1 1.0 1.0 CB C:ASP39 4.2 92.9 1.0 CG C:GLU55 4.5 81.5 1.0 CZ C:PHE49 4.5 69.6 1.0 OD1 C:ASN50 4.5 74.6 1.0 N C:ILE42 4.6 0.0 1.0 CA C:GLY44 4.6 0.5 1.0 NE2 C:HIS61 4.6 73.5 1.0 CG2 C:THR41 4.7 0.8 1.0 CE1 C:PHE49 4.8 67.8 1.0 N C:GLY44 4.8 0.7 1.0

J.Yang, Y.Wang, T.Wang, J.Jiang, C.H.Botting, H.Liu, Q.Chen, J.Yang, J.H.Naismith, X.Zhu, L.Chen. Pironetin Reacts Covalently with Cysteine-316 of Alpha-Tubulin to Destabilize Microtubule. Nat.Commun. V. 7 12103 2016.
ISSN: ISSN 2041-1723
PubMed: 27357539
DOI: 10.1038/NCOMMS12103