Calcium in PDB 5lyj: Tubulin-Combretastatin A4 Complex

The structure of Tubulin-Combretastatin A4 Complex, PDB code: 5lyj was solved by R.Gaspari, A.E.Prota, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.43 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.592, 157.170, 180.140, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 21.7

The structure of Tubulin-Combretastatin A4 Complex also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Calcium atom in the Tubulin-Combretastatin A4 Complex (pdb code 5lyj). 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-Combretastatin A4 Complex, PDB code: 5lyj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:92.0 occ:1.00 O A:GLY44 2.3 0.3 1.0 OE2 A:GLU55 2.4 85.3 1.0 OG1 A:THR41 2.5 96.5 1.0 OD2 A:ASP39 2.6 83.2 1.0 OD1 A:ASP39 2.6 88.0 1.0 O A:THR41 2.6 0.0 1.0 OE1 A:GLU55 2.8 95.0 1.0 CG A:ASP39 2.9 87.0 1.0 CD A:GLU55 2.9 90.3 1.0 C A:GLY44 3.4 1.0 1.0 CB A:THR41 3.5 99.2 1.0 C A:THR41 3.6 0.9 1.0 CA A:THR41 4.0 0.3 1.0 CA A:GLY45 4.1 0.6 1.0 N A:GLY45 4.1 0.2 1.0 OD2 A:ASP47 4.2 94.3 1.0 OD1 A:ASN50 4.3 79.2 1.0 N A:THR41 4.3 0.6 1.0 CZ A:PHE49 4.4 73.1 1.0 CG A:GLU55 4.4 88.6 1.0 CB A:ASP39 4.5 90.0 1.0 N A:GLY44 4.5 0.7 1.0 CA A:GLY44 4.5 1.0 1.0 NE2 A:HIS61 4.7 99.3 1.0 CG2 A:THR41 4.8 98.6 1.0 N A:ILE42 4.8 0.3 1.0 CE1 A:PHE49 4.8 74.8 1.0 ND2 A:ASN50 4.8 71.1 1.0

Calcium binding site 2 out of 5 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:0.2 occ:1.00 O B:HOH621 2.6 84.6 1.0 O B:HOH629 2.9 0.0 1.0 OD2 B:ASP120 4.1 84.0 1.0 OD2 B:ASP116 4.2 87.4 1.0 OD1 B:ASP120 4.3 86.8 1.0 CB B:ASP116 4.5 67.2 1.0 CG B:ASP116 4.7 76.1 1.0 CG B:ASP120 4.7 82.7 1.0

Calcium binding site 3 out of 5 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca506 b:94.6 occ:1.00 OE1 B:GLU113 2.7 96.2 1.0 OE2 B:GLU113 3.4 95.8 1.0 CD B:GLU113 3.4 92.0 1.0 OE1 B:GLU110 4.6 61.9 1.0 CG B:GLU113 4.9 81.6 1.0

Calcium binding site 4 out of 5 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:82.2 occ:1.00 O C:GLY44 2.4 77.2 1.0 O C:THR41 2.4 82.0 1.0 OE2 C:GLU55 2.5 74.8 1.0 OD2 C:ASP39 2.5 74.3 1.0 O C:HOH601 2.5 65.3 1.0 OD1 C:ASP39 2.5 74.6 1.0 OG1 C:THR41 2.6 75.3 1.0 OE1 C:GLU55 2.7 70.7 1.0 CG C:ASP39 2.9 75.3 1.0 CD C:GLU55 2.9 70.6 1.0 C C:THR41 3.5 81.8 1.0 C C:GLY44 3.5 79.7 1.0 CB C:THR41 3.5 73.0 1.0 CA C:THR41 3.9 76.8 1.0 CA C:GLY45 4.1 79.9 1.0 N C:GLY45 4.2 77.8 1.0 N C:THR41 4.2 78.8 1.0 OD2 C:ASP47 4.2 78.2 1.0 O C:HOH603 4.2 66.5 1.0 CB C:ASP39 4.4 77.1 1.0 CG C:GLU55 4.4 63.3 1.0 OD1 C:ASN50 4.4 62.4 1.0 N C:GLY44 4.5 87.4 1.0 CA C:GLY44 4.5 83.4 1.0 CZ C:PHE49 4.6 60.9 1.0 N C:ILE42 4.6 86.4 1.0 NE2 C:HIS61 4.7 63.1 1.0 CG2 C:THR41 4.9 68.6 1.0 CE1 C:PHE49 5.0 60.5 1.0

Calcium binding site 5 out of 5 in the Tubulin-Combretastatin A4 Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-Combretastatin A4 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:0.8 occ:1.00 O A:HOH630 2.5 99.6 1.0 O A:HOH617 3.1 84.9 1.0 OD2 E:ASP44 3.3 0.8 1.0 O A:GLU196 3.9 88.8 1.0 OG A:SER158 4.3 79.1 1.0 O A:HOH628 4.3 80.8 1.0 CG E:ASP44 4.4 0.5 1.0 NZ A:LYS166 4.7 80.7 1.0 CA A:HIS197 4.7 75.6 1.0 OD1 E:ASP44 4.8 0.5 1.0 CB A:SER158 4.9 77.0 1.0 OD1 A:ASP199 4.9 83.4 1.0

R.Gaspari, A.E.Prota, K.Bargsten, A.Cavalli, M.O.Steinmetz. Structural Basis of Cis- and Trans-Combretastatin Binding to Tubulin Chem 2017.
ISSN: ESSN 2451-9294
DOI: 10.1016/J.CHEMPR.2016.12.005