Calcium in PDB 8r67: Tubulin-Cryptophycin Complex

The structure of Tubulin-Cryptophycin Complex, PDB code: 8r67 was solved by A.C.Abel, T.Muehlethaler, C.Dessin, M.O.Steinmetz, N.Sewald, A.E.Prota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.52 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.75, 158.66, 180.28, 90, 90, 90
R / Rfree (%)	19.4 / 22.9

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

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Cryptophycin Complex (pdb code 8r67). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tubulin-Cryptophycin Complex, PDB code: 8r67:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Cryptophycin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:82.0 occ:1.00 OE2 A:GLU55 2.2 74.8 1.0 O A:GLY44 2.3 80.1 1.0 O A:HOH642 2.4 71.6 1.0 O A:THR41 2.5 87.3 1.0 OG1 A:THR41 2.5 79.9 1.0 OD2 A:ASP39 2.6 80.8 1.0 OE1 A:GLU55 2.6 84.0 1.0 CD A:GLU55 2.7 79.9 1.0 OD1 A:ASP39 2.8 81.6 1.0 CG A:ASP39 3.0 82.0 1.0 C A:GLY44 3.2 85.7 1.0 CB A:THR41 3.5 84.2 1.0 C A:THR41 3.5 88.7 1.0 CA A:GLY45 3.6 88.2 1.0 N A:GLY45 3.8 88.8 1.0 CA A:THR41 4.0 91.9 1.0 CG A:GLU55 4.2 80.4 1.0 N A:GLY44 4.3 85.8 1.0 CA A:GLY44 4.3 88.7 1.0 OD1 A:ASN50 4.4 73.1 1.0 N A:THR41 4.4 83.6 1.0 CB A:ASP39 4.5 80.0 1.0 CZ A:PHE49 4.6 70.4 1.0 N A:ILE42 4.7 86.7 1.0 CE1 A:PHE49 4.7 79.4 1.0 ND2 A:ASN50 4.8 81.9 1.0 NE2 A:HIS61 4.8 79.1 1.0 CG2 A:THR41 4.8 77.5 1.0 OD2 A:ASP47 5.0 84.2 1.0

Calcium binding site 2 out of 4 in the Tubulin-Cryptophycin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:108.9 occ:1.00 O E:HOH304 2.3 77.5 1.0 O A:HOH647 2.5 83.7 1.0 O A:HOH629 2.9 70.4 1.0 O A:HOH661 3.1 65.0 1.0 O A:HOH704 3.1 84.8 1.0 O A:HOH626 3.7 88.8 1.0 OD2 E:ASP44 3.8 104.8 1.0 O A:HOH682 4.3 78.8 1.0 OG A:SER158 4.3 71.2 1.0 O A:GLY162 4.4 71.8 1.0 O A:GLU196 4.5 72.9 1.0 NZ A:LYS166 4.6 77.2 1.0 CB A:SER158 4.7 62.3 1.0 OD1 A:ASP199 4.7 75.2 1.0 CG E:ASP44 4.8 97.1 1.0 OD1 E:ASP44 5.0 77.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Cryptophycin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca507 b:112.0 occ:1.00 O B:HOH629 2.3 72.9 1.0 OE1 B:GLU113 2.8 82.1 1.0 OE1 B:GLU110 3.3 56.9 1.0 CD B:GLU113 3.9 82.8 1.0 CD B:GLU110 4.1 64.1 1.0 OE2 B:GLU110 4.1 69.5 1.0 O B:HOH677 4.2 67.2 1.0 OE2 B:GLU113 4.3 85.8 1.0

Calcium binding site 4 out of 4 in the Tubulin-Cryptophycin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Cryptophycin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:64.8 occ:1.00 O C:THR41 2.3 67.5 1.0 O C:HOH604 2.4 51.1 1.0 OD2 C:ASP39 2.4 60.6 1.0 OE1 C:GLU55 2.4 61.1 1.0 OE2 C:GLU55 2.4 61.4 1.0 OD1 C:ASP39 2.5 65.5 1.0 OG1 C:THR41 2.5 69.1 1.0 O C:GLY44 2.5 67.1 1.0 CD C:GLU55 2.8 60.8 1.0 CG C:ASP39 2.8 61.0 1.0 C C:THR41 3.3 70.0 1.0 CB C:THR41 3.5 72.4 1.0 C C:GLY44 3.6 66.8 1.0 CA C:THR41 3.8 66.0 1.0 N C:THR41 4.0 64.8 1.0 O C:HOH622 4.2 61.6 1.0 O C:HOH610 4.2 71.7 1.0 CG C:GLU55 4.3 57.0 1.0 CB C:ASP39 4.3 64.5 1.0 OD2 C:ASP47 4.3 63.7 1.0 CA C:GLY45 4.3 65.8 1.0 N C:GLY45 4.3 74.3 1.0 N C:GLY44 4.4 69.2 1.0 CA C:GLY44 4.5 68.7 1.0 N C:ILE42 4.5 63.0 1.0 NE2 C:HIS61 4.5 54.2 1.0 OD1 C:ASN50 4.6 61.7 1.0 CZ C:PHE49 4.7 52.8 1.0 CG2 C:THR41 4.8 56.8 1.0 CE1 C:PHE49 4.9 59.2 1.0 CA C:ILE42 5.0 68.3 1.0 ND2 C:ASN50 5.0 48.4 1.0

A.C.Abel, T.Muhlethaler, C.Dessin, T.Schachtsiek, B.Sammet, T.Sharpe, M.O.Steinmetz, N.Sewald, A.E.Prota. Bridging the Maytansine and Vinca Sites: Cryptophycins Target Beta-Tubulin'S T5-Loop. J.Biol.Chem. 07363 2024.
ISSN: ESSN 1083-351X
PubMed: 38735475
DOI: 10.1016/J.JBC.2024.107363