Calcium in PDB 7l05: Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase)

The structure of Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase), PDB code: 7l05 was solved by M.C.Franklin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.62 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.088, 158.036, 181.014, 90, 90, 90
R / Rfree (%)	18.6 / 21.7

The structure of Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase) also contains other interesting chemical elements:

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

The binding sites of Calcium atom in the Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase) (pdb code 7l05). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase), PDB code: 7l05:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:44.0 occ:1.00 O A:THR41 2.4 73.0 1.0 O A:HOH604 2.4 38.8 1.0 OE2 A:GLU55 2.5 60.2 1.0 O A:GLY44 2.5 68.0 1.0 OG1 A:THR41 2.5 67.9 1.0 OD2 A:ASP39 2.5 64.2 1.0 OE1 A:GLU55 2.6 62.7 1.0 OD1 A:ASP39 2.6 64.8 1.0 CD A:GLU55 2.9 58.6 1.0 CG A:ASP39 2.9 64.3 1.0 C A:THR41 3.5 73.2 1.0 CB A:THR41 3.5 70.9 1.0 C A:GLY44 3.5 67.6 1.0 CA A:THR41 3.9 72.7 1.0 CA A:GLY45 4.2 64.2 1.0 N A:GLY45 4.2 66.0 1.0 N A:THR41 4.3 73.2 1.0 CG A:GLU55 4.4 56.8 1.0 O A:HOH607 4.4 40.6 1.0 N A:GLY44 4.5 69.6 1.0 CB A:ASP39 4.5 64.2 1.0 OD1 A:ASP47 4.5 55.3 1.0 CA A:GLY44 4.5 68.7 1.0 CZ A:PHE49 4.6 47.1 1.0 OD1 A:ASN50 4.6 44.1 1.0 N A:ILE42 4.7 74.2 1.0 NE2 A:HIS61 4.8 51.7 1.0 CG2 A:THR41 4.8 70.2 1.0 CE1 A:PHE49 4.9 46.9 1.0 ND2 A:ASN50 4.9 43.4 1.0

Calcium binding site 2 out of 4 in the Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:69.9 occ:1.00 O A:HOH707 2.4 65.3 1.0 O A:HOH768 2.5 58.9 1.0 OD2 E:ASP44 3.9 69.5 1.0 OG A:SER158 4.2 38.2 1.0 NZ A:LYS166 4.3 37.3 1.0 O A:GLU196 4.5 40.6 1.0 O A:GLY162 4.5 48.1 1.0 OD2 A:ASP199 4.6 38.5 1.0 O A:HIS197 4.7 37.5 1.0 CB A:SER158 4.9 39.4 1.0 CA A:HIS197 5.0 36.8 1.0

Calcium binding site 3 out of 4 in the Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:61.5 occ:1.00 OE2 B:GLU111 2.5 45.0 1.0 O B:HOH602 2.5 39.5 1.0 OE1 B:GLU111 2.9 47.4 1.0 CD B:GLU111 3.0 43.9 1.0 CG B:GLU111 4.5 41.0 1.0

Calcium binding site 4 out of 4 in the Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Novel Maytansinoid M24 Bound to T2R-Ttl (Two Tubulin Alpha/Beta Heterodimers, RB3 Stathmin-Like Domain, and Tubulin Tyrosine Ligase) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:28.5 occ:1.00 O C:THR41 2.4 47.5 1.0 O C:HOH611 2.4 22.6 1.0 OG1 C:THR41 2.5 46.5 1.0 O C:GLY44 2.5 46.8 1.0 OE2 C:GLU55 2.5 39.6 1.0 OD2 C:ASP39 2.5 44.9 1.0 OE1 C:GLU55 2.6 40.6 1.0 OD1 C:ASP39 2.6 44.0 1.0 CD C:GLU55 2.8 36.7 1.0 CG C:ASP39 2.9 43.7 1.0 C C:THR41 3.5 47.0 1.0 CB C:THR41 3.5 47.5 1.0 C C:GLY44 3.5 46.9 1.0 CA C:THR41 3.9 47.6 1.0 N C:THR41 4.2 48.0 1.0 N C:GLY45 4.3 46.6 1.0 CG C:GLU55 4.4 34.5 1.0 O C:HOH606 4.4 32.9 1.0 CA C:GLY45 4.4 46.1 1.0 CB C:ASP39 4.4 44.1 1.0 OD1 C:ASP47 4.4 40.7 1.0 N C:GLY44 4.4 46.6 1.0 CA C:GLY44 4.5 46.6 1.0 CZ C:PHE49 4.6 29.5 1.0 OD1 C:ASN50 4.6 24.8 1.0 N C:ILE42 4.6 47.6 1.0 NE2 C:HIS61 4.7 27.9 1.0 CG2 C:THR41 4.8 47.3 1.0 CE1 C:PHE49 4.9 29.1 1.0 ND2 C:ASN50 4.9 24.9 1.0

J.O.Dasilva, K.Yang, O.Surriga, T.Nittoli, A.Kunz, M.C.Franklin, F.J.Delfino, S.Mao, F.Zhao, J.T.Giurleo, M.P.Kelly, S.Makonnen, C.Hickey, P.Krueger, R.Foster, Z.Chen, M.W.Retter, R.Slim, T.M.Young, W.C.Olson, G.Thurston, C.Daly. A Biparatopic Antibody-Drug Conjugate to Treat Met-Expressing Cancers, Including Those That Are Unresponsive to Met Pathway Blockade. Mol.Cancer Ther. V. 20 1966 2021.
ISSN: ESSN 1538-8514
PubMed: 34315762
DOI: 10.1158/1535-7163.MCT-21-0009