Magnesium 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
Calcium	(Ca)	4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 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 Magnesium with other atoms in the Mg 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:Mg502 b:21.6 occ:1.00 O A:HOH620 2.1 21.6 1.0 O A:HOH738 2.1 19.5 1.0 O A:HOH690 2.1 22.2 1.0 O A:HOH683 2.1 19.7 1.0 O1G A:GTP501 2.1 17.3 1.0 O1B A:GTP501 2.1 17.6 1.0 PG A:GTP501 3.3 19.4 1.0 PB A:GTP501 3.3 17.7 1.0 O3B A:GTP501 3.6 19.3 1.0 O2G A:GTP501 3.7 20.1 1.0 O3A A:GTP501 3.9 18.8 1.0 OD2 A:ASP69 4.0 28.3 1.0 OE1 A:GLU71 4.0 45.1 1.0 NZ B:LYS252 4.0 23.6 1.0 OD1 A:ASP69 4.1 28.6 1.0 CB A:GLN11 4.2 22.3 1.0 CG A:GLU71 4.3 42.6 1.0 N A:GLN11 4.4 22.3 1.0 OD2 A:ASP98 4.4 27.7 1.0 CB A:ASP98 4.4 27.8 1.0 O A:HOH751 4.4 61.0 1.0 CG A:ASP69 4.5 29.0 1.0 O1A A:GTP501 4.5 19.6 1.0 O3G A:GTP501 4.6 18.1 1.0 O2B A:GTP501 4.6 19.9 1.0 CD A:GLU71 4.6 44.9 1.0 CG A:ASP98 4.8 27.5 1.0 PA A:GTP501 4.8 19.2 1.0 CA A:GLN11 4.8 22.4 1.0 OE1 A:GLN11 4.9 23.5 1.0

Magnesium binding site 2 out of 5 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 Magnesium with other atoms in the Mg 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 B:Mg502 b:13.5 occ:1.00 O B:HOH646 2.0 22.6 1.0 OE1 B:GLN11 2.1 23.8 1.0 O C:HOH817 2.2 32.1 1.0 O1A B:GDP501 2.3 17.6 1.0 O B:HOH717 2.3 46.1 1.0 O B:HOH677 2.3 26.6 1.0 O B:HOH612 2.4 29.4 1.0 CD B:GLN11 3.3 23.7 1.0 PA B:GDP501 3.6 15.9 1.0 O3A B:GDP501 3.8 16.3 1.0 OD1 B:ASP177 3.8 29.4 1.0 CB B:GLN11 4.2 22.1 1.0 CG B:GLN11 4.2 22.9 1.0 OD1 B:ASN99 4.3 21.1 1.0 NE2 B:GLN11 4.3 24.4 1.0 C5' B:GDP501 4.4 18.5 1.0 O5' B:GDP501 4.4 16.9 1.0 O C:HOH663 4.4 49.1 1.0 O1B B:GDP501 4.7 13.6 1.0 OE1 C:GLU254 4.7 30.9 1.0 CG B:ASP177 4.7 29.3 1.0 O2A B:GDP501 4.8 14.7 1.0 C8 B:GDP501 4.8 17.3 1.0 PB B:GDP501 4.9 15.1 1.0 ND2 B:ASN99 5.0 20.9 1.0

Magnesium binding site 3 out of 5 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 Magnesium with other atoms in the Mg 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 C:Mg502 b:17.8 occ:1.00 O1G C:GTP501 2.1 15.5 1.0 O C:HOH617 2.1 17.1 1.0 O C:HOH683 2.1 16.1 1.0 O C:HOH809 2.1 19.8 1.0 O C:HOH672 2.1 20.8 1.0 O1B C:GTP501 2.1 14.1 1.0 PG C:GTP501 3.2 16.2 1.0 PB C:GTP501 3.2 14.4 1.0 O3B C:GTP501 3.5 15.1 1.0 O2G C:GTP501 3.6 16.9 1.0 O3A C:GTP501 3.8 14.7 1.0 NZ D:LYS252 3.9 22.2 1.0 OE1 C:GLU71 3.9 30.6 1.0 OD2 C:ASP69 4.0 21.6 1.0 CB C:GLN11 4.2 17.8 1.0 OD1 C:ASP69 4.2 21.5 1.0 OD2 C:ASP98 4.3 27.0 1.0 CG C:GLU71 4.3 28.7 1.0 O C:HOH710 4.4 48.5 1.0 N C:GLN11 4.4 17.5 1.0 CB C:ASP98 4.4 26.6 1.0 O3G C:GTP501 4.5 14.0 1.0 O1A C:GTP501 4.5 15.0 1.0 O2B C:GTP501 4.6 13.1 1.0 CG C:ASP69 4.6 21.6 1.0 CD C:GLU71 4.7 29.8 1.0 PA C:GTP501 4.7 16.1 1.0 CG C:ASP98 4.8 26.7 1.0 O C:HOH786 4.8 47.8 1.0 CA C:GLN11 4.9 17.6 1.0 OE1 C:GLN11 4.9 18.4 1.0 CE D:LYS252 5.0 22.1 1.0

Magnesium binding site 4 out of 5 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 Magnesium with other atoms in the Mg 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 D:Mg502 b:47.7 occ:1.00 O D:HOH674 1.8 40.4 1.0 O D:HOH617 2.2 44.2 1.0 OE1 D:GLN11 2.3 50.4 1.0 O1A D:GDP501 2.4 40.3 1.0 O D:HOH636 2.5 37.2 1.0 CD D:GLN11 3.5 49.5 1.0 PA D:GDP501 3.6 40.4 1.0 O3A D:GDP501 3.7 36.1 1.0 CB D:GLN11 4.1 45.4 1.0 CG D:GLN11 4.3 47.5 1.0 O1B D:GDP501 4.3 33.0 1.0 NE2 D:GLN11 4.5 50.4 1.0 O5' D:GDP501 4.5 39.4 1.0 OD1 D:ASN99 4.5 51.2 1.0 C5' D:GDP501 4.6 40.6 1.0 O2A D:GDP501 4.7 41.7 1.0 PB D:GDP501 4.7 37.7 1.0 O D:HOH602 4.9 32.5 1.0

Magnesium binding site 5 out of 5 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 Magnesium with other atoms in the Mg binding site number 5 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 F:Mg501 b:62.0 occ:1.00 O2B F:ACP502 2.1 78.2 1.0 OE1 F:GLU331 2.2 68.3 1.0 O1G F:ACP502 2.2 77.2 1.0 OE2 F:GLU331 2.8 69.5 1.0 CD F:GLU331 2.8 62.7 1.0 OD1 F:ASN333 2.9 53.1 1.0 PB F:ACP502 3.4 83.2 1.0 PG F:ACP502 3.5 94.5 1.0 CG F:ASN333 3.9 49.0 1.0 C3B F:ACP502 4.0 86.4 1.0 NZ F:LYS74 4.1 64.1 1.0 O1B F:ACP502 4.2 86.8 1.0 CG F:GLU331 4.2 55.9 1.0 ND2 F:ASN333 4.3 49.5 1.0 O3G F:ACP502 4.4 87.9 1.0 O3A F:ACP502 4.5 78.6 1.0 O2G F:ACP502 4.5 91.2 1.0 O2A F:ACP502 4.7 74.6 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