Magnesium in PDB 4i50: Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex, PDB code: 4i50 was solved by A.E.Prota, K.Bargsten, D.Zurwerra, J.J.Field, J.F.Diaz, K.H.Altmann, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	77.57 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.620, 155.130, 180.410, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.6

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex also contains other interesting chemical elements:

Calcium	(Ca)	6 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex (pdb code 4i50). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex, PDB code: 4i50:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:58.7 occ:1.00 O A:HOH612 2.5 29.9 1.0 O1G A:GTP501 2.9 28.5 1.0 HB2 A:GLN11 2.9 34.8 1.0 O A:HOH609 2.9 31.8 1.0 HZ1 B:LYS254 2.9 62.1 1.0 O1A A:GTP501 3.0 34.8 1.0 O1B A:GTP501 3.1 32.4 1.0 HB3 A:GLN11 3.2 34.8 1.0 HZ3 B:LYS254 3.2 62.1 1.0 NZ B:LYS254 3.4 51.7 1.0 HZ2 B:LYS254 3.4 62.1 1.0 OE1 A:GLN11 3.4 51.6 1.0 CB A:GLN11 3.5 29.0 1.0 O3A A:GTP501 3.5 43.6 1.0 CD A:GLN11 3.8 38.9 1.0 PA A:GTP501 3.8 46.0 1.0 PB A:GTP501 3.9 34.1 1.0 H A:GLN11 4.0 41.5 1.0 O A:HOH610 4.2 37.8 1.0 PG A:GTP501 4.2 42.6 1.0 CG A:GLN11 4.2 36.5 1.0 O B:HOH650 4.3 51.7 1.0 O3B A:GTP501 4.5 52.7 1.0 NE2 A:GLN11 4.6 50.3 1.0 OE1 A:GLU71 4.6 82.6 1.0 N A:GLN11 4.7 34.5 1.0 CA A:GLN11 4.7 45.3 1.0 HE22 A:GLN11 4.7 60.3 1.0 O2A A:GTP501 4.7 38.4 1.0 CE B:LYS254 4.8 45.2 1.0 HG3 A:GLN11 4.8 43.8 1.0 O3G A:GTP501 4.8 37.8 1.0 H8 A:GTP501 4.9 42.5 1.0 HG2 A:GLN11 4.9 43.8 1.0 HG21 A:VAL74 5.0 65.1 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:35.7 occ:1.00 O1A B:GDP501 2.2 35.7 1.0 O B:HOH609 2.3 40.2 1.0 O C:HOH717 2.5 52.2 1.0 OE1 B:GLN11 2.5 48.7 1.0 O B:HOH610 2.6 40.1 1.0 O B:HOH614 2.7 42.0 1.0 CD B:GLN11 3.3 72.1 1.0 HB3 B:GLN11 3.4 61.5 1.0 PA B:GDP501 3.5 37.0 1.0 H8 B:GDP501 3.6 40.0 1.0 OD1 B:ASP179 3.8 59.7 1.0 O3A B:GDP501 3.8 35.7 1.0 HE22 B:GLN11 3.9 0.0 1.0 HB2 B:GLN11 3.9 61.5 1.0 NE2 B:GLN11 4.0 0.5 1.0 CB B:GLN11 4.0 51.2 1.0 OE1 C:GLU254 4.1 93.4 1.0 CG B:GLN11 4.3 60.5 1.0 C5' B:GDP501 4.3 37.1 1.0 O5' B:GDP501 4.3 22.9 1.0 OD1 B:ASN101 4.3 53.3 1.0 HD22 B:ASN101 4.6 58.4 1.0 O2A B:GDP501 4.6 33.1 1.0 C8 B:GDP501 4.6 33.3 1.0 HE21 B:GLN11 4.7 0.0 1.0 HG2 B:GLN11 4.7 72.6 1.0 O2B B:GDP501 4.7 28.3 1.0 CG B:ASP179 4.8 58.3 1.0 PB B:GDP501 4.9 37.6 1.0 HG3 B:GLN11 5.0 72.6 1.0 HB3 B:ASP179 5.0 50.1 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:39.4 occ:1.00 O C:HOH646 2.2 45.5 1.0 O1G C:GTP501 2.3 27.1 1.0 O C:HOH620 2.3 32.6 1.0 O C:HOH622 2.3 41.7 1.0 O C:HOH613 2.4 32.8 1.0 O1B C:GTP501 2.5 32.7 1.0 HZ1 D:LYS254 3.3 54.9 1.0 HB2 C:GLN11 3.4 28.8 1.0 PG C:GTP501 3.5 39.7 1.0 OE1 C:GLU71 3.6 75.5 1.0 PB C:GTP501 3.6 33.4 1.0 HB2 C:ASP98 3.7 46.1 1.0 H C:GLN11 3.7 40.5 1.0 HB3 C:GLU71 3.8 66.1 1.0 O2G C:GTP501 3.8 33.6 1.0 O3B C:GTP501 3.9 51.7 1.0 OD2 C:ASP69 4.0 38.5 1.0 HZ2 D:LYS254 4.0 54.9 1.0 HB3 C:ASP98 4.0 46.1 1.0 NZ D:LYS254 4.0 45.8 1.0 OD1 C:ASP69 4.1 36.3 1.0 O3A C:GTP501 4.2 48.7 1.0 OD2 C:ASP98 4.2 41.9 1.0 CB C:ASP98 4.2 38.5 1.0 CB C:GLN11 4.3 24.0 1.0 HB3 C:GLN11 4.3 28.8 1.0 HZ3 D:LYS254 4.4 54.9 1.0 CD C:GLU71 4.4 77.3 1.0 CG C:ASP69 4.5 46.0 1.0 N C:GLN11 4.5 33.7 1.0 CG C:ASP98 4.6 43.5 1.0 CB C:GLU71 4.6 55.1 1.0 HG23 C:VAL74 4.6 58.6 1.0 O3G C:GTP501 4.7 25.4 1.0 OE1 C:GLN11 4.8 55.2 1.0 HB2 C:GLU71 4.8 66.1 1.0 HA2 C:GLY10 4.9 44.6 1.0 O2B C:GTP501 4.9 38.3 1.0 HB C:THR145 4.9 47.0 1.0 CA C:GLN11 4.9 29.2 1.0 O1A C:GTP501 4.9 38.4 1.0 HG1 C:THR145 5.0 43.5 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:57.0 occ:1.00 HE22 D:GLN11 2.3 0.3 1.0 O1A D:GDP501 2.5 74.7 1.0 NE2 D:GLN11 2.6 86.1 1.0 HE21 D:GLN11 2.7 0.3 1.0 OD1 D:ASP179 2.7 0.5 1.0 O D:HOH616 2.7 53.8 1.0 HD22 D:ASN101 3.4 0.1 1.0 CD D:GLN11 3.5 84.0 1.0 PA D:GDP501 3.7 58.0 1.0 HB3 D:GLN11 3.7 63.5 1.0 H8 D:GDP501 3.7 58.1 1.0 O3A D:GDP501 3.9 51.7 1.0 CG D:ASP179 3.9 0.3 1.0 OE1 D:GLN11 4.1 82.1 1.0 HB2 D:GLN11 4.2 63.5 1.0 ND2 D:ASN101 4.2 95.9 1.0 CB D:GLN11 4.3 52.9 1.0 C5' D:GDP501 4.3 62.4 1.0 O5' D:GDP501 4.5 55.2 1.0 CG D:GLN11 4.5 64.0 1.0 OD2 D:ASP179 4.6 0.9 1.0 HD21 D:ASN101 4.6 0.1 1.0 C8 D:GDP501 4.8 48.4 1.0 O2A D:GDP501 4.8 56.2 1.0 H2' D:GDP501 4.8 59.2 1.0 HB3 D:ASP179 4.9 0.3 1.0 HG2 D:GLN11 4.9 76.8 1.0 O2B D:GDP501 4.9 41.8 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:0.7 occ:1.00 HH21 F:ARG222 2.5 0.7 1.0 H5'2 F:ACP401 2.6 0.3 1.0 O1G F:ACP401 2.6 0.4 1.0 HO3' F:ACP401 2.7 0.9 1.0 HH22 F:ARG222 2.8 0.7 1.0 NH2 F:ARG222 2.9 0.1 1.0 H3' F:ACP401 3.1 0.8 1.0 O3' F:ACP401 3.3 97.5 1.0 OD2 F:ASP318 3.4 0.8 1.0 OD1 F:ASP200 3.4 0.2 1.0 O1A F:ACP401 3.5 0.8 1.0 C5' F:ACP401 3.6 97.8 1.0 C3' F:ACP401 3.6 93.2 1.0 CG F:ASP318 3.6 89.3 1.0 HB3 F:ASP318 3.7 93.5 1.0 H3B1 F:ACP401 3.7 97.2 1.0 PG F:ACP401 3.8 0.9 1.0 CG F:ASP200 4.0 90.4 1.0 H5'1 F:ACP401 4.0 0.3 1.0 CZ F:ARG222 4.0 0.9 1.0 OD1 F:ASP318 4.1 72.1 1.0 C4' F:ACP401 4.1 88.1 1.0 CB F:ASP318 4.2 77.9 1.0 C3B F:ACP401 4.3 81.0 1.0 O3G F:ACP401 4.3 98.3 1.0 OD2 F:ASP200 4.3 89.0 1.0 O5' F:ACP401 4.4 99.5 1.0 HE F:ARG222 4.4 0.3 1.0 H4' F:ACP401 4.4 0.8 1.0 HOG3 F:ACP401 4.4 0.0 1.0 OD1 F:ASN242 4.5 0.8 1.0 PA F:ACP401 4.5 0.1 1.0 HD13 F:ILE330 4.5 94.8 1.0 HB2 F:ASP318 4.6 93.5 1.0 HD12 F:ILE330 4.6 94.8 1.0 NE F:ARG222 4.6 0.1 1.0 HH21 F:ARG202 4.7 0.1 1.0 HB2 F:ASP200 4.8 0.0 1.0 HG21 F:ILE330 4.8 0.4 1.0 HH12 F:ARG222 4.8 0.8 1.0 HG2 F:GLU331 4.8 0.3 1.0 NH1 F:ARG222 4.9 0.0 1.0 CB F:ASP200 4.9 90.0 1.0 C2' F:ACP401 4.9 87.6 1.0 HB3 F:ASP200 5.0 0.0 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Tubulin-Stathmin-Ttl-Epothilone A Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg403 b:97.5 occ:1.00 OE1 F:GLU331 2.8 0.2 1.0 HE2 F:LYS74 2.8 0.8 1.0 HE3 F:LYS74 2.9 0.8 1.0 HD22 F:ASN333 3.0 0.9 1.0 HD21 F:ASN333 3.1 0.9 1.0 HOB2 F:ACP401 3.3 0.1 1.0 CE F:LYS74 3.3 1.0 1.0 ND2 F:ASN333 3.4 1.0 1.0 HOG2 F:ACP401 3.5 0.0 1.0 CD F:GLU331 3.5 0.4 1.0 O2G F:ACP401 3.6 94.2 1.0 O2B F:ACP401 3.6 88.4 1.0 OE2 F:GLU331 3.7 0.7 1.0 HD3 F:LYS74 3.9 0.3 1.0 CD F:LYS74 4.2 0.1 1.0 HZ1 F:LYS74 4.3 0.8 1.0 NZ F:LYS74 4.4 94.0 1.0 O F:CYS72 4.5 88.9 1.0 CG F:ASN333 4.7 0.2 1.0 HA F:ASN333 4.8 91.5 1.0 HG2 F:LYS74 4.8 1.0 1.0 HB2 F:GLU331 4.8 0.5 1.0 HD2 F:LYS74 4.9 0.3 1.0 CG F:GLU331 4.9 0.3 1.0 HZ3 F:LYS74 4.9 0.8 1.0 HZ2 F:LYS74 5.0 0.8 1.0

A.E.Prota, K.Bargsten, D.Zurwerra, J.J.Field, J.F.Diaz, K.H.Altmann, M.O.Steinmetz. Molecular Mechanism of Action of Microtubule-Stabilizing Anticancer Agents. Science V. 339 587 2013.
ISSN: ISSN 0036-8075
PubMed: 23287720
DOI: 10.1126/SCIENCE.1230582