Magnesium in PDB 4i4t: Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex

The structure of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex, PDB code: 4i4t was solved by A.E.Prota, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	79.32 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.770, 158.640, 179.240, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 20.4

The structure of Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex also contains other interesting chemical elements:

Calcium	(Ca)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide Complex (pdb code 4i4t). 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-RB3-Ttl-Zampanolide Complex, PDB code: 4i4t:
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-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:28.0 occ:1.00 O1G A:GTP501 2.1 22.5 1.0 O1B A:GTP501 2.1 21.6 1.0 O A:HOH872 2.1 23.9 1.0 O A:HOH681 2.2 25.2 1.0 O A:HOH683 2.2 24.9 1.0 O A:HOH602 2.2 24.9 1.0 HZ1 B:LYS254 3.1 34.4 1.0 PG A:GTP501 3.1 24.0 1.0 PB A:GTP501 3.2 24.8 1.0 HB2 A:GLN11 3.4 26.7 1.0 O3B A:GTP501 3.5 24.8 1.0 O2G A:GTP501 3.6 28.5 1.0 H A:GLN11 3.7 28.7 1.0 HG2 A:GLU71 3.8 54.8 1.0 O3A A:GTP501 3.8 26.8 1.0 NZ B:LYS254 3.9 28.7 1.0 HZ2 B:LYS254 3.9 34.4 1.0 HB2 A:ASP98 3.9 33.6 1.0 OE1 A:GLU71 3.9 49.1 1.0 HG3 A:GLU71 3.9 54.8 1.0 OD2 A:ASP69 4.0 28.6 1.0 HB3 A:GLN11 4.1 26.7 1.0 OD1 A:ASP69 4.2 27.8 1.0 CB A:GLN11 4.2 22.3 1.0 OD2 A:ASP98 4.2 29.5 1.0 HZ3 B:LYS254 4.2 34.4 1.0 CG A:GLU71 4.3 45.6 1.0 HB3 A:ASP98 4.3 33.6 1.0 N A:GLN11 4.4 23.9 1.0 O3G A:GTP501 4.4 22.9 1.0 CB A:ASP98 4.4 28.0 1.0 O2B A:GTP501 4.5 26.1 1.0 CG A:ASP69 4.5 29.9 1.0 O1A A:GTP501 4.6 28.6 1.0 CD A:GLU71 4.6 48.4 1.0 O A:HOH809 4.6 48.2 1.0 CG A:ASP98 4.7 26.8 1.0 PA A:GTP501 4.7 25.9 1.0 HB A:THR145 4.8 29.4 1.0 HG1 A:THR145 4.8 33.6 1.0 HA2 A:GLY10 4.8 27.0 1.0 CA A:GLN11 4.9 25.4 1.0 HE3 B:LYS254 5.0 35.2 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:21.0 occ:1.00 OE1 B:GLN11 2.3 30.9 1.0 O B:HOH694 2.3 28.8 1.0 O1A B:GDP501 2.3 25.1 1.0 O C:HOH794 2.4 33.6 1.0 O B:HOH623 2.5 37.6 1.0 O B:HOH695 2.5 27.9 1.0 O B:HOH791 2.7 59.9 1.0 CD B:GLN11 3.5 32.5 1.0 HB3 B:GLN11 3.5 29.2 1.0 PA B:GDP501 3.6 24.2 1.0 H8 B:GDP501 3.7 35.9 1.0 OD1 B:ASP179 3.9 31.9 1.0 O3A B:GDP501 3.9 23.8 1.0 HB2 B:GLN11 3.9 29.2 1.0 CB B:GLN11 4.0 24.3 1.0 CG B:GLN11 4.2 28.0 1.0 HG2 B:GLN11 4.4 33.6 1.0 HD22 B:ASN101 4.4 30.1 1.0 O C:HOH668 4.5 38.5 1.0 OE1 C:GLU254 4.5 34.1 1.0 OD1 B:ASN101 4.5 29.9 1.0 NE2 B:GLN11 4.5 39.0 1.0 O5' B:GDP501 4.5 24.4 1.0 HE21 B:GLN11 4.5 46.8 1.0 C5' B:GDP501 4.6 22.9 1.0 O2B B:GDP501 4.6 24.1 1.0 O2A B:GDP501 4.7 25.6 1.0 C8 B:GDP501 4.7 29.9 1.0 CG B:ASP179 4.9 30.1 1.0 PB B:GDP501 4.9 24.1 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:23.7 occ:1.00 O1G C:GTP501 2.1 23.3 1.0 O1B C:GTP501 2.1 17.0 1.0 O C:HOH949 2.1 23.5 1.0 O C:HOH771 2.2 23.1 1.0 O C:HOH839 2.2 23.7 1.0 O C:HOH791 2.2 23.8 1.0 HZ1 D:LYS254 3.1 28.9 1.0 PB C:GTP501 3.2 24.2 1.0 PG C:GTP501 3.2 22.6 1.0 HB2 C:GLN11 3.5 21.2 1.0 O3B C:GTP501 3.6 22.7 1.0 H C:GLN11 3.6 26.4 1.0 O2G C:GTP501 3.7 22.6 1.0 O3A C:GTP501 3.8 24.9 1.0 HG2 C:GLU71 3.8 39.0 1.0 HB2 C:ASP98 3.9 30.7 1.0 NZ D:LYS254 3.9 24.1 1.0 HZ2 D:LYS254 3.9 28.9 1.0 HB3 C:GLN11 4.0 21.2 1.0 OD2 C:ASP69 4.1 26.9 1.0 HG3 C:GLU71 4.1 39.0 1.0 OE1 C:GLU71 4.1 38.7 1.0 CB C:GLN11 4.2 17.6 1.0 OD1 C:ASP69 4.3 23.9 1.0 HZ3 D:LYS254 4.3 28.9 1.0 OD2 C:ASP98 4.3 28.0 1.0 N C:GLN11 4.4 22.0 1.0 CG C:GLU71 4.4 32.5 1.0 HB3 C:ASP98 4.4 30.7 1.0 O2B C:GTP501 4.5 22.9 1.0 CB C:ASP98 4.5 25.6 1.0 O1A C:GTP501 4.5 23.2 1.0 O3G C:GTP501 4.6 23.4 1.0 O C:HOH884 4.6 50.0 1.0 CG C:ASP69 4.6 28.0 1.0 O C:HOH649 4.6 38.5 1.0 CG C:ASP98 4.7 28.0 1.0 CD C:GLU71 4.8 43.5 1.0 PA C:GTP501 4.8 23.1 1.0 HB C:THR145 4.8 29.3 1.0 HA2 C:GLY10 4.8 25.2 1.0 CA C:GLN11 4.9 20.4 1.0 HE3 D:LYS254 4.9 28.7 1.0 HG21 C:VAL74 4.9 38.8 1.0 OE1 C:GLN11 4.9 32.2 1.0 CE D:LYS254 5.0 23.9 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:63.0 occ:1.00 OE1 D:GLN11 2.3 46.3 1.0 O1A D:GDP501 2.3 41.0 1.0 O D:HOH829 2.5 53.4 1.0 O D:HOH809 2.7 35.8 1.0 O D:HOH784 2.9 66.8 1.0 OD1 D:ASP179 3.3 74.5 1.0 CD D:GLN11 3.5 54.8 1.0 HB3 D:GLN11 3.6 45.8 1.0 HD21 D:ASN101 3.6 64.1 1.0 PA D:GDP501 3.6 41.7 1.0 O D:HOH814 3.8 69.3 1.0 H8 D:GDP501 3.8 42.8 1.0 HB2 D:GLN11 4.1 45.8 1.0 O3A D:GDP501 4.1 37.7 1.0 CB D:GLN11 4.1 38.2 1.0 CG D:GLN11 4.3 40.4 1.0 O2B D:GDP501 4.4 33.8 1.0 ND2 D:ASN101 4.4 53.5 1.0 C5' D:GDP501 4.5 37.6 1.0 NE2 D:GLN11 4.5 52.5 1.0 HG2 D:GLN11 4.5 48.4 1.0 CG D:ASP179 4.5 84.9 1.0 HE22 D:GLN11 4.5 63.0 1.0 O5' D:GDP501 4.5 37.9 1.0 O2A D:GDP501 4.7 42.2 1.0 HB3 D:ASP179 4.8 0.5 1.0 C8 D:GDP501 4.8 35.6 1.0 HD22 D:ASN101 4.9 64.1 1.0 PB D:GDP501 5.0 38.2 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg701 b:68.0 occ:1.00 H5'1 F:ACP703 2.4 68.1 1.0 H3B1 F:ACP703 2.5 69.4 1.0 H5'2 F:ACP703 2.7 68.1 1.0 H3' F:ACP703 2.8 59.3 1.0 O2A F:ACP703 2.9 93.5 1.0 HB3 F:ASP318 2.9 46.0 1.0 C5' F:ACP703 3.0 56.8 1.0 HG21 F:ILE330 3.0 72.2 1.0 OD2 F:ASP318 3.1 41.1 1.0 HG2 F:GLU331 3.3 51.9 1.0 HB2 F:ASP318 3.4 46.0 1.0 C3' F:ACP703 3.5 49.4 1.0 CB F:ASP318 3.5 38.3 1.0 C3B F:ACP703 3.5 57.9 1.0 HO3' F:ACP703 3.6 97.6 1.0 CG F:ASP318 3.6 46.0 1.0 H3B2 F:ACP703 3.6 69.4 1.0 O3' F:ACP703 3.7 81.3 1.0 HB F:ILE330 3.7 43.7 1.0 CG2 F:ILE330 3.8 60.2 1.0 C4' F:ACP703 3.8 59.1 1.0 HG22 F:ILE330 3.8 72.2 1.0 OE2 F:GLU331 3.9 83.3 1.0 PA F:ACP703 4.1 56.9 1.0 HH11 F:ARG222 4.1 61.2 1.0 O5' F:ACP703 4.1 72.5 1.0 CB F:ILE330 4.2 36.4 1.0 H4' F:ACP703 4.2 71.0 1.0 CG F:GLU331 4.3 43.2 1.0 HG13 F:ILE330 4.3 65.5 1.0 HOG3 F:ACP703 4.4 79.5 1.0 OD1 F:ASP200 4.4 55.5 1.0 O3A F:ACP703 4.4 90.1 1.0 HH12 F:ARG222 4.5 61.2 1.0 O3G F:ACP703 4.5 66.2 1.0 HB2 F:ASP200 4.5 46.7 1.0 CD F:GLU331 4.5 58.4 1.0 CG F:ASP200 4.6 54.6 1.0 PB F:ACP703 4.6 63.7 1.0 HG23 F:ILE330 4.6 72.2 1.0 NH1 F:ARG222 4.6 51.0 1.0 OD1 F:ASP318 4.7 43.4 1.0 PG F:ACP703 4.8 65.6 1.0 CG1 F:ILE330 4.8 54.5 1.0 HG3 F:GLU331 4.8 51.9 1.0 OD2 F:ASP200 4.8 59.7 1.0 C2' F:ACP703 4.8 48.3 1.0 HB3 F:GLU331 4.9 64.6 1.0 H8 F:ACP703 4.9 51.5 1.0 CA F:ASP318 4.9 35.0 1.0 CB F:ASP200 5.0 38.9 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of Tubulin-RB3-Ttl-Zampanolide 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-RB3-Ttl-Zampanolide Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:38.5 occ:1.00 O1G F:ACP703 2.3 49.1 1.0 HD22 F:ASN333 2.3 0.1 1.0 O F:HOH955 2.3 60.3 1.0 O2B F:ACP703 2.3 87.0 1.0 HOB2 F:ACP703 2.3 0.5 1.0 O F:HOH802 2.4 68.0 1.0 OE1 F:GLU331 2.6 50.3 1.0 O F:HOH936 2.6 51.4 1.0 OE2 F:GLU331 2.7 83.3 1.0 HD21 F:ASN333 2.8 0.1 1.0 ND2 F:ASN333 2.8 85.9 1.0 CD F:GLU331 3.0 58.4 1.0 HZ3 F:LYS74 3.2 65.0 1.0 PB F:ACP703 3.5 63.7 1.0 PG F:ACP703 3.6 65.6 1.0 HZ2 F:LYS74 3.7 65.0 1.0 NZ F:LYS74 3.8 54.2 1.0 O1B F:ACP703 4.0 98.1 1.0 HB2 A:GLU450 4.0 1.0 1.0 O F:HOH878 4.0 57.6 1.0 O A:HOH801 4.0 52.7 1.0 CG F:ASN333 4.1 77.6 1.0 C3B F:ACP703 4.1 57.9 1.0 HZ1 F:LYS74 4.1 65.0 1.0 H3B1 F:ACP703 4.3 69.4 1.0 HG3 A:GLU450 4.3 0.3 1.0 O3G F:ACP703 4.4 66.2 1.0 CG F:GLU331 4.5 43.2 1.0 O F:HOH962 4.6 66.0 1.0 O F:HOH981 4.6 89.7 1.0 HOG2 F:ACP703 4.6 85.9 1.0 OD1 F:ASN333 4.6 91.4 1.0 O2G F:ACP703 4.6 71.6 1.0 HG3 F:GLU331 4.7 51.9 1.0 O3A F:ACP703 4.8 90.1 1.0 CB A:GLU450 4.8 0.8 1.0 O2A F:ACP703 4.8 93.5 1.0 HA F:ASN333 4.9 50.3 1.0 CG A:GLU450 4.9 0.2 1.0 HG2 F:GLU331 5.0 51.9 1.0 HB2 F:GLU331 5.0 64.6 1.0 OE2 A:GLU450 5.0 0.4 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