Magnesium in PDB 4i55: Crystal Structure of Tubulin-Stathmin-Ttl Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl Complex, PDB code: 4i55 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)	71.84 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.160, 156.470, 181.490, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.8

The structure of Crystal Structure of Tubulin-Stathmin-Ttl 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-Stathmin-Ttl Complex (pdb code 4i55). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl Complex, PDB code: 4i55:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:38.2 occ:1.00 O A:HOH708 2.1 36.8 1.0 O1G A:GTP501 2.1 24.0 1.0 O1B A:GTP501 2.2 29.1 1.0 O A:HOH602 2.2 30.9 1.0 O A:HOH662 2.3 31.9 1.0 O A:HOH660 2.3 32.5 1.0 HZ1 B:LYS254 3.2 41.9 1.0 PG A:GTP501 3.2 31.2 1.0 PB A:GTP501 3.3 30.0 1.0 HB2 A:GLN11 3.4 35.8 1.0 O2G A:GTP501 3.6 31.5 1.0 H A:GLN11 3.6 36.4 1.0 O3B A:GTP501 3.6 39.0 1.0 HG2 A:GLU71 3.8 70.3 1.0 O3A A:GTP501 3.9 34.9 1.0 HG3 A:GLU71 3.9 70.3 1.0 HB2 A:ASP98 3.9 36.1 1.0 HZ2 B:LYS254 3.9 41.9 1.0 NZ B:LYS254 3.9 34.9 1.0 OD2 A:ASP69 4.0 37.5 1.0 OE1 A:GLU71 4.0 55.3 1.0 HB3 A:GLN11 4.1 35.8 1.0 CB A:GLN11 4.1 29.8 1.0 OD1 A:ASP69 4.3 36.0 1.0 CG A:GLU71 4.3 58.6 1.0 OD2 A:ASP98 4.3 36.3 1.0 N A:GLN11 4.4 30.4 1.0 HZ3 B:LYS254 4.4 41.9 1.0 HB3 A:ASP98 4.4 36.1 1.0 HE21 A:GLN11 4.5 45.4 1.0 O A:HOH727 4.5 63.6 1.0 O3G A:GTP501 4.5 28.6 1.0 CB A:ASP98 4.5 30.1 1.0 O1A A:GTP501 4.6 33.9 1.0 CG A:ASP69 4.6 40.5 1.0 O2B A:GTP501 4.6 35.2 1.0 CD A:GLU71 4.6 60.3 1.0 PA A:GTP501 4.7 30.0 1.0 CG A:ASP98 4.8 36.8 1.0 HA2 A:GLY10 4.8 43.2 1.0 HG1 A:THR145 4.8 45.0 1.0 CA A:GLN11 4.8 33.8 1.0 NE2 A:GLN11 4.8 37.8 1.0 HE3 B:LYS254 4.9 41.6 1.0 HB A:THR145 4.9 52.4 1.0 HG21 A:VAL74 5.0 52.0 1.0 CE B:LYS254 5.0 34.7 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:25.1 occ:1.00 O B:HOH729 2.2 28.6 1.0 OE1 B:GLN11 2.3 34.7 1.0 O1A B:GDP501 2.3 31.2 1.0 O C:HOH755 2.5 49.5 1.0 O B:HOH667 2.6 35.8 1.0 O B:HOH624 2.6 39.9 1.0 CD B:GLN11 3.5 44.9 1.0 HB3 B:GLN11 3.5 30.0 1.0 PA B:GDP501 3.6 27.7 1.0 H8 B:GDP501 3.7 33.3 1.0 O B:HOH666 3.7 54.3 1.0 O3A B:GDP501 3.7 33.6 1.0 OD1 B:ASP179 3.8 36.6 1.0 HB2 B:GLN11 4.1 30.0 1.0 CB B:GLN11 4.1 25.0 1.0 CG B:GLN11 4.2 29.9 1.0 HG2 B:GLN11 4.3 35.9 1.0 HD22 B:ASN101 4.3 36.8 1.0 OD1 B:ASN101 4.4 40.6 1.0 O C:HOH665 4.4 52.2 1.0 C5' B:GDP501 4.4 29.6 1.0 O5' B:GDP501 4.4 32.3 1.0 OE1 C:GLU254 4.5 43.0 1.0 NE2 B:GLN11 4.5 42.3 1.0 HE22 B:GLN11 4.6 50.8 1.0 O2A B:GDP501 4.7 30.7 1.0 O2B B:GDP501 4.7 19.8 1.0 C8 B:GDP501 4.7 27.8 1.0 CG B:ASP179 4.8 40.3 1.0 PB B:GDP501 4.8 27.1 1.0 ND2 B:ASN101 5.0 30.7 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:60.3 occ:1.00 O B:HOH689 2.6 73.3 1.0 O B:HOH746 2.8 82.5 1.0 O B:HOH680 2.8 55.8 1.0 O B:HOH747 2.8 78.8 1.0 HB3 B:ASP116 3.7 47.3 1.0 OD1 B:ASP120 4.2 52.6 1.0 OD1 B:ASP116 4.5 78.6 1.0 CB B:ASP116 4.6 39.4 1.0 OD2 B:ASP120 4.6 44.5 1.0 CG B:ASP120 4.8 44.8 1.0 CG B:ASP116 4.9 62.2 1.0 HB2 B:ASP116 4.9 47.3 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:33.5 occ:1.00 O C:HOH880 2.1 29.9 1.0 O1G C:GTP501 2.2 24.2 1.0 O C:HOH753 2.2 30.8 1.0 O1B C:GTP501 2.3 24.3 1.0 O C:HOH735 2.3 31.3 1.0 O C:HOH770 2.3 28.3 1.0 HZ1 D:LYS254 3.1 41.1 1.0 PG C:GTP501 3.2 31.4 1.0 PB C:GTP501 3.3 26.3 1.0 O2G C:GTP501 3.5 28.1 1.0 HB2 C:GLN11 3.6 25.1 1.0 O3B C:GTP501 3.6 36.3 1.0 HG2 C:GLU71 3.6 47.9 1.0 H C:GLN11 3.7 34.0 1.0 HB2 C:ASP98 3.7 37.4 1.0 O3A C:GTP501 3.9 28.2 1.0 HZ2 D:LYS254 3.9 41.1 1.0 NZ D:LYS254 3.9 34.2 1.0 OD2 C:ASP69 4.0 31.0 1.0 HG3 C:GLU71 4.0 47.9 1.0 OE1 C:GLU71 4.1 50.3 1.0 HB3 C:GLN11 4.1 25.1 1.0 HB3 C:ASP98 4.1 37.4 1.0 HZ3 D:LYS254 4.2 41.1 1.0 CG C:GLU71 4.2 39.9 1.0 OD1 C:ASP69 4.2 24.4 1.0 CB C:GLN11 4.3 20.9 1.0 CB C:ASP98 4.3 31.2 1.0 OD2 C:ASP98 4.4 40.0 1.0 N C:GLN11 4.4 28.3 1.0 O3G C:GTP501 4.5 25.4 1.0 CG C:ASP69 4.6 38.3 1.0 O2B C:GTP501 4.6 25.9 1.0 O1A C:GTP501 4.6 26.9 1.0 HG1 C:THR145 4.6 34.1 1.0 O C:HOH650 4.6 44.0 1.0 CD C:GLU71 4.7 41.7 1.0 HB C:THR145 4.7 31.1 1.0 CG C:ASP98 4.8 40.2 1.0 HA2 C:GLY10 4.8 29.6 1.0 PA C:GTP501 4.9 27.1 1.0 CA C:GLN11 4.9 27.5 1.0 OE1 C:GLN11 5.0 42.6 1.0 HE3 D:LYS254 5.0 43.0 1.0 OG1 C:THR145 5.0 28.4 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:65.0 occ:1.00 O1A D:GDP600 2.7 60.2 1.0 O D:HOH753 2.8 62.3 1.0 OE1 D:GLN11 2.9 59.2 1.0 OD1 D:ASP179 2.9 0.7 1.0 O3A D:GDP600 3.6 56.8 1.0 PA D:GDP600 3.6 58.4 1.0 OD1 D:ASN101 3.8 85.9 1.0 CD D:GLN11 4.0 69.5 1.0 HB3 D:GLN11 4.0 70.0 1.0 H8 D:GDP600 4.0 59.6 1.0 HD22 D:ASN101 4.1 0.3 1.0 CG D:ASP179 4.1 0.7 1.0 C5' D:GDP600 4.1 62.6 1.0 O5' D:GDP600 4.2 59.0 1.0 HB3 D:ASP179 4.5 0.3 1.0 HB2 D:GLN11 4.6 70.0 1.0 CB D:GLN11 4.6 58.3 1.0 CG D:ASN101 4.7 85.1 1.0 ND2 D:ASN101 4.7 96.9 1.0 HG2 D:GLN11 4.7 75.7 1.0 CG D:GLN11 4.7 63.0 1.0 O2B D:GDP600 4.8 43.1 1.0 CB D:ASP179 4.8 0.8 1.0 PB D:GDP600 4.8 55.0 1.0 O2A D:GDP600 4.9 56.2 1.0 HB2 D:ASP179 4.9 0.3 1.0 NE2 D:GLN11 5.0 65.2 1.0 HE22 D:GLN11 5.0 78.3 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl 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 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg701 b:93.2 occ:1.00 O1G F:ACP703 2.4 0.7 1.0 H5'1 F:ACP703 2.6 0.7 1.0 OD2 F:ASP318 3.0 74.0 1.0 O3A F:ACP703 3.0 86.4 1.0 OE2 F:GLU331 3.3 81.8 1.0 HH12 F:ARG222 3.4 0.8 1.0 HG2 F:GLU331 3.5 78.0 1.0 C5' F:ACP703 3.5 0.6 1.0 HB3 F:ASP318 3.5 69.5 1.0 O1A F:ACP703 3.5 69.2 1.0 CG F:ASP318 3.6 61.7 1.0 HG21 F:ILE330 3.6 0.8 1.0 H5'2 F:ACP703 3.6 0.7 1.0 HH11 F:ARG222 3.6 0.8 1.0 PA F:ACP703 3.7 0.5 1.0 H3' F:ACP703 3.7 0.5 1.0 HB2 F:ASP318 3.8 69.5 1.0 PG F:ACP703 3.8 1.0 1.0 CB F:ASP318 3.8 58.0 1.0 NH1 F:ARG222 3.8 86.5 1.0 O5' F:ACP703 3.9 0.2 1.0 HD22 F:ASN242 4.0 0.5 1.0 HO3' F:ACP703 4.0 0.7 1.0 CD F:GLU331 4.1 79.5 1.0 HG22 F:ILE330 4.2 0.8 1.0 CG F:GLU331 4.2 65.0 1.0 PB F:ACP703 4.3 0.4 1.0 OD2 F:ASP200 4.3 0.1 1.0 H3B1 F:ACP703 4.3 0.8 1.0 C3B F:ACP703 4.3 0.8 1.0 CG2 F:ILE330 4.3 87.3 1.0 C3' F:ACP703 4.4 97.9 1.0 HD21 F:ASN242 4.5 0.5 1.0 OD1 F:ASP318 4.5 61.8 1.0 ND2 F:ASN242 4.5 0.6 1.0 C4' F:ACP703 4.6 94.4 1.0 O2G F:ACP703 4.6 69.9 1.0 O3' F:ACP703 4.7 0.2 1.0 HG3 F:GLU331 4.7 78.0 1.0 HB F:ILE330 4.7 96.8 1.0 O3G F:ACP703 4.9 0.4 1.0 HOG3 F:ACP703 4.9 0.5 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Tubulin-Stathmin-Ttl Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Tubulin-Stathmin-Ttl Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg702 b:95.0 occ:1.00 HD22 F:ASN333 2.5 0.3 1.0 O2G F:ACP703 2.7 69.9 1.0 O2B F:ACP703 2.8 0.5 1.0 OE1 F:GLU331 2.8 83.8 1.0 HZ2 F:LYS74 2.9 87.6 1.0 HOG2 F:ACP703 2.9 83.8 1.0 HD21 F:ASN333 3.0 0.3 1.0 HOB2 F:ACP703 3.0 0.6 1.0 ND2 F:ASN333 3.1 99.5 1.0 OE2 F:GLU331 3.2 81.8 1.0 CD F:GLU331 3.4 79.5 1.0 OE2 A:GLU450 3.4 0.6 1.0 HZ1 F:LYS74 3.5 87.6 1.0 NZ F:LYS74 3.6 73.0 1.0 HZ3 F:LYS74 3.8 87.6 1.0 PB F:ACP703 4.1 0.4 1.0 PG F:ACP703 4.1 1.0 1.0 H3B2 F:ACP703 4.3 0.8 1.0 CG F:ASN333 4.3 92.2 1.0 C3B F:ACP703 4.4 0.8 1.0 HB3 A:GLU450 4.4 0.4 1.0 CD A:GLU450 4.5 0.5 1.0 O3A F:ACP703 4.6 86.4 1.0 CG F:GLU331 4.8 65.0 1.0 CE F:LYS74 4.9 80.4 1.0 O1G F:ACP703 4.9 0.7 1.0 HE3 F:LYS74 4.9 96.4 1.0 HB2 A:GLU450 4.9 0.4 1.0 OD1 F:ASN333 4.9 0.2 1.0 HA F:SER152 5.0 0.9 1.0 HA F:ASN333 5.0 64.1 1.0 HG3 F:GLU331 5.0 78.0 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