Magnesium in PDB 5xaf: Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 Complex, PDB code: 5xaf was solved by H.Zhang, C.Luo, Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.77 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.568, 156.509, 182.078, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 25.7

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 Complex also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 Complex (pdb code 5xaf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 Complex, PDB code: 5xaf:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 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-Compound Z1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:67.2 occ:1.00 O3G A:GTP501 2.3 59.2 1.0 O2B A:GTP501 2.4 70.7 1.0 OE1 A:GLU71 2.9 0.5 1.0 PG A:GTP501 3.4 64.1 1.0 O2G A:GTP501 3.5 48.8 1.0 PB A:GTP501 3.6 63.0 1.0 O3B A:GTP501 3.9 65.4 1.0 OD1 A:ASP69 3.9 65.3 1.0 OD2 A:ASP69 3.9 65.8 1.0 CB A:GLN11 4.1 58.3 1.0 CD A:GLU71 4.1 96.5 1.0 OD2 A:ASP98 4.2 72.1 1.0 OE1 A:GLN11 4.2 63.3 1.0 CB A:ASP98 4.2 66.9 1.0 CG A:ASP69 4.3 62.8 1.0 CG A:ASP98 4.4 66.9 1.0 O3A A:GTP501 4.5 62.3 1.0 N A:GLN11 4.5 57.8 1.0 O1B A:GTP501 4.7 70.9 1.0 O1G A:GTP501 4.8 49.4 1.0 OE2 A:GLU71 4.8 91.9 1.0 CA A:GLN11 4.9 56.7 1.0 OG1 A:THR145 4.9 58.5 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 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-Compound Z1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:58.8 occ:1.00 NE2 B:GLN11 2.4 62.5 1.0 O2A B:GDP501 2.6 51.6 1.0 OD2 B:ASP179 2.7 82.5 1.0 O B:HOH648 2.9 40.5 1.0 CD B:GLN11 3.7 71.8 1.0 ND2 B:ASN101 3.8 54.0 1.0 PA B:GDP501 3.8 43.0 1.0 CG B:ASP179 3.9 78.8 1.0 C5' B:GDP501 4.2 41.7 1.0 O3A B:GDP501 4.2 48.6 1.0 OE1 C:GLU254 4.3 68.7 1.0 OE1 B:GLN11 4.4 79.2 1.0 O5' B:GDP501 4.4 36.0 1.0 CB B:GLN11 4.7 53.2 1.0 CG B:ASN101 4.7 56.3 1.0 OD1 B:ASP179 4.7 89.2 1.0 OD1 B:ASN101 4.7 70.8 1.0 OE2 C:GLU254 4.7 66.8 1.0 CD C:GLU254 4.8 66.8 1.0 CB B:ASP179 4.8 66.2 1.0 O2B B:GDP501 4.8 52.6 1.0 CG B:GLN11 4.8 67.0 1.0 O B:HOH694 4.9 40.5 1.0 O1A B:GDP501 5.0 56.3 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 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-Compound Z1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:48.4 occ:1.00 O C:HOH678 1.9 40.5 1.0 O3G C:GTP502 2.1 45.6 1.0 O C:HOH663 2.2 47.1 1.0 O C:HOH621 2.2 50.6 1.0 O2B C:GTP502 2.5 47.6 1.0 PG C:GTP502 3.2 53.8 1.0 O2G C:GTP502 3.6 51.1 1.0 PB C:GTP502 3.6 50.4 1.0 OD2 C:ASP98 3.6 61.7 1.0 O3B C:GTP502 3.8 54.7 1.0 OE1 C:GLU71 3.9 73.2 1.0 OE2 C:GLU71 3.9 73.9 1.0 O C:HOH607 4.0 40.5 1.0 CD C:GLU71 4.1 64.1 1.0 O3A C:GTP502 4.1 56.6 1.0 CB C:ASP98 4.2 40.9 1.0 CG C:ASP98 4.3 52.1 1.0 OD1 C:ASP69 4.3 54.9 1.0 OD2 C:ASP69 4.4 48.4 1.0 OE1 C:GLN11 4.4 56.7 1.0 CB C:GLN11 4.5 41.6 1.0 O1G C:GTP502 4.5 45.9 1.0 CG C:ASP69 4.8 47.2 1.0 N C:GLN11 4.9 45.3 1.0 O1B C:GTP502 4.9 47.1 1.0 O2A C:GTP502 5.0 52.0 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 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-Compound Z1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:97.5 occ:1.00 O D:HOH652 2.5 40.5 1.0 O D:HOH613 2.8 30.0 1.0 O3A D:GDP501 2.8 0.3 1.0 OE1 D:GLN11 3.3 93.2 1.0 OD1 D:ASN101 3.3 0.2 1.0 O2B D:GDP501 3.4 0.6 1.0 PB D:GDP501 3.7 0.6 1.0 PA D:GDP501 4.0 93.9 1.0 O2A D:GDP501 4.1 79.7 1.0 CD D:GLN11 4.1 0.5 1.0 CG D:ASN101 4.3 0.2 1.0 O5' D:GDP501 4.3 81.2 1.0 CB D:GLN11 4.5 0.2 1.0 ND2 D:ASN101 4.5 97.8 1.0 O1B D:GDP501 4.5 0.0 1.0 C5' D:GDP501 4.6 72.9 1.0 O D:HOH607 4.8 40.5 1.0 NE2 D:GLN11 4.8 0.6 1.0 O3B D:GDP501 4.9 68.6 1.0 CG D:GLN11 5.0 97.5 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z1 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-Compound Z1 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:0.2 occ:1.00 NH1 F:ARG222 1.9 0.4 1.0 CZ F:ARG222 3.0 0.1 1.0 OD2 F:ASP318 3.1 0.5 1.0 CG F:ASP318 3.2 0.8 1.0 ND2 F:ASN242 3.5 0.9 1.0 OD1 F:ASP318 3.5 0.6 1.0 OD1 F:ASP200 3.6 0.5 1.0 OD2 F:ASP200 3.7 0.6 1.0 NH2 F:ARG222 3.7 0.8 1.0 CG F:ASP200 3.8 0.5 1.0 NE F:ARG222 3.8 0.1 1.0 O F:HOH515 3.9 40.5 1.0 CB F:ASP318 4.0 82.8 1.0 CG F:ASN242 4.1 0.4 1.0 OD1 F:ASN242 4.1 0.1 1.0 CB F:ASP200 4.7 0.9 1.0 NH2 F:ARG202 4.8 0.2 1.0

P.Zhou, Y.Liang, H.Zhang, H.Jiang, K.Feng, P.Xu, J.Wang, X.Wang, K.Ding, C.Luo, M.Liu, Y.Wang. Design, Synthesis, Biological Evaluation and Cocrystal Structures with Tubulin of Chiral Beta-Lactam Bridged Combretastatin A-4 Analogues As Potent Antitumor Agents Eur J Med Chem V. 144 817 2017.
ISSN: ISSN 1768-3254
PubMed: 29306206
DOI: 10.1016/J.EJMECH.2017.12.004