Magnesium in PDB 5xag: Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 Complex, PDB code: 5xag 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)	47.92 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.270, 156.117, 182.107, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 25.5

The structure of Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 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 Z2 Complex (pdb code 5xag). 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 Z2 Complex, PDB code: 5xag:
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 Z2 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 Z2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:80.4 occ:1.00 O A:HOH601 1.9 60.1 1.0 O A:HOH604 2.3 52.1 1.0 OE2 A:GLU71 2.7 84.3 1.0 O2B A:GTP501 2.7 62.4 1.0 OD2 A:ASP69 3.2 62.7 1.0 O3G A:GTP501 3.4 53.7 1.0 CB A:GLN11 3.6 60.4 1.0 CD A:GLU71 3.6 93.1 1.0 OE1 A:GLN11 3.7 55.7 1.0 OD1 A:ASP69 3.7 63.4 1.0 CG A:GLU71 3.8 89.5 1.0 CG A:ASP69 3.8 63.4 1.0 N A:GLN11 4.1 57.7 1.0 PB A:GTP501 4.2 59.7 1.0 CA A:GLN11 4.3 54.6 1.0 CG2 A:VAL74 4.3 56.6 1.0 CG A:GLN11 4.5 57.1 1.0 CD A:GLN11 4.5 55.7 1.0 PG A:GTP501 4.6 59.4 1.0 O3B A:GTP501 4.7 62.4 1.0 OE1 A:GLU71 4.8 0.9 1.0 O2G A:GTP501 4.8 52.1 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 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 Z2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:52.0 occ:1.00 O2A B:GDP501 2.3 50.1 1.0 OE1 B:GLN11 2.5 66.8 1.0 OD2 B:ASP179 2.7 80.4 1.0 ND2 B:ASN101 3.5 51.6 1.0 PA B:GDP501 3.6 66.3 1.0 CD B:GLN11 3.7 58.9 1.0 O3A B:GDP501 3.8 45.4 1.0 CG B:ASP179 3.9 76.6 1.0 C5' B:GDP501 4.1 41.5 1.0 OE1 C:GLU254 4.1 59.1 1.0 O5' B:GDP501 4.3 36.6 1.0 CG B:ASN101 4.5 53.2 1.0 NE2 B:GLN11 4.5 56.2 1.0 OD1 B:ASN101 4.5 62.8 1.0 CB B:GLN11 4.6 55.4 1.0 CB B:ASP179 4.6 65.5 1.0 O1A B:GDP501 4.7 45.4 1.0 CG B:GLN11 4.8 58.6 1.0 CD C:GLU254 4.8 60.3 1.0 OE2 C:GLU254 4.8 61.8 1.0 OD1 B:ASP179 4.8 79.8 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 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 Z2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:52.8 occ:1.00 O C:HOH607 2.0 54.8 1.0 O C:HOH602 2.2 40.8 1.0 O2B C:GTP502 2.4 53.6 1.0 O3G C:GTP502 2.6 52.1 1.0 OE2 C:GLU71 2.9 59.7 1.0 CG C:GLU71 3.5 46.5 1.0 CD C:GLU71 3.6 58.8 1.0 OD2 C:ASP69 3.7 52.3 1.0 PB C:GTP502 3.8 57.5 1.0 PG C:GTP502 3.8 54.0 1.0 OD2 C:ASP98 3.8 61.8 1.0 OD1 C:ASP69 4.0 54.3 1.0 O2G C:GTP502 4.1 54.1 1.0 CB C:GLN11 4.2 45.2 1.0 O3B C:GTP502 4.2 58.4 1.0 OE1 C:GLN11 4.3 52.0 1.0 CG C:ASP69 4.3 51.8 1.0 CB C:ASP98 4.4 49.2 1.0 CG C:ASP98 4.6 58.6 1.0 N C:GLN11 4.6 43.4 1.0 CG2 C:VAL74 4.6 58.5 1.0 O3A C:GTP502 4.7 56.1 1.0 O1B C:GTP502 4.8 45.5 1.0 OE1 C:GLU71 4.8 62.8 1.0 OD1 D:ASN249 4.8 0.1 1.0 CA C:GLN11 4.9 45.2 1.0 CB C:GLU71 4.9 48.8 1.0 O2A C:GTP502 5.0 51.4 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 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 Z2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:95.3 occ:1.00 OE1 D:GLN11 2.4 0.9 1.0 O3A D:GDP501 3.1 0.6 1.0 CD D:GLN11 3.4 0.3 1.0 OD2 D:ASP179 3.5 0.5 1.0 OD1 D:ASN101 3.6 0.8 1.0 O2A D:GDP501 3.6 89.2 1.0 ND2 D:ASN101 3.7 1.0 1.0 PA D:GDP501 3.8 95.4 1.0 C5' D:GDP501 3.9 79.0 1.0 O5' D:GDP501 4.0 83.0 1.0 NE2 D:GLN11 4.0 0.2 1.0 CG D:ASN101 4.1 0.8 1.0 O2B D:GDP501 4.3 0.1 1.0 CB D:GLN11 4.3 0.6 1.0 PB D:GDP501 4.3 99.5 1.0 CG D:GLN11 4.5 0.9 1.0 CG D:ASP179 4.8 0.8 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Tubulin-Stathmin-Ttl-Compound Z2 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 Z2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:0.0 occ:1.00 NH1 F:ARG222 2.5 1.0 1.0 ND2 F:ASN242 2.7 0.8 1.0 OD2 F:ASP318 2.8 96.7 1.0 O F:HOH509 3.0 78.0 1.0 CG F:ASP318 3.2 93.5 1.0 CZ F:ARG222 3.4 0.0 1.0 OD2 F:ASP200 3.6 0.0 1.0 OD1 F:ASP318 3.6 95.3 1.0 CG F:ASN242 3.7 0.5 1.0 O2A F:ACP402 3.8 0.7 1.0 NH2 F:ARG222 3.9 0.7 1.0 OD1 F:ASN242 3.9 0.9 1.0 CB F:ASP318 4.0 86.3 1.0 CG F:ASP200 4.2 0.6 1.0 OD1 F:ASP200 4.4 0.3 1.0 NE F:ARG222 4.4 0.5 1.0 C5' F:ACP402 4.6 0.3 1.0 O5' F:ACP402 4.6 0.7 1.0 NH2 F:ARG202 4.7 99.2 1.0 PA F:ACP402 4.7 0.5 1.0 O3A F:ACP402 4.9 0.7 1.0 CB F:ASN242 5.0 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