Magnesium in PDB 8diq: Tubulin-RB3_SLD-Ttl in Complex with SB226

The structure of Tubulin-RB3_SLD-Ttl in Complex with SB226, PDB code: 8diq was solved by S.W.White, M.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.491, 158.414, 181.226, 90, 90, 90
R / Rfree (%)	18.2 / 21

The structure of Tubulin-RB3_SLD-Ttl in Complex with SB226 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Tubulin-RB3_SLD-Ttl in Complex with SB226 (pdb code 8diq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-RB3_SLD-Ttl in Complex with SB226, PDB code: 8diq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with SB226


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-RB3_SLD-Ttl in Complex with SB226 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:39.5 occ:1.00 O2G A:GTP501 1.9 30.4 1.0 O A:HOH621 2.0 40.1 1.0 O A:HOH661 2.1 43.5 1.0 O A:HOH663 2.2 40.2 1.0 O A:HOH604 2.2 45.5 1.0 O2B A:GTP501 2.2 32.5 1.0 PG A:GTP501 3.1 42.0 1.0 PB A:GTP501 3.2 40.1 1.0 O3B A:GTP501 3.6 48.9 1.0 O3G A:GTP501 3.6 46.2 1.0 O3A A:GTP501 3.7 52.3 1.0 OE2 A:GLU71 3.7 76.5 1.0 NZ B:LYS252 4.0 61.1 1.0 OD1 A:ASP69 4.1 47.1 1.0 CB A:GLN11 4.2 38.9 1.0 OD2 A:ASP98 4.3 53.2 1.0 OD2 A:ASP69 4.3 45.0 1.0 CB A:ASP98 4.4 47.2 1.0 O1G A:GTP501 4.4 37.2 1.0 N A:GLN11 4.5 40.4 1.0 O1B A:GTP501 4.5 44.7 1.0 CD A:GLU71 4.6 63.2 1.0 OE1 A:GLN11 4.6 54.2 1.0 CG A:ASP69 4.7 49.4 1.0 CG A:ASP98 4.7 45.9 1.0 O2A A:GTP501 4.7 37.4 1.0 PA A:GTP501 4.8 39.5 1.0 CA A:GLN11 4.9 42.6 1.0 OE1 A:GLU71 5.0 75.8 1.0 OG1 A:THR145 5.0 44.0 1.0

Magnesium binding site 2 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with SB226


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-RB3_SLD-Ttl in Complex with SB226 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:46.2 occ:1.00 O B:HOH603 2.1 52.6 1.0 OE1 B:GLN11 2.2 66.2 1.0 O2A B:GDP501 2.3 45.3 1.0 O C:HOH689 2.3 59.5 1.0 O B:HOH604 2.4 51.7 1.0 O B:HOH632 2.9 55.9 1.0 CD B:GLN11 3.4 60.9 1.0 OD2 B:ASP177 3.5 67.6 1.0 PA B:GDP501 3.5 39.7 1.0 O3A B:GDP501 3.7 40.6 1.0 C5' B:GDP501 4.2 38.1 1.0 CB B:GLN11 4.2 35.8 1.0 O5' B:GDP501 4.3 40.4 1.0 CG B:GLN11 4.3 48.0 1.0 NE2 B:GLN11 4.3 57.7 1.0 OD1 B:ASN99 4.4 50.1 1.0 CG B:ASP177 4.6 63.3 1.0 O1A B:GDP501 4.6 42.1 1.0 O2B B:GDP501 4.8 34.4 1.0 C8 B:GDP501 4.8 38.4 1.0 PB B:GDP501 4.9 39.5 1.0

Magnesium binding site 3 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with SB226


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-RB3_SLD-Ttl in Complex with SB226 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:37.3 occ:1.00 O3G C:GTP501 1.9 31.0 1.0 O C:HOH636 2.0 34.9 1.0 O C:HOH650 2.1 32.8 1.0 O2B C:GTP501 2.1 35.5 1.0 O C:HOH643 2.1 32.3 1.0 O C:HOH658 2.2 37.8 1.0 PG C:GTP501 3.1 41.0 1.0 PB C:GTP501 3.2 40.5 1.0 O3B C:GTP501 3.6 42.0 1.0 O3A C:GTP501 3.6 46.9 1.0 O2G C:GTP501 3.7 40.9 1.0 OE1 C:GLU71 3.7 62.8 1.0 OD1 C:ASP69 4.1 40.7 1.0 CB C:GLN11 4.2 26.4 1.0 NZ D:LYS252 4.2 61.1 1.0 OD2 C:ASP69 4.2 37.7 1.0 O1G C:GTP501 4.4 35.6 1.0 OD2 C:ASP98 4.4 47.0 1.0 CB C:ASP98 4.4 38.4 1.0 N C:GLN11 4.5 29.0 1.0 O1B C:GTP501 4.5 45.2 1.0 OE1 C:GLN11 4.5 42.9 1.0 CG C:ASP69 4.6 39.7 1.0 O2A C:GTP501 4.7 41.0 1.0 PA C:GTP501 4.7 37.3 1.0 CG C:ASP98 4.9 40.4 1.0 CD C:GLU71 4.9 60.1 1.0 CA C:GLN11 4.9 36.9 1.0

Magnesium binding site 4 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with SB226


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-RB3_SLD-Ttl in Complex with SB226 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:97.9 occ:1.00 OE1 D:GLN11 2.2 152.1 1.0 O2A D:GTP501 2.5 84.1 1.0 CD D:GLN11 3.3 130.6 1.0 PA D:GTP501 3.6 73.8 1.0 O3A D:GTP501 3.7 75.8 1.0 O2G D:GTP501 3.7 117.7 1.0 NE2 D:GLN11 4.0 127.6 1.0 CB D:GLN11 4.3 99.0 1.0 CG D:GLN11 4.4 114.1 1.0 ND2 D:ASN99 4.4 77.6 1.0 C5' D:GTP501 4.5 67.2 1.0 O5' D:GTP501 4.6 74.0 1.0 O1A D:GTP501 4.7 69.8 1.0 O1B D:GTP501 4.8 83.5 1.0 PB D:GTP501 4.9 80.9 1.0

Magnesium binding site 5 out of 5 in the Tubulin-RB3_SLD-Ttl in Complex with SB226


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-RB3_SLD-Ttl in Complex with SB226 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:84.9 occ:1.00 O2B F:ACP402 2.2 116.3 1.0 OE1 F:GLU331 2.3 115.4 1.0 O3G F:ACP402 2.5 124.4 1.0 CD F:GLU331 3.2 112.3 1.0 OE2 F:GLU331 3.4 123.6 1.0 NZ F:LYS74 3.5 83.2 1.0 PG F:ACP402 3.5 120.7 1.0 O1G F:ACP402 3.6 124.7 1.0 PB F:ACP402 3.6 113.7 1.0 ND2 F:ASN333 3.9 96.3 1.0 C3B F:ACP402 4.2 116.3 1.0 O1B F:ACP402 4.3 116.8 1.0 CG F:GLU331 4.5 96.0 1.0 CG F:ASN333 4.6 93.7 1.0 O3A F:ACP402 4.8 106.5 1.0 O2G F:ACP402 4.8 113.6 1.0 CE F:LYS74 4.9 81.8 1.0

S.Deng, S.Banerjee, H.Chen, S.Pochampally, Y.Wang, M.K.Yun, S.W.White, K.Parmar, B.Meibohm, K.L.Hartman, Z.Wu, D.D.Miller, W.Li. SB226, An Inhibitor of Tubulin Polymerization, Inhibits Paclitaxel-Resistant Melanoma Growth and Spontaneous Metastasis. Cancer Lett. 16046 2022.
ISSN: ESSN 1872-7980
PubMed: 36596380
DOI: 10.1016/J.CANLET.2022.216046