Magnesium in PDB 6gj4: Tubulin-6J Complex

The structure of Tubulin-6J Complex, PDB code: 6gj4 was solved by M.Brindisi, C.Ulivieri, G.Alfano, S.Gemma, F.D.A.Balaguer, T.Khan, A.Grillo, G.Chemi, G.Menchon, A.E.Prota, N.Olieric, D.L.Agell, I.Barasoain, J.F.Diaz, A.Nebbioso, M.R.Conte, L.Lopresti, S.Magnano, R.Amet, P.Kinsella, D.M.Zisterer, O.Ibrahim, J.O'sullivan, L.Morbidelli, R.Spaccapelo, C.Baldari, S.Butini, E.Novellino, G.Campiani, L.Altucci, M.O.Steinmetz, S.Brogi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.02 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.970, 157.810, 181.220, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.1

The structure of Tubulin-6J Complex also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Tubulin-6J Complex (pdb code 6gj4). 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-6J Complex, PDB code: 6gj4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-6J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-6J Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:69.0 occ:1.00 O2G A:GTP501 1.8 56.5 1.0 O A:HOH617 1.9 39.4 1.0 O A:HOH613 2.1 46.4 1.0 O A:HOH611 2.4 40.0 1.0 O1B A:GTP501 2.7 55.4 1.0 PG A:GTP501 3.1 53.0 1.0 OE2 A:GLU71 3.5 95.7 1.0 O1G A:GTP501 3.5 46.0 1.0 PB A:GTP501 3.7 52.7 1.0 OD2 A:ASP98 3.8 58.8 1.0 O3B A:GTP501 3.8 54.4 1.0 CB A:ASP98 3.9 48.5 1.0 O3A A:GTP501 4.1 57.5 1.0 CG A:ASP98 4.2 55.6 1.0 O3G A:GTP501 4.3 55.9 1.0 OE1 A:GLN11 4.6 55.9 1.0 OD1 A:ASP69 4.6 51.5 1.0 CD A:GLU71 4.6 89.0 1.0 CB A:GLN11 4.7 43.2 1.0 OD2 A:ASP69 4.8 60.5 1.0 O1A A:GTP501 4.9 49.6 1.0

Magnesium binding site 2 out of 5 in the Tubulin-6J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-6J Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:48.1 occ:1.00 OE1 B:GLN11 2.2 69.2 1.0 O C:HOH641 2.2 50.1 1.0 O B:HOH604 2.3 53.3 1.0 O1A B:GDP501 2.5 49.1 1.0 CD B:GLN11 3.4 63.7 1.0 OD2 B:ASP179 3.5 77.8 1.0 PA B:GDP501 3.7 44.1 1.0 O3A B:GDP501 4.0 62.5 1.0 CB B:GLN11 4.2 45.0 1.0 NE2 B:GLN11 4.3 72.1 1.0 CG B:GLN11 4.3 54.7 1.0 OD1 B:ASN101 4.4 59.5 1.0 C5' B:GDP501 4.4 51.3 1.0 O5' B:GDP501 4.5 38.1 1.0 CG B:ASP179 4.6 68.5 1.0 O1B B:GDP501 4.6 51.4 1.0 OE1 C:GLU254 4.8 81.1 1.0 O2A B:GDP501 4.9 43.7 1.0 PB B:GDP501 5.0 85.8 1.0 C8 B:GDP501 5.0 42.5 1.0

Magnesium binding site 3 out of 5 in the Tubulin-6J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-6J Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:49.3 occ:1.00 O C:HOH615 1.9 41.1 1.0 O C:HOH614 2.0 47.1 1.0 O C:HOH623 2.1 47.6 1.0 O C:HOH643 2.2 49.0 1.0 O1G C:GTP501 2.2 38.6 1.0 O1B C:GTP501 2.3 40.7 1.0 PG C:GTP501 3.4 52.7 1.0 PB C:GTP501 3.4 43.9 1.0 OE1 C:GLU71 3.6 84.5 1.0 O3B C:GTP501 3.8 53.6 1.0 O2G C:GTP501 3.9 50.5 1.0 O3A C:GTP501 4.0 55.8 1.0 OD1 C:ASP69 4.0 50.9 1.0 CB C:GLN11 4.0 36.5 1.0 OD2 C:ASP69 4.1 47.2 1.0 N C:GLN11 4.4 35.6 1.0 CB C:ASP98 4.4 39.5 1.0 OD2 C:ASP98 4.4 59.2 1.0 CG C:ASP69 4.5 51.3 1.0 OE1 C:GLN11 4.5 55.4 1.0 CD C:GLU71 4.6 83.4 1.0 O3G C:GTP501 4.7 32.6 1.0 O1A C:GTP501 4.7 41.3 1.0 O2B C:GTP501 4.7 63.5 1.0 CA C:GLN11 4.8 35.8 1.0 PA C:GTP501 4.9 39.1 1.0 CG C:ASP98 4.9 47.1 1.0 CB C:GLU71 4.9 52.7 1.0

Magnesium binding site 4 out of 5 in the Tubulin-6J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-6J Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:65.5 occ:1.00 OE1 D:GLN11 1.9 0.6 1.0 O D:HOH616 2.1 69.7 1.0 O1A D:GDP501 2.2 83.3 1.0 O D:HOH605 2.3 64.2 1.0 O D:HOH611 2.4 50.9 1.0 CD D:GLN11 3.1 0.8 1.0 PA D:GDP501 3.6 70.6 1.0 CB D:GLN11 3.9 84.8 1.0 CG D:GLN11 4.0 94.1 1.0 NE2 D:GLN11 4.0 80.6 1.0 O2A D:GDP501 4.2 52.5 1.0 O1B D:GDP501 4.5 67.2 1.0 O3A D:GDP501 4.5 71.2 1.0 C5' D:GDP501 4.6 60.8 1.0 O5' D:GDP501 4.6 66.7 1.0 OD1 D:ASN101 4.9 80.3 1.0 C8 D:GDP501 4.9 66.6 1.0 PB D:GDP501 5.0 78.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-6J Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-6J Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:87.3 occ:1.00 OD2 F:ASP318 2.0 0.9 1.0 O2G F:ACP401 2.4 0.2 1.0 O1A F:ACP401 2.5 0.4 1.0 O3G F:ACP401 2.8 0.4 1.0 OE2 F:GLU331 2.9 0.5 1.0 PG F:ACP401 3.0 0.9 1.0 CG F:ASP318 3.0 93.6 1.0 H3B1 F:ACP401 3.2 0.4 1.0 O2B F:ACP401 3.4 0.1 1.0 C3B F:ACP401 3.5 0.4 1.0 OD1 F:ASN333 3.6 0.2 1.0 CB F:ASP318 3.6 82.1 1.0 H5'1 F:ACP401 3.7 0.6 1.0 PB F:ACP401 3.9 0.2 1.0 OD1 F:ASP318 3.9 97.2 1.0 CD F:GLU331 4.0 0.6 1.0 PA F:ACP401 4.0 0.2 1.0 NH2 F:ARG222 4.1 93.5 1.0 CB F:GLU331 4.3 0.3 1.0 O1G F:ACP401 4.4 0.1 1.0 O3A F:ACP401 4.4 1.0 1.0 CG F:ASN333 4.4 0.3 1.0 ND2 F:ASN333 4.4 0.7 1.0 H3B2 F:ACP401 4.5 0.4 1.0 C5' F:ACP401 4.6 0.4 1.0 NH2 F:ARG202 4.7 92.7 1.0 CG F:GLU331 4.7 0.1 1.0 O5' F:ACP401 4.7 0.3 1.0 OE1 F:GLU331 4.8 0.6 1.0 CG2 F:ILE330 4.8 79.2 1.0 NH1 F:ARG222 4.9 0.1 1.0 CZ F:ARG222 5.0 0.2 1.0

M.Brindisi, C.Ulivieri, G.Alfano, S.Gemma, F.De Asis Balaguer, T.Khan, A.Grillo, G.Chemi, G.Menchon, A.E.Prota, N.Olieric, D.Lucena-Agell, I.Barasoain, J.F.Diaz, A.Nebbioso, M.Conte, L.Lopresti, S.Magnano, R.Amet, P.Kinsella, D.M.Zisterer, O.Ibrahim, J.O'sullivan, L.Morbidelli, R.Spaccapelo, C.Baldari, S.Butini, E.Novellino, G.Campiani, L.Altucci, M.O.Steinmetz, S.Brogi. Structure-Activity Relationships, Biological Evaluation and Structural Studies of Novel Pyrrolonaphthoxazepines As Antitumor Agents. Eur J Med Chem V. 162 290 2018.
ISSN: ISSN 1768-3254
PubMed: 30448418
DOI: 10.1016/J.EJMECH.2018.11.004