Magnesium in PDB 8clg: Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex

The structure of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clg was solved by M.Wranik, Q.Bertrand, M.W.Kepa, T.Weinert, M.Steinmetz, J.Standfuss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.26 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.76, 160.76, 180.96, 90, 90, 90
R / Rfree (%)	17.8 / 22.7

The structure of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex (pdb code 8clg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:44.7 occ:1.00 O A:HOH602 2.2 44.0 1.0 O A:HOH601 2.2 42.0 1.0 O1B A:GTP501 2.6 38.7 1.0 O2G A:GTP501 2.8 37.4 1.0 OD2 A:ASP69 3.3 55.3 1.0 OD1 A:ASP69 3.3 54.0 1.0 OE2 A:GLU71 3.4 67.0 1.0 CG A:GLU71 3.6 67.2 1.0 CG A:ASP69 3.7 54.8 1.0 PG A:GTP501 3.9 49.1 1.0 PB A:GTP501 3.9 37.6 1.0 CD A:GLU71 4.0 68.7 1.0 CB A:GLN11 4.1 43.2 1.0 O1G A:GTP501 4.2 44.7 1.0 N A:GLN11 4.2 41.8 1.0 O3B A:GTP501 4.3 56.0 1.0 OD2 A:ASP98 4.5 46.8 1.0 CB A:ASP98 4.5 46.6 1.0 CA A:GLN11 4.6 42.9 1.0 O3A A:GTP501 4.8 46.6 1.0 NZ B:LYS254 4.8 51.7 1.0 OE1 A:GLN11 4.8 46.8 1.0 O2B A:GTP501 5.0 42.1 1.0 CB A:GLU71 5.0 68.5 1.0 CG2 A:VAL74 5.0 55.3 1.0 CG A:ASP98 5.0 45.4 1.0

Magnesium binding site 2 out of 4 in the Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:45.2 occ:1.00 O1A B:GDP505 2.2 54.0 1.0 O B:HOH605 2.5 39.0 1.0 OE1 B:GLN11 2.6 50.2 1.0 OD2 B:ASP179 3.3 52.5 1.0 PA B:GDP505 3.5 39.7 1.0 ND2 B:ASN101 3.8 38.7 1.0 CD B:GLN11 3.8 51.6 1.0 O3A B:GDP505 3.9 33.5 1.0 C5' B:GDP505 4.2 32.0 1.0 O5' B:GDP505 4.3 34.6 1.0 CG B:ASP179 4.4 52.6 1.0 OE2 C:GLU254 4.4 65.2 1.0 CB B:GLN11 4.5 49.4 1.0 OD1 B:ASN101 4.6 41.1 1.0 CG B:ASN101 4.7 39.8 1.0 O1B B:GDP505 4.7 33.0 1.0 O2A B:GDP505 4.7 40.4 1.0 CG B:GLN11 4.7 51.6 1.0 NE2 B:GLN11 4.7 52.3 1.0 PB B:GDP505 4.9 44.1 1.0 CB B:ASP179 5.0 51.1 1.0

Magnesium binding site 3 out of 4 in the Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:32.7 occ:1.00 O C:HOH601 2.2 28.5 1.0 O C:HOH608 2.4 35.2 1.0 O C:HOH603 2.4 28.1 1.0 O1B C:GTP501 2.6 28.6 1.0 OD2 C:ASP69 2.9 41.1 1.0 OE2 C:GLU71 3.1 50.8 1.0 CG C:GLU71 3.6 47.9 1.0 OD1 C:ASP69 3.6 38.9 1.0 CG C:ASP69 3.6 39.5 1.0 O1G C:GTP501 3.7 24.8 1.0 CD C:GLU71 3.8 50.1 1.0 CB C:GLN11 3.9 40.2 1.0 N C:GLN11 4.0 36.6 1.0 PB C:GTP501 4.1 36.9 1.0 CA C:GLN11 4.4 38.9 1.0 CG2 C:VAL74 4.5 41.5 1.0 PG C:GTP501 4.6 41.4 1.0 O3B C:GTP501 4.7 39.0 1.0 O3G C:GTP501 4.7 31.1 1.0 OE1 C:GLN11 4.8 47.7 1.0 OD2 C:ASP98 4.9 49.6 1.0 O3A C:GTP501 4.9 48.2 1.0 CB C:ASP98 4.9 45.5 1.0 OE1 C:GLU71 5.0 49.7 1.0 C C:GLY10 5.0 44.5 1.0

Magnesium binding site 4 out of 4 in the Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Epothilone A and Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:76.3 occ:0.00 OE1 D:GLN11 2.0 84.4 1.0 O1A D:GDP502 2.1 101.1 1.0 CD D:GLN11 3.1 83.5 1.0 PA D:GDP502 3.5 59.9 1.0 NE2 D:GLN11 3.8 85.8 1.0 O2A D:GDP502 4.0 53.1 1.0 CG D:GLN11 4.2 78.9 1.0 O5' D:GDP502 4.3 53.6 1.0 C8 D:GDP502 4.3 49.4 1.0 C5' D:GDP502 4.4 54.0 1.0 CB D:GLN11 4.4 76.6 1.0 O3A D:GDP502 4.6 66.7 1.0 OD1 D:ASN101 4.9 80.4 1.0

M.Wranik, M.W.Kepa, E.V.Beale, D.James, Q.Bertrand, T.Weinert, A.Furrer, H.Glover, D.Gashi, M.Carrillo, Y.Kondo, R.T.Stipp, G.Khusainov, K.Nass, D.Ozerov, C.Cirelli, P.J.M.Johnson, F.Dworkowski, J.H.Beale, S.Stubbs, T.Zamofing, M.Schneider, K.Krauskopf, L.Gao, O.Thorn-Seshold, C.Bostedt, C.Bacellar, M.O.Steinmetz, C.Milne, J.Standfuss. A Multi-Reservoir Extruder For Time-Resolved Serial Protein Crystallography and Compound Screening at X-Ray Free-Electron Lasers. Nat Commun V. 14 7956 2023.
ISSN: ESSN 2041-1723
PubMed: 38042952
DOI: 10.1038/S41467-023-43523-5