Magnesium in PDB 8clb: Colchicine Bound to Tubulin (T2R-Ttl) Complex

The structure of Colchicine Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clb was solved by M.Wranik, M.W.Kepa, Q.Bertrand, 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)	15.18 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.71, 160.61, 180.73, 90, 90, 90
R / Rfree (%)	16.3 / 21.4

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

Calcium

(Ca)

2 atoms

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

Magnesium binding site 1 out of 4 in the 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 Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:43.2 occ:1.00 O1B A:GTP501 2.1 47.0 1.0 O A:HOH601 2.1 30.1 1.0 O A:HOH603 2.4 44.4 1.0 O1G A:GTP501 3.0 30.9 1.0 HB2 A:GLN11 3.2 53.2 1.0 OE2 A:GLU71 3.3 59.1 1.0 HG3 A:GLU71 3.4 61.4 1.0 OD1 A:ASP69 3.4 53.8 1.0 OD2 A:ASP69 3.5 53.1 1.0 PB A:GTP501 3.5 47.5 1.0 H A:GLN11 3.6 49.1 1.0 HG2 A:GLU71 3.6 61.4 1.0 HD21 B:ASN249 3.8 118.8 1.0 PG A:GTP501 3.8 58.0 1.0 CG A:ASP69 3.9 55.1 1.0 CG A:GLU71 3.9 61.4 1.0 HZ1 B:LYS254 3.9 62.8 1.0 O2G A:GTP501 3.9 57.6 1.0 HB3 A:GLN11 4.0 53.2 1.0 CB A:GLN11 4.0 53.2 1.0 O3B A:GTP501 4.0 65.7 1.0 CD A:GLU71 4.0 62.5 1.0 HB2 A:ASP98 4.0 56.7 1.0 HB3 A:ASP98 4.1 56.7 1.0 N A:GLN11 4.2 49.1 1.0 HD22 B:ASN249 4.2 118.8 1.0 ND2 B:ASN249 4.3 118.8 1.0 O3A A:GTP501 4.4 50.9 1.0 HA2 A:GLY10 4.5 44.5 1.0 O2B A:GTP501 4.5 50.9 1.0 CB A:ASP98 4.5 56.7 1.0 CA A:GLN11 4.6 49.2 1.0 HG21 A:VAL74 4.6 50.4 1.0 HG1 A:THR145 4.7 51.4 1.0 NZ B:LYS254 4.7 62.8 1.0 HA A:GLN11 4.8 49.2 1.0 OE1 A:GLN11 4.8 58.3 1.0 HZ3 B:LYS254 4.8 62.8 1.0 HG23 A:VAL74 4.8 50.4 1.0 HB A:THR145 4.8 45.5 1.0 OD2 A:ASP98 5.0 59.5 1.0

Magnesium binding site 2 out of 4 in the 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 Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:43.2 occ:1.00 O1A B:GDP501 2.4 52.6 1.0 O B:HOH603 2.5 30.4 1.0 OE1 B:GLN11 2.7 66.0 1.0 OD2 B:ASP179 2.8 57.3 1.0 H5'' B:GDP501 3.6 42.9 1.0 PA B:GDP501 3.8 48.1 1.0 CD B:GLN11 3.9 67.2 1.0 OD1 B:ASN101 3.9 40.2 1.0 CG B:ASP179 4.0 58.7 1.0 H8 B:GDP501 4.1 42.1 1.0 O3A B:GDP501 4.3 55.7 1.0 HB3 B:ASP179 4.3 55.4 1.0 HB3 B:GLN11 4.3 60.0 1.0 C5' B:GDP501 4.3 42.9 1.0 H5' B:GDP501 4.3 42.9 1.0 HD21 B:ASN101 4.4 45.7 1.0 OE1 C:GLU254 4.4 74.6 1.0 HE22 B:GLN11 4.4 73.2 1.0 CB B:ASP179 4.6 55.4 1.0 O5' B:GDP501 4.6 39.1 1.0 NE2 B:GLN11 4.6 73.2 1.0 HB2 B:GLN11 4.7 60.0 1.0 HB2 B:ASP179 4.8 55.4 1.0 OE2 C:GLU254 4.8 71.6 1.0 CB B:GLN11 4.8 60.0 1.0 CG B:ASN101 4.9 40.1 1.0 OD1 B:ASP179 4.9 60.8 1.0 O2A B:GDP501 4.9 46.2 1.0 CG B:GLN11 5.0 62.4 1.0 ND2 B:ASN101 5.0 45.7 1.0 CD C:GLU254 5.0 70.9 1.0

Magnesium binding site 3 out of 4 in the 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 Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:37.6 occ:1.00 O C:HOH601 1.8 37.8 1.0 O1B C:GTP501 2.3 51.8 1.0 O1G C:GTP501 2.6 33.7 1.0 OE2 C:GLU71 3.1 54.6 1.0 HG3 C:GLU71 3.4 53.4 1.0 HG2 C:GLU71 3.5 53.4 1.0 HB2 C:GLN11 3.5 40.2 1.0 OD2 C:ASP69 3.5 42.5 1.0 OD1 C:ASP69 3.6 42.4 1.0 H C:GLN11 3.6 36.7 1.0 PB C:GTP501 3.6 37.4 1.0 CG C:GLU71 3.8 53.4 1.0 PG C:GTP501 3.8 45.8 1.0 CD C:GLU71 3.9 56.2 1.0 HB2 C:ASP98 3.9 46.7 1.0 CG C:ASP69 4.0 42.6 1.0 O3B C:GTP501 4.0 50.0 1.0 HB3 C:ASP98 4.1 46.7 1.0 HB3 C:GLN11 4.2 40.2 1.0 HZ1 D:LYS254 4.2 53.9 1.0 CB C:GLN11 4.3 40.2 1.0 O2G C:GTP501 4.3 55.7 1.0 N C:GLN11 4.4 36.7 1.0 OD2 C:ASP98 4.4 50.2 1.0 CB C:ASP98 4.4 46.7 1.0 HD22 D:ASN249 4.5 98.5 1.0 O3A C:GTP501 4.5 56.3 1.0 HG21 C:VAL74 4.7 45.3 1.0 HD21 D:ASN249 4.7 98.5 1.0 HA2 C:GLY10 4.7 46.8 1.0 ND2 D:ASN249 4.7 98.5 1.0 O2B C:GTP501 4.7 38.8 1.0 OE1 C:GLN11 4.8 47.2 1.0 HG23 C:VAL74 4.8 45.3 1.0 HZ2 D:LYS254 4.8 53.9 1.0 CG C:ASP98 4.9 47.3 1.0 HB C:THR145 4.9 38.4 1.0 CA C:GLN11 4.9 37.0 1.0 NZ D:LYS254 4.9 53.9 1.0 HG1 C:THR145 4.9 42.2 1.0 H C:GLU71 4.9 46.6 1.0 HZ3 D:LYS254 5.0 53.9 1.0

Magnesium binding site 4 out of 4 in the 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 Colchicine Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:84.7 occ:1.00 O1A D:GDP501 2.7 112.8 1.0 OE1 D:GLN11 2.8 96.3 1.0 OD2 D:ASP179 3.1 132.7 1.0 HD21 D:ASN101 3.2 84.8 1.0 H5'' D:GDP501 3.6 76.0 1.0 OD1 D:ASN101 3.7 83.5 1.0 O3A D:GDP501 3.9 93.3 1.0 PA D:GDP501 3.9 84.3 1.0 ND2 D:ASN101 4.0 84.8 1.0 CD D:GLN11 4.0 95.5 1.0 CG D:ASP179 4.2 136.5 1.0 CG D:ASN101 4.3 83.2 1.0 HB3 D:ASP179 4.3 134.5 1.0 HB3 D:GLN11 4.3 94.6 1.0 C5' D:GDP501 4.3 76.0 1.0 H8 D:GDP501 4.3 54.8 1.0 H5' D:GDP501 4.4 76.0 1.0 HE22 D:GLN11 4.5 97.8 1.0 O5' D:GDP501 4.6 77.2 1.0 HB2 D:GLN11 4.7 94.6 1.0 HD22 D:ASN101 4.7 84.8 1.0 NE2 D:GLN11 4.7 97.8 1.0 CB D:ASP179 4.7 134.5 1.0 CB D:GLN11 4.9 94.6 1.0 HB2 D:ASP179 4.9 134.5 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