Magnesium in PDB 8clc: Tubulin (T2R-Ttl) Complex

The structure of Tubulin (T2R-Ttl) Complex, PDB code: 8clc 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)	15.20 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.53, 160.48, 181.24, 90, 90, 90
R / Rfree (%)	18.6 / 23.4

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

Calcium

(Ca)

2 atoms

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

Magnesium binding site 1 out of 3 in the 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 Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.0 occ:1.00 O1B A:GTP501 2.1 37.1 1.0 O A:HOH607 2.2 44.4 1.0 O A:HOH608 2.2 50.1 1.0 O2G A:GTP501 2.3 43.1 1.0 O A:HOH603 2.3 48.3 1.0 PB A:GTP501 3.3 48.8 1.0 PG A:GTP501 3.5 54.4 1.0 O3B A:GTP501 3.7 73.5 1.0 CB A:GLN11 3.7 47.9 1.0 O3A A:GTP501 3.8 61.1 1.0 NZ B:LYS254 3.9 55.7 1.0 O1A A:GTP501 4.1 48.1 1.0 O1G A:GTP501 4.2 45.7 1.0 OE1 A:GLN11 4.2 60.7 1.0 OE2 A:GLU71 4.3 79.1 1.0 N A:GLN11 4.3 46.2 1.0 PA A:GTP501 4.4 52.3 1.0 OD1 A:ASP69 4.6 57.0 1.0 CG A:GLU71 4.6 78.7 1.0 O2B A:GTP501 4.6 57.0 1.0 CA A:GLN11 4.6 49.0 1.0 OD2 A:ASP69 4.7 64.2 1.0 CD A:GLN11 4.7 51.9 1.0 O3G A:GTP501 4.7 42.6 1.0 CG A:GLN11 4.8 53.9 1.0 O2A A:GTP501 4.9 49.5 1.0 CD A:GLU71 4.9 79.1 1.0

Magnesium binding site 2 out of 3 in the 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 Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:57.5 occ:1.00 O B:HOH620 2.5 57.1 1.0 O1A B:GDP501 2.5 62.2 1.0 NE2 B:GLN11 2.5 67.2 1.0 OD2 B:ASP179 3.0 67.2 1.0 OD1 B:ASN101 3.7 56.4 1.0 CD B:GLN11 3.8 74.1 1.0 PA B:GDP501 3.9 58.6 1.0 CG B:ASP179 4.1 67.0 1.0 O3A B:GDP501 4.2 52.4 1.0 OE1 C:GLU254 4.4 87.0 1.0 C5' B:GDP501 4.4 42.2 1.0 OE1 B:GLN11 4.5 77.2 1.0 O5' B:GDP501 4.6 34.9 1.0 CG B:ASN101 4.7 55.3 1.0 CB B:GLN11 4.7 61.1 1.0 CB B:ASP179 4.7 61.9 1.0 ND2 B:ASN101 4.7 54.0 1.0 CG B:GLN11 4.8 64.8 1.0 O1B B:GDP501 4.9 51.4 1.0 OE2 C:GLU254 4.9 86.6 1.0 O2A B:GDP501 5.0 44.5 1.0

Magnesium binding site 3 out of 3 in the 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 Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:45.8 occ:1.00 O1G C:GTP501 1.9 38.0 1.0 O C:HOH612 2.1 34.9 1.0 O C:HOH615 2.3 43.9 1.0 O C:HOH617 2.4 38.7 1.0 O1B C:GTP501 2.7 37.4 1.0 PG C:GTP501 3.3 46.5 1.0 OE2 C:GLU71 3.4 70.5 1.0 OD2 C:ASP98 3.5 56.4 1.0 NZ D:LYS254 3.5 57.1 1.0 PB C:GTP501 3.8 45.6 1.0 O2G C:GTP501 3.8 43.8 1.0 O3B C:GTP501 3.8 59.1 1.0 CG C:GLU71 3.9 64.0 1.0 CD C:GLU71 4.0 65.7 1.0 CB C:ASP98 4.0 51.4 1.0 CG C:ASP98 4.2 53.0 1.0 O3A C:GTP501 4.4 58.1 1.0 OD2 C:ASP69 4.4 45.5 1.0 O3G C:GTP501 4.4 39.2 1.0 OD1 C:ASP69 4.5 43.7 1.0 OE1 C:GLN11 4.6 68.2 1.0 CE D:LYS254 4.7 50.6 1.0 CB C:GLN11 4.7 54.5 1.0 CB C:GLU71 4.8 61.3 1.0 CG C:ASP69 4.9 43.6 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