Magnesium in PDB 8cld: Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex

The structure of Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8cld 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)	15.10 / 3.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.06, 159.61, 180.61, 90, 90, 90
R / Rfree (%)	20 / 24.1

The structure of Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex (pdb code 8cld). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8cld:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Ansamitocin P3 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 Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:36.9 occ:1.00 O1G A:GTP501 2.7 38.1 1.0 O1B A:GTP501 2.8 47.6 1.0 O2G A:GTP501 2.9 37.7 1.0 O3A A:GTP501 3.1 45.3 1.0 PG A:GTP501 3.2 42.9 1.0 PB A:GTP501 3.4 41.3 1.0 O3B A:GTP501 3.6 52.5 1.0 NZ B:LYS252 3.8 60.6 1.0 OE1 A:GLU71 3.9 69.9 1.0 OD2 A:ASP98 4.3 44.7 1.0 CB A:GLN11 4.4 53.8 1.0 OD1 A:ASP69 4.4 49.3 1.0 CB A:ASP98 4.5 50.5 1.0 PA A:GTP501 4.5 37.8 1.0 O1A A:GTP501 4.5 41.9 1.0 O3G A:GTP501 4.6 33.6 1.0 CG A:ASP98 4.7 46.1 1.0 OD2 A:ASP69 4.7 51.2 1.0 N A:GLN11 4.7 49.0 1.0 OE1 A:GLN11 4.8 53.1 1.0 O2B A:GTP501 4.8 44.3 1.0 CE B:LYS252 4.9 55.2 1.0

Magnesium binding site 2 out of 3 in the Ansamitocin P3 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 Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:39.3 occ:1.00 O1A B:GDP501 2.5 50.1 1.0 NE2 B:GLN11 2.5 56.5 1.0 O1B B:GDP501 3.4 42.2 1.0 CD B:GLN11 3.7 59.3 1.0 OE2 C:GLU254 3.8 77.2 1.0 OD1 B:ASN99 3.9 45.7 1.0 PA B:GDP501 3.9 37.4 1.0 OD2 B:ASP177 4.2 55.7 1.0 OE1 B:GLN11 4.3 60.7 1.0 CB B:GLN11 4.4 55.5 1.0 O3A B:GDP501 4.4 38.2 1.0 PB B:GDP501 4.4 34.8 1.0 ND2 B:ASN99 4.6 38.4 1.0 CG B:GLN11 4.6 57.3 1.0 CG B:ASN99 4.7 43.2 1.0 O3B B:GDP501 4.8 43.4 1.0 O2A B:GDP501 4.8 31.9 1.0 O5' B:GDP501 4.8 38.2 1.0 C5' B:GDP501 4.9 39.3 1.0 CD C:GLU254 5.0 69.6 1.0

Magnesium binding site 3 out of 3 in the Ansamitocin P3 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 Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:29.1 occ:1.00 O1G C:GTP501 2.5 39.2 1.0 OE1 C:GLU71 2.9 48.4 1.0 O1B C:GTP501 2.9 51.5 1.0 CD C:GLU71 3.8 53.1 1.0 OD2 C:ASP69 3.8 42.8 1.0 PG C:GTP501 3.9 43.2 1.0 O3A C:GTP501 3.9 44.6 1.0 PB C:GTP501 3.9 42.3 1.0 OD1 C:ASP69 4.0 37.9 1.0 NZ D:LYS252 4.1 41.5 1.0 O3B C:GTP501 4.2 37.5 1.0 OE2 C:GLU71 4.3 58.4 1.0 CG C:ASP69 4.3 42.9 1.0 OD2 C:ASP98 4.4 47.7 1.0 CB C:ASP98 4.4 48.4 1.0 O3G C:GTP501 4.4 32.8 1.0 CB C:GLN11 4.5 43.7 1.0 CB C:GLU71 4.6 50.7 1.0 N C:GLN11 4.7 42.0 1.0 OE1 C:GLN11 4.7 46.3 1.0 CG C:GLU71 4.8 53.4 1.0 CG C:ASP98 4.9 49.7 1.0 CG2 C:VAL74 4.9 51.7 1.0 O2G C:GTP501 5.0 45.5 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