Calcium 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:

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8cld:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca503 b:79.0 occ:1.00 OG1 A:THR41 2.4 87.8 1.0 OD2 A:ASP39 2.4 73.1 1.0 OD1 A:ASP39 2.5 80.3 1.0 OE2 A:GLU55 2.6 82.3 1.0 O A:GLY44 2.6 90.2 1.0 CG A:ASP39 2.8 77.1 1.0 O A:THR41 3.2 87.3 1.0 CD A:GLU55 3.3 82.3 1.0 OE1 A:GLU55 3.3 86.1 1.0 CB A:THR41 3.5 87.9 1.0 OD1 A:ASP47 3.5 69.5 1.0 C A:GLY44 3.6 89.7 1.0 CA A:GLY45 3.9 101.7 1.0 CZ A:PHE49 3.9 69.9 1.0 C A:THR41 4.0 91.3 1.0 OD1 A:ASN50 4.1 75.1 1.0 N A:GLY45 4.1 99.4 1.0 CA A:THR41 4.2 92.0 1.0 ND2 A:ASN50 4.3 66.6 1.0 CB A:ASP39 4.3 78.4 1.0 N A:THR41 4.4 90.8 1.0 CG A:ASP47 4.5 64.5 1.0 CE1 A:PHE49 4.5 69.2 1.0 CG A:ASN50 4.6 71.1 1.0 CG2 A:THR41 4.6 82.5 1.0 C A:GLY45 4.7 101.9 1.0 CE1 A:HIS61 4.8 73.2 1.0 CA A:GLY44 4.8 96.4 1.0 CG A:GLU55 4.8 81.2 1.0 CE2 A:PHE49 4.8 69.3 1.0 N A:GLY44 4.9 96.5 1.0

Calcium binding site 2 out of 2 in the Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ansamitocin P3 Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:64.4 occ:1.00 OD1 C:ASP39 2.2 61.0 1.0 OE2 C:GLU55 2.3 60.9 1.0 OD2 C:ASP39 2.3 61.2 1.0 OG1 C:THR41 2.3 70.7 1.0 CG C:ASP39 2.6 60.8 1.0 O C:THR41 2.6 66.0 1.0 OE1 C:GLU55 2.7 60.6 1.0 CD C:GLU55 2.8 58.6 1.0 O C:GLY44 3.0 66.1 1.0 CB C:THR41 3.5 70.5 1.0 C C:THR41 3.6 71.1 1.0 CA C:THR41 3.9 75.6 1.0 C C:GLY44 3.9 64.2 1.0 N C:THR41 4.0 74.0 1.0 CB C:ASP39 4.1 63.9 1.0 CZ C:PHE49 4.3 43.7 1.0 CA C:GLY45 4.3 60.7 1.0 OD2 C:ASP47 4.3 76.1 1.0 CG C:GLU55 4.3 53.5 1.0 OD1 C:ASN50 4.4 51.6 1.0 N C:GLY45 4.5 57.1 1.0 NE2 C:HIS61 4.5 66.2 1.0 CE1 C:PHE49 4.5 42.0 1.0 ND2 C:ASN50 4.7 49.1 1.0 CG2 C:THR41 4.7 69.1 1.0 N C:ILE42 4.8 86.5 1.0 CA C:ASP39 4.9 63.3 1.0 C C:ASP39 4.9 67.0 1.0 N C:GLY44 5.0 63.8 1.0 CG C:ASN50 5.0 47.4 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