Calcium in PDB 8clf: Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex

The structure of Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clf was solved by M.Wranik, Q.Bertrand, M.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)	15.35 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.65, 160.33, 180.95, 90, 90, 90
R / Rfree (%)	16.8 / 21.7

The structure of Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Magnesium	(Mg)	4 atoms

The binding sites of Calcium atom in the Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex (pdb code 8clf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex, PDB code: 8clf:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Z-SOLQ2BR 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 Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:109.9 occ:1.00 O A:GLY44 2.2 122.2 1.0 OG1 A:THR41 2.3 141.8 1.0 OD2 A:ASP39 2.4 109.5 1.0 OE1 A:GLU55 2.5 122.6 1.0 OD1 A:ASP39 2.6 117.2 1.0 O A:THR41 2.7 134.2 1.0 CG A:ASP39 2.9 105.1 1.0 OE2 A:GLU55 3.0 117.9 1.0 HA3 A:GLY45 3.0 136.9 1.0 CD A:GLU55 3.1 122.9 1.0 C A:GLY44 3.4 126.3 1.0 CB A:THR41 3.7 127.0 1.0 C A:THR41 3.7 131.6 1.0 HZ A:PHE49 3.8 93.5 1.0 HE1 A:HIS61 3.8 88.0 1.0 OD1 A:ASP47 3.8 118.0 1.0 H A:GLY44 3.8 129.5 1.0 H A:THR41 3.9 136.8 1.0 CA A:GLY45 3.9 136.9 1.0 HE2 A:PHE49 4.0 97.2 1.0 CA A:THR41 4.1 130.2 1.0 N A:GLY45 4.1 132.8 1.0 HB A:THR41 4.1 127.0 1.0 HD21 A:ASN50 4.2 115.0 1.0 N A:THR41 4.3 136.8 1.0 HA2 A:GLY45 4.4 136.9 1.0 CB A:ASP39 4.4 101.1 1.0 N A:GLY44 4.4 129.5 1.0 CZ A:PHE49 4.5 93.5 1.0 CA A:GLY44 4.5 127.0 1.0 HG23 A:THR41 4.5 120.8 1.0 CG A:GLU55 4.5 109.6 1.0 CE2 A:PHE49 4.6 97.2 1.0 OD1 A:ASN50 4.6 107.6 1.0 CG2 A:THR41 4.6 120.8 1.0 CE1 A:HIS61 4.7 88.0 1.0 HB2 A:ASP39 4.7 101.1 1.0 HG21 A:THR41 4.7 120.8 1.0 HB3 A:ASP39 4.8 101.1 1.0 HG2 A:GLU55 4.8 109.6 1.0 N A:ILE42 4.9 119.3 1.0 ND2 A:ASN50 4.9 115.0 1.0 CG A:ASP47 4.9 102.1 1.0 HG3 A:GLU55 4.9 109.6 1.0 C A:GLY45 5.0 138.0 1.0 H A:GLY45 5.0 132.8 1.0 HA A:ILE42 5.0 126.9 1.0

Calcium binding site 2 out of 2 in the Z-SOLQ2BR 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 Z-SOLQ2BR Bound to Tubulin (T2R-Ttl) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:94.4 occ:1.00 OG1 C:THR41 2.2 107.4 1.0 OE2 C:GLU55 2.3 93.9 1.0 OD2 C:ASP39 2.3 91.9 1.0 O C:GLY44 2.4 92.0 1.0 O C:THR41 2.4 99.3 1.0 OD1 C:ASP39 2.6 89.0 1.0 OE1 C:GLU55 2.6 93.8 1.0 CD C:GLU55 2.8 85.8 1.0 CG C:ASP39 2.8 87.6 1.0 C C:THR41 3.5 98.5 1.0 CB C:THR41 3.5 97.5 1.0 H C:THR41 3.5 94.8 1.0 C C:GLY44 3.6 91.6 1.0 HA3 C:GLY45 3.7 96.6 1.0 HE2 C:HIS61 3.8 62.0 1.0 CA C:THR41 3.9 98.2 1.0 H C:GLY44 3.9 98.1 1.0 HZ C:PHE49 3.9 68.0 1.0 HD21 C:ASN50 4.0 80.8 1.0 HG23 C:THR41 4.1 103.3 1.0 HB C:THR41 4.1 97.5 1.0 N C:THR41 4.1 94.8 1.0 OD2 C:ASP47 4.1 98.0 1.0 CG2 C:THR41 4.3 103.3 1.0 CG C:GLU55 4.3 79.2 1.0 CB C:ASP39 4.3 86.2 1.0 HE1 C:PHE49 4.3 71.7 1.0 HG21 C:THR41 4.4 103.3 1.0 CA C:GLY45 4.5 96.6 1.0 N C:GLY44 4.5 98.1 1.0 N C:GLY45 4.5 91.3 1.0 CA C:GLY44 4.6 96.1 1.0 NE2 C:HIS61 4.6 62.0 1.0 OD1 C:ASN50 4.6 78.1 1.0 HG3 C:GLU55 4.6 79.2 1.0 HB3 C:ASP39 4.6 86.2 1.0 N C:ILE42 4.7 109.7 1.0 CZ C:PHE49 4.7 68.0 1.0 HG2 C:GLU55 4.7 79.2 1.0 HA C:ILE42 4.7 110.6 1.0 HB2 C:ASP39 4.7 86.2 1.0 ND2 C:ASN50 4.8 80.8 1.0 HA2 C:GLY44 4.8 96.1 1.0 HA C:THR41 4.8 98.2 1.0 CE1 C:PHE49 4.9 71.7 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