Calcium in PDB 5s58: Tubulin-Z2856434826-Complex

The structure of Tubulin-Z2856434826-Complex, PDB code: 5s58 was solved by T.Muehlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.14 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.28, 157.51, 179.79, 90, 90, 90
R / Rfree (%)	20.9 / 24.6

The structure of Tubulin-Z2856434826-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z2856434826-Complex (pdb code 5s58). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Tubulin-Z2856434826-Complex, PDB code: 5s58:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:96.7 occ:1.00 OE2 A:GLU55 2.3 96.0 1.0 O A:GLY44 2.3 109.9 1.0 OD1 A:ASP39 2.4 100.7 1.0 OD2 A:ASP39 2.4 93.8 1.0 OG1 A:THR41 2.4 104.6 1.0 CG A:ASP39 2.7 95.1 1.0 O A:THR41 2.8 104.2 1.0 CD A:GLU55 3.0 96.0 1.0 OE1 A:GLU55 3.0 100.5 1.0 C A:GLY44 3.4 110.5 1.0 CB A:THR41 3.7 105.4 1.0 CA A:GLY45 3.8 108.1 1.0 C A:THR41 3.8 107.1 1.0 N A:GLY45 4.1 109.5 1.0 OD2 A:ASP47 4.1 88.1 1.0 CZ A:PHE49 4.1 84.7 1.0 OD1 A:ASN50 4.2 91.2 1.0 CA A:THR41 4.2 106.8 1.0 CB A:ASP39 4.2 94.0 1.0 N A:THR41 4.4 106.5 1.0 CG A:GLU55 4.5 88.2 1.0 ND2 A:ASN50 4.6 82.3 1.0 CA A:GLY44 4.6 111.0 1.0 C A:GLY45 4.6 104.8 1.0 N A:GLY44 4.7 110.1 1.0 CE1 A:PHE49 4.7 78.4 1.0 CG A:ASN50 4.8 83.7 1.0 CG2 A:THR41 4.8 99.0 1.0 NE2 A:HIS61 4.8 85.3 1.0 O A:GLY45 4.9 102.7 1.0 CE2 A:PHE49 5.0 81.1 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:92.8 occ:1.00 O A:HOH647 2.5 81.6 1.0 O A:HOH652 2.9 70.5 1.0 O A:HOH637 3.1 59.1 1.0 NZ A:LYS166 3.9 65.8 1.0 O A:HOH655 3.9 78.0 1.0 OG A:SER158 3.9 69.3 1.0 OD2 E:ASP44 4.0 96.2 1.0 CB A:SER158 4.3 63.5 1.0 O A:GLY162 4.4 90.5 1.0 O A:GLU196 4.5 72.5 1.0 O A:HIS197 4.6 62.5 1.0 CA A:HIS197 4.8 65.4 1.0 OD1 A:ASP199 4.9 71.6 1.0 O A:LYS164 5.0 81.7 1.0 CA A:SER158 5.0 66.6 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:106.1 occ:1.00 OE1 B:GLU113 2.3 76.7 1.0 CD B:GLU113 3.1 77.4 1.0 OE2 B:GLU113 3.2 73.7 1.0 OE1 B:GLU110 4.5 60.4 1.0 CG B:GLU113 4.5 59.3 1.0 CB B:GLU113 4.9 59.0 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z2856434826-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z2856434826-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:73.9 occ:1.00 O C:GLY44 2.4 73.6 1.0 OG1 C:THR41 2.5 77.8 1.0 OE2 C:GLU55 2.5 63.9 1.0 OE1 C:GLU55 2.5 71.3 1.0 OD2 C:ASP39 2.5 67.3 1.0 O C:THR41 2.5 80.0 1.0 OD1 C:ASP39 2.6 73.1 1.0 O C:HOH604 2.7 66.0 1.0 CD C:GLU55 2.8 68.8 1.0 CG C:ASP39 2.9 72.1 1.0 CB C:THR41 3.4 78.4 1.0 C C:THR41 3.5 83.5 1.0 C C:GLY44 3.6 76.1 1.0 CA C:THR41 3.9 79.3 1.0 N C:THR41 4.2 78.2 1.0 CA C:GLY45 4.3 77.8 1.0 OD2 C:ASP47 4.3 78.4 1.0 CG C:GLU55 4.3 65.7 1.0 N C:GLY45 4.4 81.1 1.0 CB C:ASP39 4.4 73.5 1.0 N C:GLY44 4.5 81.7 1.0 OD1 C:ASN50 4.5 67.0 1.0 CA C:GLY44 4.6 81.0 1.0 CZ C:PHE49 4.6 62.9 1.0 N C:ILE42 4.6 83.3 1.0 NE2 C:HIS61 4.6 66.6 1.0 ND2 C:ASN50 4.7 63.2 1.0 CG2 C:THR41 4.7 74.5 1.0 CE1 C:PHE49 5.0 63.6 1.0

T.Muhlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz. Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273