Calcium in PDB 5s51: Tubulin-Z1251207602-Complex

The structure of Tubulin-Z1251207602-Complex, PDB code: 5s51 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)	78.73 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.42, 157.45, 179.36, 90, 90, 90
R / Rfree (%)	20.3 / 24.5

The structure of Tubulin-Z1251207602-Complex also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Tubulin-Z1251207602-Complex (pdb code 5s51). 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-Z1251207602-Complex, PDB code: 5s51:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:112.3 occ:1.00 OD1 A:ASP39 2.2 108.7 1.0 O A:GLY44 2.3 112.0 1.0 OG1 A:THR41 2.4 109.8 1.0 OE2 A:GLU55 2.4 102.7 1.0 O A:THR41 2.8 115.3 1.0 CG A:ASP39 2.9 106.0 1.0 OD2 A:ASP39 2.9 105.7 1.0 CD A:GLU55 3.2 104.3 1.0 OE1 A:GLU55 3.2 108.3 1.0 CB A:THR41 3.4 108.4 1.0 C A:GLY44 3.5 114.5 1.0 C A:THR41 3.7 115.8 1.0 CA A:GLY45 3.8 118.2 1.0 OD2 A:ASP47 3.9 108.7 1.0 CA A:THR41 4.0 111.2 1.0 N A:GLY45 4.1 115.3 1.0 CZ A:PHE49 4.1 94.2 1.0 N A:THR41 4.2 113.5 1.0 OD1 A:ASN50 4.3 105.1 1.0 CB A:ASP39 4.3 104.9 1.0 CG A:GLU55 4.6 102.0 1.0 C A:GLY45 4.6 113.5 1.0 N A:GLY44 4.7 112.5 1.0 CG2 A:THR41 4.7 110.0 1.0 CA A:GLY44 4.7 111.2 1.0 ND2 A:ASN50 4.8 91.2 1.0 CE2 A:PHE49 4.9 92.8 1.0 CG A:ASP47 4.9 106.5 1.0 CA A:ASP39 4.9 109.3 1.0 CE1 A:PHE49 4.9 96.7 1.0 O A:GLY45 5.0 107.4 1.0 CG A:ASN50 5.0 95.3 1.0 N A:ILE42 5.0 115.7 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:106.3 occ:1.00 O E:HOH204 2.4 94.4 1.0 O A:HOH636 3.0 83.2 1.0 OD2 E:ASP44 3.6 115.8 1.0 OG A:SER158 3.7 82.2 1.0 NZ A:LYS166 4.0 81.0 1.0 CB A:SER158 4.3 80.8 1.0 O A:GLY162 4.4 106.5 1.0 O A:GLU196 4.6 86.2 1.0 O A:HOH641 4.8 72.8 1.0 CG E:ASP44 4.8 117.5 1.0 CA A:SER158 4.9 81.1 1.0 OD1 A:ASP199 4.9 89.4 1.0 O A:HIS197 4.9 74.2 1.0 CA A:HIS197 4.9 77.4 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:112.8 occ:1.00 OE1 B:GLU113 2.6 90.7 1.0 CD B:GLU113 3.4 93.7 1.0 OE2 B:GLU113 3.5 93.8 1.0 OE1 B:GLU110 4.5 66.6 1.0 CG B:GLU113 4.8 77.5 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z1251207602-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z1251207602-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:82.2 occ:1.00 OE2 C:GLU55 2.3 81.7 1.0 O C:GLY44 2.4 89.8 1.0 O C:THR41 2.4 93.5 1.0 OD2 C:ASP39 2.5 78.1 1.0 OG1 C:THR41 2.5 88.7 1.0 OD1 C:ASP39 2.5 77.8 1.0 O C:HOH608 2.6 73.4 1.0 OE1 C:GLU55 2.6 89.8 1.0 CD C:GLU55 2.8 80.8 1.0 CG C:ASP39 2.8 78.8 1.0 C C:THR41 3.4 93.8 1.0 CB C:THR41 3.4 88.9 1.0 C C:GLY44 3.6 93.5 1.0 CA C:THR41 3.8 88.3 1.0 N C:THR41 4.1 91.5 1.0 CA C:GLY45 4.3 94.5 1.0 CG C:GLU55 4.3 78.4 1.0 CB C:ASP39 4.3 82.9 1.0 N C:GLY45 4.4 95.7 1.0 OD2 C:ASP47 4.4 85.5 1.0 CZ C:PHE49 4.5 68.0 1.0 N C:GLY44 4.5 98.3 1.0 N C:ILE42 4.6 96.5 1.0 CA C:GLY44 4.6 98.4 1.0 NE2 C:HIS61 4.7 73.3 1.0 OD1 C:ASN50 4.7 81.6 1.0 CG2 C:THR41 4.8 80.2 1.0 ND2 C:ASN50 4.9 71.6 1.0 CE1 C:PHE49 5.0 72.6 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