Calcium in PDB 5s62: Tubulin-Z100642432-Complex

The structure of Tubulin-Z100642432-Complex, PDB code: 5s62 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)	63.60 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.48, 159.44, 179.83, 90, 90, 90
R / Rfree (%)	21.1 / 26.7

The structure of Tubulin-Z100642432-Complex also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Bromine	(Br)	1 atom
Magnesium	(Mg)	5 atoms

The binding sites of Calcium atom in the Tubulin-Z100642432-Complex (pdb code 5s62). 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-Z100642432-Complex, PDB code: 5s62:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:114.6 occ:1.00 OE2 A:GLU55 2.3 114.7 1.0 OD2 A:ASP39 2.4 115.1 1.0 O A:GLY44 2.5 127.5 1.0 OG1 A:THR41 2.6 117.7 1.0 OD1 A:ASP39 2.6 119.6 1.0 OE1 A:GLU55 2.7 123.0 1.0 CG A:ASP39 2.8 117.2 1.0 O A:THR41 2.8 122.4 1.0 CD A:GLU55 2.8 119.3 1.0 C A:GLY44 3.4 128.3 1.0 CB A:THR41 3.6 121.2 1.0 C A:THR41 3.8 122.5 1.0 CA A:GLY45 4.0 137.4 1.0 N A:GLY45 4.1 133.4 1.0 CA A:THR41 4.1 124.6 1.0 OD1 A:ASN50 4.2 117.3 1.0 CZ A:PHE49 4.2 107.0 1.0 N A:GLY44 4.3 128.2 1.0 CB A:ASP39 4.3 119.8 1.0 CG A:GLU55 4.3 118.5 1.0 N A:THR41 4.4 121.1 1.0 CA A:GLY44 4.4 125.8 1.0 OD2 A:ASP47 4.5 107.3 1.0 ND2 A:ASN50 4.6 108.1 1.0 CE1 A:PHE49 4.7 109.3 1.0 C A:GLY45 4.8 136.3 1.0 CG2 A:THR41 4.9 121.8 1.0 CG A:ASN50 4.9 113.0 1.0 O A:GLY45 4.9 130.6 1.0 NE2 A:HIS61 5.0 110.5 1.0

Calcium binding site 2 out of 4 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:116.9 occ:1.00 O A:HOH607 3.1 98.3 1.0 NZ A:LYS166 3.6 98.7 1.0 OG A:SER158 3.9 90.2 1.0 O A:GLY162 4.0 132.0 1.0 OD2 E:ASP44 4.2 132.1 1.0 CB A:SER158 4.3 87.8 1.0 O A:LYS164 4.7 121.1 1.0 CE A:LYS166 4.7 83.6 1.0 CA A:SER158 4.8 92.1 1.0 O A:HIS197 4.9 89.6 1.0 O A:GLU196 4.9 96.8 1.0 OD1 A:ASP199 5.0 117.6 1.0

Calcium binding site 3 out of 4 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:117.3 occ:1.00 OE1 B:GLU113 2.9 106.9 1.0 OE2 B:GLU113 3.6 103.2 1.0 CD B:GLU113 3.6 108.4 1.0 OE1 B:GLU110 4.7 88.2 1.0

Calcium binding site 4 out of 4 in the Tubulin-Z100642432-Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Z100642432-Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:95.3 occ:1.00 OG1 C:THR41 2.3 119.1 1.0 OD2 C:ASP39 2.4 103.2 1.0 OE2 C:GLU55 2.4 97.9 1.0 O C:THR41 2.4 120.5 1.0 O C:GLY44 2.4 124.6 1.0 OD1 C:ASP39 2.5 107.1 1.0 OE1 C:GLU55 2.6 109.9 1.0 CG C:ASP39 2.7 102.1 1.0 CD C:GLU55 2.8 97.5 1.0 CB C:THR41 3.4 121.0 1.0 C C:THR41 3.4 120.8 1.0 C C:GLY44 3.6 123.2 1.0 CA C:THR41 3.8 120.6 1.0 OD2 C:ASP47 3.9 93.7 1.0 N C:THR41 4.0 119.8 1.0 CB C:ASP39 4.2 100.6 1.0 CG C:GLU55 4.3 92.8 1.0 CA C:GLY45 4.3 113.3 1.0 N C:GLY45 4.4 118.7 1.0 N C:GLY44 4.6 125.1 1.0 N C:ILE42 4.6 115.8 1.0 OD1 C:ASN50 4.6 93.2 1.0 CZ C:PHE49 4.6 85.1 1.0 CA C:GLY44 4.6 123.0 1.0 CG2 C:THR41 4.7 122.4 1.0 CE1 C:PHE49 4.8 82.8 1.0 NE2 C:HIS61 4.8 93.9 1.0 ND2 C:ASN50 4.9 85.6 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