Calcium in PDB 5nfz: Tubulin-Mtc Complex

The structure of Tubulin-Mtc Complex, PDB code: 5nfz was solved by J.J.Field, B.Pera, J.Estevez Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, A.E.Prota, G.Menchon, J.H.Miller, K.-H.Altmann, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.78 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.163, 158.787, 180.376, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.8

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

Magnesium

(Mg)

5 atoms

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

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Mtc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:69.1 occ:1.00 O A:GLY44 2.3 80.4 1.0 OD2 A:ASP39 2.3 70.9 1.0 OD1 A:ASP39 2.5 73.2 1.0 O A:THR41 2.5 82.4 1.0 O A:HOH603 2.6 66.1 1.0 OE2 A:GLU55 2.6 61.4 1.0 OG1 A:THR41 2.6 70.5 1.0 OE1 A:GLU55 2.7 71.4 1.0 CG A:ASP39 2.7 71.0 1.0 CD A:GLU55 2.9 66.5 1.0 C A:GLY44 3.4 83.8 1.0 C A:THR41 3.6 81.3 1.0 CB A:THR41 3.6 80.3 1.0 CA A:THR41 4.0 85.6 1.0 CA A:GLY45 4.2 80.4 1.0 N A:GLY45 4.2 84.6 1.0 CB A:ASP39 4.3 71.4 1.0 N A:THR41 4.3 89.7 1.0 O A:HOH661 4.3 61.4 1.0 CZ A:PHE49 4.4 65.6 1.0 N A:GLY44 4.4 82.6 1.0 CG A:GLU55 4.4 65.7 1.0 CA A:GLY44 4.5 85.2 1.0 OD2 A:ASP47 4.5 78.9 1.0 OD1 A:ASN50 4.6 63.6 1.0 CE1 A:PHE49 4.7 69.0 1.0 N A:ILE42 4.7 83.4 1.0 NE2 A:HIS61 4.8 65.2 1.0 ND2 A:ASN50 4.9 61.9 1.0 CG2 A:THR41 4.9 74.3 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Mtc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:96.9 occ:1.00 O E:HOH204 2.4 70.2 1.0 O A:HOH655 2.9 63.1 1.0 O A:HOH683 3.3 66.8 1.0 OD2 E:ASP44 3.8 0.2 1.0 OG A:SER158 3.9 54.0 1.0 NZ A:LYS166 4.0 46.4 1.0 O A:GLY162 4.0 76.8 1.0 O A:HOH636 4.2 67.0 1.0 O A:HOH664 4.3 70.7 1.0 CB A:SER158 4.5 53.1 1.0 O A:LYS164 4.8 53.2 1.0 O A:HIS197 4.8 53.3 1.0 CA A:SER158 4.9 56.4 1.0 O A:GLU196 4.9 61.8 1.0 CG E:ASP44 5.0 0.4 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Mtc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:86.4 occ:1.00 O B:HOH642 2.4 59.8 1.0 OE1 B:GLU113 2.5 78.1 1.0 OE2 B:GLU113 3.1 80.8 1.0 CD B:GLU113 3.2 74.1 1.0 CG B:GLU113 4.6 63.6 1.0 OE1 B:GLU110 4.7 52.1 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Mtc Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:54.0 occ:1.00 OE1 C:GLU55 2.4 44.9 1.0 O C:HOH602 2.4 45.9 1.0 O C:THR41 2.4 58.6 1.0 OD2 C:ASP39 2.4 55.0 1.0 O C:GLY44 2.5 61.6 1.0 OG1 C:THR41 2.5 53.9 1.0 OE2 C:GLU55 2.5 47.7 1.0 OD1 C:ASP39 2.6 59.8 1.0 CD C:GLU55 2.8 46.8 1.0 CG C:ASP39 2.8 54.9 1.0 C C:THR41 3.5 61.8 1.0 C C:GLY44 3.5 68.5 1.0 CB C:THR41 3.6 54.5 1.0 CA C:THR41 3.9 58.3 1.0 N C:THR41 4.2 58.4 1.0 N C:GLY45 4.3 70.0 1.0 CA C:GLY45 4.3 70.4 1.0 OD2 C:ASP47 4.3 65.8 1.0 CG C:GLU55 4.3 43.1 1.0 CB C:ASP39 4.3 57.5 1.0 O C:HOH620 4.4 60.5 1.0 N C:GLY44 4.4 70.2 1.0 CA C:GLY44 4.5 66.5 1.0 OD1 C:ASN50 4.6 47.3 1.0 N C:ILE42 4.6 64.0 1.0 NE2 C:HIS61 4.6 45.6 1.0 CZ C:PHE49 4.7 49.6 1.0 CG2 C:THR41 4.9 48.0 1.0 CE1 C:PHE49 4.9 46.3 1.0 ND2 C:ASN50 5.0 43.4 1.0

J.J.Field, B.Pera, J.E.Gallego, E.Calvo, J.Rodriguez-Salarichs, G.Saez-Calvo, D.Zuwerra, M.Jordi, J.M.Andreu, A.E.Prota, G.Menchon, J.H.Miller, K.H.Altmann, J.F.Diaz. Zampanolide Binding to Tubulin Indicates Cross-Talk of Taxane Site with Colchicine and Nucleotide Sites. J. Nat. Prod. V. 81 494 2018.
ISSN: ESSN 1520-6025
PubMed: 29023132
DOI: 10.1021/ACS.JNATPROD.7B00704