Calcium in PDB 8jjc: Tubulin-Y62

The structure of Tubulin-Y62, PDB code: 8jjc was solved by J.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.74 / 2.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.493, 157.005, 180.398, 90, 90, 90
R / Rfree (%)	23.5 / 26.4

The structure of Tubulin-Y62 also contains other interesting chemical elements:

Magnesium	(Mg)	5 atoms
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Tubulin-Y62 (pdb code 8jjc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Tubulin-Y62, PDB code: 8jjc:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:77.7 occ:0.00 HZ A:PHE49 2.0 90.0 1.0 OG1 A:THR41 2.3 82.5 1.0 OE2 A:GLU55 2.4 82.3 1.0 HG1 A:THR41 2.4 99.0 1.0 OD1 A:ASP39 2.5 79.4 1.0 OD2 A:ASP39 2.6 78.4 1.0 OD2 A:ASP47 2.7 76.0 1.0 CG A:ASP39 2.7 78.5 1.0 CZ A:PHE49 2.8 75.0 1.0 CD A:GLU55 3.4 82.8 1.0 HE1 A:PHE49 3.5 89.1 1.0 HA3 A:GLY45 3.5 96.0 1.0 O A:GLY44 3.5 75.6 1.0 CE1 A:PHE49 3.6 74.2 1.0 HD21 A:ASN50 3.6 85.2 1.0 CE2 A:PHE49 3.7 74.2 1.0 HE2 A:PHE49 3.7 89.1 1.0 OD1 A:ASN50 3.7 77.4 1.0 CB A:THR41 3.7 82.7 1.0 OE1 A:GLU55 3.8 81.1 1.0 CG A:ASP47 3.9 75.9 1.0 O A:THR41 3.9 84.4 1.0 HG23 A:THR41 3.9 94.7 1.0 HB2 A:ASP47 4.0 86.3 1.0 H A:THR41 4.0 95.8 1.0 CB A:ASP39 4.1 76.0 1.0 HB2 A:ASP39 4.1 91.3 1.0 HB A:THR41 4.2 99.3 1.0 ND2 A:ASN50 4.3 70.9 1.0 CG2 A:THR41 4.3 78.9 1.0 CG A:ASN50 4.4 72.3 1.0 HG21 A:THR41 4.4 94.7 1.0 CA A:GLY45 4.5 80.0 1.0 CB A:ASP47 4.5 71.9 1.0 H A:ASP47 4.5 87.7 1.0 C A:GLY44 4.5 76.9 1.0 HA A:ASP39 4.6 92.1 1.0 CA A:THR41 4.6 79.6 1.0 N A:THR41 4.7 79.8 1.0 C A:THR41 4.7 81.6 1.0 HB3 A:ASP39 4.7 91.3 1.0 CG A:GLU55 4.7 77.6 1.0 HD2 A:HIS61 4.8 95.6 1.0 OD1 A:ASP47 4.8 82.0 1.0 CD1 A:PHE49 4.8 72.2 1.0 HG3 A:GLU55 4.8 93.2 1.0 NE2 A:HIS61 4.9 81.5 1.0 HG2 A:GLU55 4.9 93.2 1.0 CA A:ASP39 4.9 76.7 1.0 CD2 A:PHE49 4.9 74.0 1.0 N A:GLY45 4.9 76.3 1.0

Calcium binding site 2 out of 6 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:64.8 occ:0.00 HZ1 A:LYS166 3.7 82.3 1.0 HG A:SER158 3.9 83.0 1.0 HZ3 A:LYS166 4.0 82.3 1.0 HA A:HIS197 4.0 75.4 1.0 HB3 A:SER158 4.0 77.3 1.0 OG A:SER158 4.2 69.1 1.0 O A:GLY162 4.2 70.2 1.0 NZ A:LYS166 4.3 68.6 1.0 O A:GLU196 4.5 65.5 1.0 CB A:SER158 4.6 64.3 1.0 HZ2 A:LYS166 4.7 82.3 1.0 HA A:SER158 4.8 76.3 1.0 OD1 A:ASP199 4.9 54.5 1.0 CA A:HIS197 4.9 62.8 1.0

Calcium binding site 3 out of 6 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:67.1 occ:0.00 HB3 B:ASP114 3.3 71.4 1.0 OD2 B:ASP114 3.7 71.8 1.0 CG B:ASP114 4.1 61.3 1.0 CB B:ASP114 4.1 59.5 1.0 OD1 B:ASP118 4.4 59.8 1.0 OD2 B:ASP118 4.4 64.8 1.0 HB2 B:ASP114 4.7 71.4 1.0 HH22 B:ARG121 4.8 84.7 1.0 CG B:ASP118 4.8 63.6 1.0 OD1 B:ASP114 4.9 55.3 1.0 HH21 B:ARG121 5.0 84.7 1.0

Calcium binding site 4 out of 6 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:70.0 occ:0.00 OE2 B:GLU111 2.6 76.2 1.0 CD B:GLU111 3.4 73.2 1.0 OE1 B:GLU111 3.5 76.7 1.0 OE1 B:GLU108 4.7 63.8 1.0 CG B:GLU111 4.8 60.1 1.0 HB2 B:GLU111 4.9 71.5 1.0

Calcium binding site 5 out of 6 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:63.1 occ:0.00 OG1 C:THR41 2.1 73.1 1.0 OE2 C:GLU55 2.1 65.9 1.0 OD2 C:ASP39 2.2 62.5 1.0 O C:GLY44 2.3 62.1 1.0 O C:THR41 2.3 65.5 1.0 OE1 C:GLU55 2.4 64.9 1.0 OD1 C:ASP39 2.5 65.1 1.0 CD C:GLU55 2.6 63.2 1.0 CG C:ASP39 2.7 62.5 1.0 C C:THR41 3.4 63.7 1.0 CB C:THR41 3.4 68.0 1.0 HA3 C:GLY45 3.4 74.1 1.0 C C:GLY44 3.5 62.2 1.0 HZ C:PHE49 3.6 66.9 1.0 H C:GLY44 3.7 72.3 1.0 HB C:THR41 3.7 81.7 1.0 H C:THR41 3.7 74.3 1.0 CA C:THR41 3.8 63.0 1.0 HD21 C:ASN50 3.9 66.8 1.0 OD2 C:ASP47 3.9 65.6 1.0 HE2 C:PHE49 4.0 66.6 1.0 CG C:GLU55 4.1 56.9 1.0 N C:THR41 4.2 61.9 1.0 CB C:ASP39 4.2 63.9 1.0 CA C:GLY45 4.3 61.7 1.0 OD1 C:ASN50 4.3 62.6 1.0 N C:GLY45 4.3 63.9 1.0 N C:GLY44 4.4 60.2 1.0 CZ C:PHE49 4.4 55.7 1.0 O C:HOH605 4.4 53.4 1.0 HG3 C:GLU55 4.4 68.3 1.0 CA C:GLY44 4.5 62.0 1.0 CG2 C:THR41 4.5 59.6 1.0 HB3 C:ASP39 4.5 76.7 1.0 N C:ILE42 4.5 62.4 1.0 HG23 C:THR41 4.6 71.5 1.0 HG2 C:GLU55 4.6 68.3 1.0 CE2 C:PHE49 4.6 55.4 1.0 HB2 C:ASP39 4.6 76.7 1.0 ND2 C:ASN50 4.6 55.6 1.0 HA C:ILE42 4.6 72.1 1.0 HA C:THR41 4.7 75.6 1.0 HG21 C:THR41 4.7 71.5 1.0 NE2 C:HIS61 4.8 59.0 1.0 HA2 C:GLY45 4.8 74.1 1.0 HA2 C:GLY44 4.8 74.4 1.0 HB3 C:GLU55 4.9 70.3 1.0 CG C:ASN50 4.9 57.9 1.0 H C:GLY43 5.0 80.0 1.0 HB2 C:GLU55 5.0 70.3 1.0 CB C:GLU55 5.0 58.6 1.0

Calcium binding site 6 out of 6 in the Tubulin-Y62


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Tubulin-Y62 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:76.5 occ:0.00 HG13 D:VAL175 3.3 98.3 1.0 CZ D:TYR222 3.9 70.5 1.0 CE2 D:TYR222 3.9 71.4 1.0 CE1 D:TYR222 4.2 73.0 1.0 HA D:THR221 4.2 99.2 1.0 HE2 D:TYR222 4.2 85.8 1.0 CG1 D:VAL175 4.2 81.9 1.0 O D:PRO220 4.2 85.2 1.0 O D:VAL175 4.2 90.1 1.0 CD2 D:TYR222 4.2 74.4 1.0 OH D:TYR222 4.3 73.2 1.0 HH D:TYR222 4.4 88.0 1.0 HA D:VAL175 4.4 100.3 1.0 CD1 D:TYR222 4.4 71.8 1.0 H D:TYR222 4.4 92.0 1.0 HG12 D:VAL175 4.4 98.3 1.0 CG D:TYR222 4.5 72.3 1.0 HG11 D:VAL175 4.5 98.3 1.0 HE1 D:TYR222 4.5 87.7 1.0 HD2 D:TYR222 4.6 89.3 1.0 N D:TYR222 4.7 76.7 1.0 HD1 D:TYR222 5.0 86.2 1.0 C D:VAL175 5.0 86.3 1.0

C.Zhang, W.Yan, Y.Liu, M.Tang, Y.Teng, F.Wang, X.Hu, M.Zhao, J.Yang, Y.Li. Structure-Based Design and Synthesis of BML284 Derivatives: A Novel Class of Colchicine-Site Noncovalent Tubulin Degradation Agents. Eur.J.Med.Chem. V. 268 16265 2024.
ISSN: ISSN 0223-5234
PubMed: 38430854
DOI: 10.1016/J.EJMECH.2024.116265