Calcium in PDB 7cld: Crystal Structure of T2R-Ttl-Cevipabulin Complex

The structure of Crystal Structure of T2R-Ttl-Cevipabulin Complex, PDB code: 7cld was solved by L.J.Chen, Q.Chen, Y.Yu, J.H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.03 / 2.61
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.422, 160.778, 174.764, 90, 90, 90
R / Rfree (%)	20.7 / 25.8

The structure of Crystal Structure of T2R-Ttl-Cevipabulin Complex also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	5 atoms
Fluorine	(F)	10 atoms

The binding sites of Calcium atom in the Crystal Structure of T2R-Ttl-Cevipabulin Complex (pdb code 7cld). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of T2R-Ttl-Cevipabulin Complex, PDB code: 7cld:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of T2R-Ttl-Cevipabulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of T2R-Ttl-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:75.1 occ:1.00 OG1 A:THR41 2.2 82.0 1.0 OE2 A:GLU55 2.3 75.4 1.0 O A:THR41 2.4 87.0 1.0 OD1 A:ASP39 2.4 65.1 1.0 O A:GLY44 2.4 78.9 1.0 OD2 A:ASP39 2.4 71.6 1.0 CG A:ASP39 2.7 68.5 1.0 OE1 A:GLU55 2.8 76.3 1.0 CD A:GLU55 2.9 73.8 1.0 CB A:THR41 3.3 81.3 1.0 C A:THR41 3.4 84.1 1.0 HA3 A:GLY45 3.4 100.1 1.0 HB A:THR41 3.5 97.4 1.0 H A:THR41 3.5 103.8 1.0 HZ A:PHE49 3.6 91.2 1.0 C A:GLY44 3.6 81.3 1.0 CA A:THR41 3.7 84.3 1.0 H A:GLY44 3.8 99.7 1.0 HD21 A:ASN50 3.8 56.3 1.0 N A:THR41 4.0 86.7 1.0 OD2 A:ASP47 4.2 65.2 1.0 CA A:GLY45 4.2 83.6 1.0 CB A:ASP39 4.3 69.8 1.0 CG A:GLU55 4.4 67.2 1.0 CZ A:PHE49 4.4 76.2 1.0 N A:GLY45 4.4 83.3 1.0 OD1 A:ASN50 4.4 47.3 1.0 HE2 A:PHE49 4.4 91.5 1.0 NE2 A:HIS61 4.5 55.5 1.0 N A:GLY44 4.5 83.3 1.0 N A:ILE42 4.6 80.1 1.0 HB2 A:ASP39 4.6 83.6 1.0 ND2 A:ASN50 4.6 47.1 1.0 CG2 A:THR41 4.6 78.5 1.0 HA2 A:GLY45 4.6 100.1 1.0 HG3 A:GLU55 4.7 80.4 1.0 HA A:THR41 4.7 100.9 1.0 HA A:ILE42 4.7 92.9 1.0 HB3 A:ASP39 4.7 83.6 1.0 CA A:GLY44 4.7 82.1 1.0 HG2 A:GLU55 4.8 80.4 1.0 HG21 A:THR41 4.8 94.0 1.0 HG23 A:THR41 4.8 94.0 1.0 CE2 A:PHE49 4.8 76.4 1.0 HA A:ASP39 4.9 86.7 1.0 CG A:ASN50 5.0 49.1 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of T2R-Ttl-Cevipabulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of T2R-Ttl-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:98.4 occ:1.00 O E:HOH202 2.6 71.3 1.0 O A:HOH666 2.8 46.3 1.0 O A:GLY162 3.5 56.4 1.0 HG A:SER158 3.8 42.3 1.0 HZ3 A:LYS166 4.1 42.8 1.0 OG A:SER158 4.2 35.5 1.0 HZ1 A:LYS166 4.2 42.8 1.0 HB3 A:SER158 4.3 33.7 1.0 OD2 E:ASP44 4.4 75.9 1.0 HA A:SER158 4.4 37.2 1.0 HA A:HIS197 4.6 50.5 1.0 NZ A:LYS166 4.6 35.9 1.0 C A:GLY162 4.7 57.7 1.0 CB A:SER158 4.7 28.3 1.0 HA2 A:GLY162 4.7 65.7 1.0 HZ2 A:LYS166 4.9 42.8 1.0 O A:LYS164 4.9 39.4 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of T2R-Ttl-Cevipabulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of T2R-Ttl-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:119.9 occ:1.00 O B:HOH653 2.4 48.2 1.0 HB3 B:ASP114 3.4 42.4 1.0 CB B:ASP114 4.3 35.5 1.0 HB2 B:ASP114 4.4 42.4 1.0 OD2 B:ASP118 4.4 40.4 1.0 OD1 B:ASP118 4.4 38.9 1.0 CG B:ASP118 4.8 37.3 1.0 CG B:ASP114 4.9 44.7 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of T2R-Ttl-Cevipabulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of T2R-Ttl-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:72.5 occ:1.00 OE2 B:GLU111 3.7 71.4 1.0 OE1 B:GLU108 3.9 35.8 1.0 CD B:GLU108 4.7 37.1 1.0 CD B:GLU111 4.7 69.6 1.0 OE2 B:GLU108 4.8 37.7 1.0 HA B:GLU108 4.8 35.2 1.0 HB2 B:GLU111 4.9 62.8 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of T2R-Ttl-Cevipabulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of T2R-Ttl-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:98.5 occ:1.00 HA2 C:GLY59 2.4 39.2 1.0 HA C:ILE42 2.5 44.1 1.0 HG23 C:ILE42 2.8 44.3 1.0 H C:GLY43 2.8 59.5 1.0 HE1 C:HIS61 2.8 38.0 1.0 OE1 C:GLU55 2.9 29.1 1.0 CA C:GLY59 3.3 32.9 1.0 HB3 C:GLU55 3.4 32.4 1.0 CA C:ILE42 3.4 37.0 1.0 CE1 C:HIS61 3.4 31.9 1.0 CG2 C:ILE42 3.5 37.1 1.0 N C:GLY43 3.5 49.8 1.0 O C:THR41 3.6 45.6 1.0 HG22 C:ILE42 3.7 44.3 1.0 OD2 C:ASP39 3.7 47.9 1.0 HA3 C:GLY59 3.8 39.2 1.0 C C:GLY59 3.8 28.7 1.0 O C:GLY59 3.8 30.1 1.0 HG12 C:ILE42 3.9 43.9 1.0 CD C:GLU55 3.9 30.2 1.0 CB C:ILE42 4.0 35.8 1.0 C C:ILE42 4.0 44.2 1.0 H C:GLY59 4.0 40.8 1.0 NE2 C:HIS61 4.1 32.0 1.0 O C:THR56 4.2 33.2 1.0 N C:GLY59 4.2 34.2 1.0 ND1 C:HIS61 4.2 32.2 1.0 CB C:GLU55 4.2 27.2 1.0 HG2 C:GLU55 4.3 35.0 1.0 HG21 C:ILE42 4.3 44.3 1.0 N C:ILE42 4.3 39.9 1.0 C C:THR41 4.4 43.5 1.0 CG C:GLU55 4.4 29.4 1.0 CG1 C:ILE42 4.5 36.8 1.0 CA C:CA505 4.5 30.8 1.0 H C:GLY44 4.6 52.2 1.0 HB2 C:GLU55 4.6 32.4 1.0 CG C:ASP39 4.7 51.6 1.0 N C:LYS60 4.7 25.4 1.0 CA C:GLY43 4.7 50.9 1.0 HA2 C:GLY43 4.7 60.8 1.0 HB3 C:ASP39 4.8 68.6 1.0 HB C:ILE42 4.8 42.7 1.0 OE2 C:GLU55 4.9 29.9 1.0 O C:LYS60 4.9 25.2 1.0 H C:LYS60 5.0 30.3 1.0 H C:THR56 5.0 42.0 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of T2R-Ttl-Cevipabulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of T2R-Ttl-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca505 b:30.8 occ:1.00 O C:THR41 2.2 45.6 1.0 OG1 C:THR41 2.4 42.1 1.0 O C:GLY44 2.5 40.2 1.0 OD2 C:ASP39 2.5 47.9 1.0 OE1 C:GLU55 2.5 29.1 1.0 OE2 C:GLU55 2.5 29.9 1.0 O C:HOH617 2.7 25.1 1.0 OD1 C:ASP39 2.7 51.6 1.0 CD C:GLU55 2.8 30.2 1.0 CG C:ASP39 2.9 51.6 1.0 C C:THR41 3.2 43.5 1.0 CB C:THR41 3.5 39.7 1.0 HA3 C:GLY45 3.5 48.0 1.0 C C:GLY44 3.6 41.7 1.0 HZ C:PHE49 3.6 28.3 1.0 HB C:THR41 3.6 47.4 1.0 H C:THR41 3.8 53.5 1.0 CA C:THR41 3.8 41.6 1.0 H C:GLY44 3.9 52.2 1.0 N C:THR41 4.2 44.8 1.0 HA C:ILE42 4.2 44.1 1.0 HD21 C:ASN50 4.3 41.6 1.0 N C:ILE42 4.3 39.9 1.0 CA C:GLY45 4.3 40.2 1.0 N C:GLY45 4.4 41.5 1.0 CG C:GLU55 4.4 29.4 1.0 HE1 C:PHE49 4.4 34.1 1.0 CZ C:PHE49 4.4 23.8 1.0 OD1 C:ASN50 4.4 21.5 1.0 CB C:ASP39 4.4 57.4 1.0 N C:GLY44 4.5 43.7 1.0 CA C:CA503 4.5 98.5 1.0 CA C:GLY44 4.5 43.4 1.0 OD2 C:ASP47 4.6 56.2 1.0 NE2 C:HIS61 4.6 32.0 1.0 HA2 C:GLY44 4.7 51.9 1.0 HA C:THR41 4.7 49.6 1.0 CA C:ILE42 4.7 37.0 1.0 HG3 C:GLU55 4.7 35.0 1.0 HG2 C:GLU55 4.8 35.0 1.0 CG2 C:THR41 4.8 40.1 1.0 HA2 C:GLY45 4.8 48.0 1.0 HB3 C:ASP39 4.8 68.6 1.0 HB2 C:ASP39 4.8 68.6 1.0 CE1 C:PHE49 4.8 28.6 1.0 HG21 C:THR41 5.0 48.0 1.0 HG23 C:THR41 5.0 48.0 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of T2R-Ttl-Cevipabulin Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of T2R-Ttl-Cevipabulin Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca502 b:78.2 occ:1.00 HG13 D:VAL175 3.6 60.3 1.0 O D:VAL175 3.8 58.5 1.0 CZ D:TYR222 4.0 55.8 1.0 CE2 D:TYR222 4.1 56.3 1.0 HA D:THR221 4.2 78.8 1.0 CE1 D:TYR222 4.3 55.2 1.0 O D:PRO220 4.3 58.8 1.0 HG12 D:VAL175 4.3 60.3 1.0 HE2 D:TYR222 4.3 67.3 1.0 OH D:TYR222 4.4 56.5 1.0 CD2 D:TYR222 4.4 60.0 1.0 CG1 D:VAL175 4.4 50.5 1.0 H D:TYR222 4.4 71.7 1.0 HA D:VAL175 4.5 69.0 1.0 HH D:TYR222 4.5 67.5 1.0 CD1 D:TYR222 4.6 54.1 1.0 HE1 D:TYR222 4.6 66.0 1.0 CG D:TYR222 4.6 55.8 1.0 C D:VAL175 4.8 58.8 1.0 HD2 D:TYR222 4.8 71.8 1.0 N D:TYR222 4.8 60.0 1.0 O D:HOH628 4.8 43.3 1.0

J.Yang, Y.Yu, Y.Li, W.Yan, H.Ye, L.Niu, M.Tang, Z.Wang, Z.Yang, H.Pei, H.Wei, M.Zhao, J.Wen, L.Yang, L.Ouyang, Y.Wei, Q.Chen, W.Li, L.Chen. Cevipabulin-Tubulin Complex Reveals A Novel Agent Binding Site on Alpha-Tubulin with Tubulin Degradation Effect. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 34138737
DOI: 10.1126/SCIADV.ABG4168