Calcium in PDB 7ogn: Crystal Structure of T2R-Ttl -Mebendazole Complex

The structure of Crystal Structure of T2R-Ttl -Mebendazole Complex, PDB code: 7ogn was solved by M.A.Oliva, F.Bonato, J.F.Diaz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.35 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.9, 158.01, 179.689, 90, 90, 90
R / Rfree (%)	20.9 / 23.4

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

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	7 atoms

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

Calcium binding site 1 out of 4 in the Crystal Structure of T2R-Ttl -Mebendazole 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 -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:68.3 occ:1.00 O A:GLY44 2.3 65.4 1.0 O A:HOH628 2.4 67.4 1.0 OD2 A:ASP39 2.4 73.0 1.0 O A:THR41 2.4 77.4 1.0 OE2 A:GLU55 2.4 70.7 1.0 OG1 A:THR41 2.4 73.4 1.0 OD1 A:ASP39 2.4 85.0 1.0 OE1 A:GLU55 2.5 83.3 1.0 CG A:ASP39 2.7 77.3 1.0 CD A:GLU55 2.8 75.9 1.0 HA3 A:GLY45 3.4 82.9 1.0 C A:THR41 3.4 84.3 1.0 C A:GLY44 3.4 69.2 1.0 CB A:THR41 3.5 86.2 1.0 HB A:THR41 3.6 85.4 1.0 H A:GLY44 3.6 77.2 1.0 HZ A:PHE49 3.7 79.2 1.0 H A:THR41 3.7 82.0 1.0 CA A:THR41 3.8 87.5 1.0 HE2 A:HIS61 3.9 75.0 1.0 N A:THR41 4.1 82.6 1.0 HD21 A:ASN50 4.2 78.0 1.0 CA A:GLY45 4.2 83.1 1.0 CB A:ASP39 4.3 70.7 1.0 N A:GLY45 4.3 82.8 1.0 N A:GLY44 4.3 76.9 1.0 CG A:GLU55 4.3 70.5 1.0 CA A:GLY44 4.5 72.8 1.0 CZ A:PHE49 4.5 80.8 1.0 OD1 A:ASN50 4.6 84.0 1.0 N A:ILE42 4.6 80.1 1.0 HE1 A:PHE49 4.6 75.2 1.0 HB2 A:ASP39 4.6 71.4 1.0 HA A:ILE42 4.6 78.4 1.0 NE2 A:HIS61 4.6 75.7 1.0 HB3 A:ASP39 4.7 71.4 1.0 HG3 A:GLU55 4.7 70.7 1.0 HG2 A:GLU55 4.7 70.7 1.0 HA A:THR41 4.8 86.5 1.0 HA2 A:GLY45 4.8 82.9 1.0 OD2 A:ASP47 4.8 89.1 1.0 CG2 A:THR41 4.8 104.5 1.0 HA2 A:GLY44 4.9 73.2 1.0 H A:GLY43 4.9 78.6 1.0 HG21 A:THR41 4.9 103.3 1.0 HB3 A:GLU55 5.0 78.9 1.0 CE1 A:PHE49 5.0 76.4 1.0 ND2 A:ASN50 5.0 78.9 1.0 HA A:ASP39 5.0 76.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of T2R-Ttl -Mebendazole 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 -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:76.4 occ:1.00 O B:HOH631 2.3 59.9 1.0 OE1 B:GLU113 2.5 78.2 1.0 CD B:GLU113 3.2 79.6 1.0 OE2 B:GLU113 3.3 87.7 1.0 CG B:GLU113 4.7 72.3 1.0 HB2 B:GLU113 4.9 60.5 1.0 OE1 B:GLU110 4.9 54.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of T2R-Ttl -Mebendazole 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 -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca504 b:56.3 occ:1.00 O C:THR41 2.4 61.8 1.0 OE2 C:GLU55 2.4 56.1 1.0 OG1 C:THR41 2.4 60.8 1.0 O C:GLY44 2.4 60.4 1.0 OD2 C:ASP39 2.4 52.2 1.0 O C:HOH610 2.4 46.5 1.0 OE1 C:GLU55 2.4 65.5 1.0 OD1 C:ASP39 2.5 57.2 1.0 CD C:GLU55 2.8 56.2 1.0 CG C:ASP39 2.8 54.9 1.0 HA3 C:GLY45 3.4 70.5 1.0 C C:THR41 3.4 68.0 1.0 CB C:THR41 3.5 67.7 1.0 C C:GLY44 3.5 62.7 1.0 HB C:THR41 3.6 67.4 1.0 H C:THR41 3.7 68.4 1.0 HZ C:PHE49 3.8 64.6 1.0 CA C:THR41 3.9 69.5 1.0 H C:GLY44 3.9 68.3 1.0 HE2 C:HIS61 4.0 57.9 1.0 HD21 C:ASN50 4.1 53.1 1.0 N C:THR41 4.2 69.0 1.0 CA C:GLY45 4.2 70.9 1.0 HE1 C:PHE49 4.2 61.2 1.0 N C:GLY45 4.3 71.7 1.0 CG C:GLU55 4.3 52.6 1.0 CB C:ASP39 4.3 59.0 1.0 OD2 C:ASP47 4.4 73.4 1.0 N C:GLY44 4.5 68.0 1.0 N C:ILE42 4.5 66.1 1.0 HA C:ILE42 4.5 63.5 1.0 CZ C:PHE49 4.6 65.3 1.0 CA C:GLY44 4.6 63.5 1.0 OD1 C:ASN50 4.6 60.4 1.0 HB3 C:ASP39 4.6 59.3 1.0 HG2 C:GLU55 4.6 52.7 1.0 HG3 C:GLU55 4.7 52.7 1.0 HA2 C:GLY45 4.7 70.5 1.0 NE2 C:HIS61 4.7 58.1 1.0 HB2 C:ASP39 4.7 59.3 1.0 CE1 C:PHE49 4.8 61.7 1.0 CG2 C:THR41 4.8 69.1 1.0 HA C:THR41 4.8 68.8 1.0 ND2 C:ASN50 4.8 53.5 1.0 HA2 C:GLY44 4.8 64.0 1.0 HG21 C:THR41 4.9 68.6 1.0 HG23 C:THR41 5.0 68.6 1.0 CA C:ILE42 5.0 62.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of T2R-Ttl -Mebendazole 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 -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca201 b:83.6 occ:1.00 O A:HOH643 2.4 66.5 1.0 O A:HOH638 2.4 65.6 1.0 OD2 E:ASP88 3.3 104.2 1.0 O A:HOH615 3.5 54.9 1.0 HG A:SER158 3.9 55.6 1.0 HZ1 A:LYS166 4.1 80.2 1.0 OG A:SER158 4.1 55.2 1.0 HA A:HIS197 4.1 56.4 1.0 HB3 A:SER158 4.2 61.9 1.0 HZ3 A:LYS166 4.4 80.2 1.0 O A:GLU196 4.4 65.2 1.0 CG E:ASP88 4.5 115.3 1.0 O A:GLY162 4.5 59.6 1.0 NZ A:LYS166 4.6 81.8 1.0 CB A:SER158 4.7 62.1 1.0 HZ2 A:LYS166 4.8 80.2 1.0 HA A:SER158 4.8 64.8 1.0 OD1 A:ASP199 4.9 75.4 1.0 OD1 E:ASP88 4.9 116.1 1.0

M.A.Oliva, C.Tosat-Bitrian, L.Barrado-Gil, F.Bonato, I.Galindo, U.Garaigorta, B.Alvarez-Bernad, R.Paris-Ogayar, D.Lucena-Agell, J.F.Gimenez-Abian, I.Garcia-Dorival, J.Urquiza, P.Gastaminza, J.F.Diaz, V.Palomo, C.Alonso. Effect of Clinically Used Microtubule Targeting Drugs on Viral Infection and Transport Function. Int J Mol Sci V. 23 2022.
ISSN: ESSN 1422-0067
PubMed: 35408808
DOI: 10.3390/IJMS23073448