Magnesium 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
Calcium	(Ca)	4 atoms

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

Magnesium binding site 1 out of 7 in the Crystal Structure of T2R-Ttl -Mebendazole Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of T2R-Ttl -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:39.5 occ:1.00 O A:HOH603 2.1 39.9 1.0 O A:HOH606 2.1 39.5 1.0 O A:HOH631 2.1 41.8 1.0 O A:HOH618 2.1 44.7 1.0 O3G A:GTP501 2.2 38.5 1.0 O2B A:GTP501 2.2 35.9 1.0 HZ1 B:LYS254 3.3 64.3 1.0 PB A:GTP501 3.3 37.6 1.0 PG A:GTP501 3.3 41.9 1.0 HB2 A:GLN11 3.4 40.7 1.0 H A:GLN11 3.6 43.9 1.0 O1G A:GTP501 3.7 36.8 1.0 O3B A:GTP501 3.7 41.6 1.0 O3A A:GTP501 3.8 43.7 1.0 OE2 A:GLU71 3.8 51.9 1.0 HG3 A:GLU71 3.8 52.5 1.0 HG2 A:GLU71 3.8 52.5 1.0 HB2 A:ASP98 3.9 48.4 1.0 OD1 A:ASP69 3.9 43.8 1.0 HB3 A:GLN11 4.0 40.7 1.0 NZ B:LYS254 4.0 66.1 1.0 CB A:GLN11 4.1 40.7 1.0 HZ2 B:LYS254 4.1 64.3 1.0 OD2 A:ASP69 4.2 44.7 1.0 HB3 A:ASP98 4.2 48.4 1.0 HZ3 B:LYS254 4.2 64.3 1.0 CG A:GLU71 4.2 52.6 1.0 OD2 A:ASP98 4.2 41.9 1.0 N A:GLN11 4.3 44.0 1.0 CB A:ASP98 4.4 47.4 1.0 CG A:ASP69 4.5 47.8 1.0 CD A:GLU71 4.5 55.2 1.0 OE1 A:GLN11 4.6 54.2 1.0 O2G A:GTP501 4.6 35.6 1.0 O1B A:GTP501 4.6 38.0 1.0 O2A A:GTP501 4.7 38.8 1.0 HA2 A:GLY10 4.7 39.9 1.0 CG A:ASP98 4.7 44.0 1.0 HB A:THR145 4.8 43.3 1.0 PA A:GTP501 4.8 41.4 1.0 CA A:GLN11 4.8 41.3 1.0 HG1 A:THR145 4.9 47.9 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of T2R-Ttl -Mebendazole Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of T2R-Ttl -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:71.9 occ:1.00 O A:HOH625 2.1 77.3 1.0 OE1 A:GLU420 2.1 97.1 1.0 CD A:GLU420 3.4 95.6 1.0 HA A:GLU417 3.5 30.8 1.0 HB2 A:GLU420 3.6 73.1 1.0 C A:GLY416 3.8 53.8 1.0 N A:GLU417 3.8 54.3 1.0 HA3 A:GLY416 3.9 62.3 1.0 O A:GLY416 4.0 53.5 1.0 HB2 A:GLU417 4.1 30.8 1.0 CA A:GLU417 4.1 53.8 1.0 H A:GLU417 4.1 30.8 1.0 OE2 A:GLU420 4.1 88.2 1.0 HB3 A:GLU420 4.2 73.1 1.0 CB A:GLU420 4.2 74.2 1.0 CG A:GLU420 4.4 80.7 1.0 CA A:GLY416 4.4 62.7 1.0 CB A:GLU417 4.6 53.2 1.0 HG3 A:GLU420 4.7 79.3 1.0 HB2 A:GLU414 4.9 70.7 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of T2R-Ttl -Mebendazole Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of T2R-Ttl -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:30.1 occ:1.00 OE1 B:GLN11 2.1 40.4 1.0 O C:HOH656 2.1 41.5 1.0 O B:HOH618 2.1 35.0 1.0 O B:HOH601 2.1 38.2 1.0 O B:HOH614 2.1 44.6 1.0 O1A B:GDP501 2.3 39.9 1.0 CD B:GLN11 3.3 50.7 1.0 PA B:GDP501 3.6 36.6 1.0 HB3 B:GLN11 3.6 36.3 1.0 OD2 B:ASP179 3.6 44.6 1.0 H8 B:GDP501 3.7 41.8 1.0 O3A B:GDP501 3.9 43.7 1.0 HB2 B:GLN11 4.0 36.3 1.0 CB B:GLN11 4.1 35.4 1.0 CG B:GLN11 4.2 50.7 1.0 HD21 B:ASN101 4.2 41.1 1.0 HE22 B:GLN11 4.2 57.7 1.0 NE2 B:GLN11 4.3 57.9 1.0 OD1 B:ASN101 4.3 35.0 1.0 HG2 B:GLN11 4.3 51.2 1.0 C5' B:GDP501 4.3 36.2 1.0 OE1 C:GLU254 4.4 53.5 1.0 O5' B:GDP501 4.4 36.6 1.0 O1B B:GDP501 4.6 44.9 1.0 C8 B:GDP501 4.7 41.8 1.0 O2A B:GDP501 4.7 39.5 1.0 CG B:ASP179 4.7 45.0 1.0 ND2 B:ASN101 4.9 40.8 1.0 HB3 B:ASP179 4.9 42.7 1.0 PB B:GDP501 4.9 40.7 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of T2R-Ttl -Mebendazole Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of T2R-Ttl -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:80.0 occ:1.00 O B:HOH643 2.1 69.2 1.0 O B:HOH646 2.1 74.8 1.0 O B:HOH603 2.1 64.7 1.0 OD2 B:ASP120 4.0 73.1 1.0 HB3 B:ASP116 4.1 58.9 1.0 OD1 B:ASP120 4.2 69.6 1.0 CG B:ASP120 4.5 70.1 1.0 CB B:ASP116 5.0 58.8 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of T2R-Ttl -Mebendazole Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of T2R-Ttl -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:37.3 occ:1.00 O2G C:GTP502 1.9 37.0 1.0 O C:HOH636 2.1 33.1 1.0 O C:HOH643 2.1 39.0 1.0 O C:HOH686 2.1 33.5 1.0 O2B C:GTP502 2.1 34.8 1.0 O C:HOH655 2.1 41.3 1.0 PG C:GTP502 3.0 37.3 1.0 PB C:GTP502 3.1 33.1 1.0 HZ1 D:LYS254 3.1 46.2 1.0 O3B C:GTP502 3.4 42.7 1.0 HB2 C:GLN11 3.5 34.6 1.0 O3G C:GTP502 3.6 44.2 1.0 O3A C:GTP502 3.6 36.5 1.0 H C:GLN11 3.7 36.9 1.0 HB2 C:ASP98 3.7 38.4 1.0 HG2 C:GLU71 3.7 45.8 1.0 NZ D:LYS254 3.8 46.0 1.0 HZ3 D:LYS254 3.8 46.2 1.0 HZ2 D:LYS254 4.0 46.2 1.0 HG3 C:GLU71 4.0 45.8 1.0 OD1 C:ASP69 4.1 41.2 1.0 OD2 C:ASP98 4.2 47.5 1.0 HB3 C:ASP98 4.2 38.4 1.0 OE2 C:GLU71 4.2 47.2 1.0 HB3 C:GLN11 4.3 34.6 1.0 O1G C:GTP502 4.3 37.0 1.0 OD2 C:ASP69 4.3 34.5 1.0 CG C:GLU71 4.3 45.8 1.0 CB C:GLN11 4.3 34.2 1.0 CB C:ASP98 4.4 38.6 1.0 O1B C:GTP502 4.4 34.9 1.0 N C:GLN11 4.4 36.2 1.0 O2A C:GTP502 4.6 34.6 1.0 CG C:ASP69 4.6 40.0 1.0 HB C:THR145 4.7 43.6 1.0 PA C:GTP502 4.7 34.6 1.0 HG1 C:THR145 4.7 48.1 1.0 CG C:ASP98 4.7 43.1 1.0 OE1 C:GLN11 4.7 58.2 1.0 HA2 C:GLY10 4.7 38.4 1.0 CD C:GLU71 4.8 50.5 1.0 CA C:GLN11 5.0 35.2 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of T2R-Ttl -Mebendazole Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of T2R-Ttl -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:72.9 occ:1.00 O D:HOH609 2.1 76.3 1.0 O D:HOH601 2.1 75.1 1.0 O D:HOH604 2.1 72.4 1.0 OE1 D:GLN11 2.1 96.6 1.0 O1A D:GDP500 2.2 63.5 1.0 CD D:GLN11 3.1 92.1 1.0 HB3 D:GLN11 3.4 71.5 1.0 PA D:GDP500 3.6 63.9 1.0 H8 D:GDP500 3.6 64.4 1.0 OD2 D:ASP179 3.7 71.1 0.4 HB2 D:GLN11 3.8 71.5 1.0 HE22 D:GLN11 3.8 98.1 1.0 NE2 D:GLN11 3.9 100.6 1.0 CB D:GLN11 3.9 72.5 1.0 CG D:GLN11 4.1 81.7 1.0 O3A D:GDP500 4.1 66.6 1.0 C5' D:GDP500 4.3 65.0 1.0 HD21 D:ASN101 4.4 75.1 1.0 HG2 D:GLN11 4.4 80.3 1.0 O5' D:GDP500 4.5 62.8 1.0 O1B D:GDP500 4.5 75.7 1.0 C8 D:GDP500 4.6 64.4 1.0 O2A D:GDP500 4.6 65.8 1.0 HE21 D:GLN11 4.6 98.1 1.0 HG3 D:GLN11 4.8 80.3 1.0 CG D:ASP179 4.8 63.0 0.4 OD1 D:ASN101 4.9 91.5 1.0 PB D:GDP500 5.0 65.0 1.0 HB3 D:ASP179 5.0 59.7 0.4

Magnesium binding site 7 out of 7 in the Crystal Structure of T2R-Ttl -Mebendazole Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of T2R-Ttl -Mebendazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg501 b:113.5 occ:1.00 OE2 F:GLU331 1.8 114.5 1.0 OD1 F:ASN333 2.1 107.2 1.0 OE1 F:GLU331 2.2 100.1 1.0 CD F:GLU331 2.2 102.3 1.0 O1B F:ACP500 2.7 99.3 1.0 O3G F:ACP500 2.8 101.6 1.0 HD21 F:ASN333 3.0 102.3 1.0 CG F:ASN333 3.1 100.1 1.0 ND2 F:ASN333 3.4 103.2 1.0 CG F:GLU331 3.6 87.6 1.0 H3B2 F:ACP500 3.7 93.8 1.0 HG3 F:GLU331 3.8 86.1 1.0 PG F:ACP500 3.8 104.2 1.0 PB F:ACP500 3.8 98.2 1.0 HE2 F:LYS74 3.9 111.2 1.0 C3B F:ACP500 4.0 93.8 1.0 HB3 A:GLU450 4.1 125.4 1.0 HG2 F:GLU331 4.1 86.1 1.0 HE3 F:LYS74 4.2 111.2 1.0 HD22 F:ASN333 4.2 102.3 1.0 HA F:ASN333 4.3 77.5 1.0 HB2 F:GLU331 4.3 78.3 1.0 O2G F:ACP500 4.3 96.6 1.0 CB F:ASN333 4.4 84.4 1.0 O2B F:ACP500 4.5 104.2 1.0 CE F:LYS74 4.5 105.6 1.0 OE2 A:GLU450 4.5 121.2 1.0 CB F:GLU331 4.6 79.3 1.0 CD A:GLU450 4.6 113.2 1.0 OE1 A:GLU450 4.7 103.0 1.0 O F:VAL332 4.8 69.5 1.0 HB3 F:ASN333 4.8 84.5 1.0 CA F:ASN333 4.8 76.6 1.0 HZ1 F:LYS74 4.9 107.0 1.0 HB3 F:GLU331 4.9 78.3 1.0 CB A:GLU450 4.9 126.5 1.0 H3B1 F:ACP500 5.0 93.8 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