Magnesium in PDB 7cek: Crystal Structure of T2R-Ttl-Bml-284 Complex

The structure of Crystal Structure of T2R-Ttl-Bml-284 Complex, PDB code: 7cek 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)	48.26 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.571, 158.078, 181.292, 90, 90, 90
R / Rfree (%)	22.8 / 27.1

The structure of Crystal Structure of T2R-Ttl-Bml-284 Complex also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	6 atoms

The binding sites of Magnesium atom in the Crystal Structure of T2R-Ttl-Bml-284 Complex (pdb code 7cek). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of T2R-Ttl-Bml-284 Complex, PDB code: 7cek:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:53.6 occ:1.00 O A:HOH628 1.9 51.0 1.0 O A:HOH607 1.9 54.6 1.0 O A:HOH620 2.0 48.8 1.0 O2G A:GTP501 2.1 47.1 1.0 O A:HOH612 2.1 58.7 1.0 O1B A:GTP501 2.3 50.0 1.0 HZ1 B:LYS252 3.1 68.0 1.0 PG A:GTP501 3.3 47.2 1.0 PB A:GTP501 3.5 50.4 1.0 OE2 A:GLU71 3.5 61.5 1.0 HB2 A:GLN11 3.6 67.8 1.0 HG2 A:GLU71 3.6 72.7 1.0 O3B A:GTP501 3.7 56.8 1.0 HG3 A:GLU71 3.7 72.7 1.0 HB2 A:ASP98 3.8 64.8 1.0 O1G A:GTP501 3.8 47.6 1.0 H A:GLN11 3.8 65.5 1.0 NZ B:LYS252 3.9 56.1 1.0 O3A A:GTP501 4.0 49.3 1.0 OD1 A:ASP69 4.0 56.0 1.0 CG A:GLU71 4.0 60.1 1.0 HB3 A:ASP98 4.1 64.8 1.0 HZ2 B:LYS252 4.1 68.0 1.0 HB3 A:GLN11 4.2 67.8 1.0 CD A:GLU71 4.2 60.4 1.0 HZ3 B:LYS252 4.2 68.0 1.0 OD2 A:ASP69 4.3 57.9 1.0 CB A:ASP98 4.3 53.5 1.0 CB A:GLN11 4.3 56.0 1.0 OD1 B:ASN247 4.3 70.6 1.0 HE21 A:GLN11 4.4 72.0 1.0 OD2 A:ASP98 4.5 55.5 1.0 HG1 A:THR145 4.5 60.9 1.0 O1A A:GTP501 4.5 54.7 1.0 N A:GLN11 4.5 54.1 1.0 O3G A:GTP501 4.6 49.1 1.0 CG A:ASP69 4.6 57.7 1.0 CG A:ASP98 4.6 52.3 1.0 O2B A:GTP501 4.7 55.3 1.0 HB3 B:ASN247 4.7 93.4 1.0 HB A:THR145 4.8 62.4 1.0 NE2 A:GLN11 4.8 59.5 1.0 HA2 A:GLY10 4.9 65.6 1.0 PA A:GTP501 4.9 49.7 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:55.8 occ:1.00 O B:HOH606 2.0 56.4 1.0 O C:HOH630 2.2 57.4 1.0 O B:HOH611 2.2 52.1 1.0 O1A B:GDP501 2.3 61.2 1.0 OE1 B:GLN11 2.5 57.5 1.0 O B:HOH623 2.7 56.6 1.0 O B:HOH621 2.7 61.5 1.0 CD B:GLN11 3.5 59.5 1.0 PA B:GDP501 3.7 46.2 1.0 HB3 B:GLN11 3.8 69.2 1.0 OD2 B:ASP177 3.8 57.6 1.0 HB2 B:GLN11 4.0 69.2 1.0 HE22 B:GLN11 4.0 75.5 1.0 NE2 B:GLN11 4.2 62.4 1.0 O3B B:GDP501 4.2 54.8 1.0 OD1 B:ASN99 4.2 54.1 1.0 CB B:GLN11 4.2 57.1 1.0 HD21 B:ASN99 4.3 63.7 1.0 H8 B:GDP501 4.3 66.5 1.0 C5' B:GDP501 4.4 56.0 1.0 O5' B:GDP501 4.4 47.6 1.0 O3A B:GDP501 4.4 50.6 1.0 CG B:GLN11 4.5 59.5 1.0 OE1 C:GLU254 4.5 60.0 1.0 O2A B:GDP501 4.7 51.2 1.0 PB B:GDP501 4.7 49.1 1.0 O1B B:GDP501 4.8 52.2 1.0 ND2 B:ASN99 4.9 52.5 1.0 HE21 B:GLN11 4.9 75.5 1.0 CG B:ASP177 4.9 58.2 1.0 HG3 B:GLN11 4.9 72.0 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:44.3 occ:1.00 O C:HOH601 1.8 44.3 1.0 O C:HOH623 1.9 46.7 1.0 O1B C:GTP501 2.0 46.2 1.0 O C:HOH633 2.1 53.2 1.0 O1G C:GTP501 2.1 44.1 1.0 O C:HOH619 2.2 47.2 1.0 HZ1 D:LYS252 3.2 63.4 1.0 PB C:GTP501 3.3 38.5 1.0 PG C:GTP501 3.3 39.4 1.0 HZ3 D:LYS252 3.5 63.4 1.0 HB2 C:GLN11 3.5 56.7 1.0 OE2 C:GLU71 3.6 54.7 1.0 O3B C:GTP501 3.7 47.1 1.0 HG2 C:GLU71 3.7 61.3 1.0 HG3 C:GLU71 3.7 61.3 1.0 NZ D:LYS252 3.7 52.3 1.0 O2G C:GTP501 3.8 44.7 1.0 HB2 C:ASP98 3.8 59.3 1.0 O3A C:GTP501 3.8 47.0 1.0 H C:GLN11 3.9 50.6 1.0 OD2 C:ASP69 3.9 44.2 1.0 OD1 C:ASP69 3.9 44.9 1.0 HE21 C:GLN11 3.9 64.6 1.0 CG C:GLU71 4.1 50.6 1.0 HZ2 D:LYS252 4.1 63.4 1.0 CD C:GLU71 4.3 51.2 1.0 HB3 C:GLN11 4.3 56.7 1.0 CG C:ASP69 4.4 43.7 1.0 CB C:GLN11 4.4 46.7 1.0 HB3 C:ASP98 4.4 59.3 1.0 O2B C:GTP501 4.5 46.8 1.0 HG1 C:THR145 4.5 55.7 1.0 CB C:ASP98 4.5 48.9 1.0 NE2 C:GLN11 4.6 53.3 1.0 O3G C:GTP501 4.6 48.4 1.0 N C:GLN11 4.6 41.6 1.0 OD2 C:ASP98 4.6 53.4 1.0 O1A C:GTP501 4.6 48.1 1.0 HG21 C:VAL74 4.7 60.4 1.0 HB C:THR145 4.8 56.4 1.0 HE22 C:GLN11 4.8 64.6 1.0 HA2 C:GLY10 4.8 53.1 1.0 PA C:GTP501 4.9 42.7 1.0 OD1 D:ASN247 4.9 59.5 1.0 HD21 D:ASN247 4.9 71.1 1.0 CG D:ASN247 4.9 59.0 1.0 ND2 D:ASN247 5.0 58.7 1.0 HG23 C:VAL74 5.0 60.4 1.0 CE D:LYS252 5.0 52.4 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:79.4 occ:1.00 O D:HOH613 1.9 71.2 1.0 O3G D:GTP504 2.5 76.6 1.0 O D:HOH605 2.5 69.6 1.0 O2G D:GTP504 3.0 74.6 1.0 O2B D:GTP504 3.1 73.1 1.0 HB3 D:GLU69 3.3 101.3 1.0 PG D:GTP504 3.3 83.2 1.0 HB2 D:GLN11 3.4 91.2 1.0 HB2 D:GLU69 3.5 101.3 1.0 CB D:GLU69 3.8 83.9 1.0 OD2 D:ASP67 3.8 74.7 1.0 H D:GLN11 3.9 86.5 1.0 HG2 D:GLU69 3.9 108.6 1.0 OD1 D:ASP67 3.9 72.3 1.0 O3B D:GTP504 4.2 77.5 1.0 PB D:GTP504 4.2 74.6 1.0 OE1 D:GLU69 4.2 89.8 1.0 HG1 D:THR143 4.2 92.1 1.0 CG D:ASP67 4.3 74.4 1.0 CG D:GLU69 4.3 90.0 1.0 HG23 D:THR72 4.3 100.7 1.0 CB D:GLN11 4.3 75.5 1.0 HG21 D:THR72 4.4 100.7 1.0 N D:GLN11 4.5 71.5 1.0 O1G D:GTP504 4.5 75.3 1.0 O2A D:GTP504 4.6 78.1 1.0 HB3 D:GLN11 4.6 91.2 1.0 CD D:GLU69 4.6 94.2 1.0 HA2 D:GLY10 4.7 81.0 1.0 HE21 D:GLN11 4.7 88.4 1.0 CG2 D:THR72 4.8 83.3 1.0 OG1 D:THR143 4.8 76.2 1.0 CA D:GLN11 4.9 72.0 1.0 O D:HOH604 4.9 69.4 1.0 HG22 D:THR72 4.9 100.7 1.0 H D:GLU69 5.0 100.6 1.0 HA D:GLN11 5.0 87.1 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of T2R-Ttl-Bml-284 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-Bml-284 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:106.2 occ:1.00 O2B F:ACP402 2.6 107.8 1.0 HZ1 F:LYS74 2.9 127.0 1.0 O1G F:ACP402 3.3 105.1 1.0 HZ3 F:LYS74 3.4 127.0 1.0 OG F:SER152 3.5 109.1 1.0 OE1 F:GLU331 3.5 98.0 1.0 NZ F:LYS74 3.5 105.3 1.0 HD21 F:ASN333 3.6 114.0 1.0 O1B F:ACP402 3.7 113.2 1.0 HG F:SER152 3.7 131.6 1.0 PB F:ACP402 3.7 114.8 1.0 HA F:SER152 3.8 144.5 1.0 OE2 F:GLU331 3.9 99.9 1.0 ND2 F:ASN333 4.0 94.5 1.0 HZ2 F:LYS74 4.1 127.0 1.0 HD22 F:ASN333 4.1 114.0 1.0 CD F:GLU331 4.1 94.9 1.0 HE2 F:LYS74 4.3 129.9 1.0 PG F:ACP402 4.5 115.4 1.0 CB F:SER152 4.5 114.6 1.0 CE F:LYS74 4.6 107.8 1.0 CA F:SER152 4.6 119.9 1.0 O F:SER152 4.7 123.9 1.0 HB2 F:ASN333 4.7 99.8 1.0 C3B F:ACP402 4.8 111.0 1.0 HB2 F:SER152 4.8 138.2 1.0 O3G F:ACP402 4.9 103.8 1.0 CG F:ASN333 5.0 86.2 1.0 HE3 F:LYS74 5.0 129.9 1.0

L.J.Chen, Q.Chen, J.H.Yang, Y.Yu. Small Molecular Promote Selective Destabilization and Degradation of Tubular Heterodimers By Specific Charging of GLU198 of Beta-Tubulin Through A Low Barrier Hydrogen Bond To Be Published.