Magnesium in PDB 6y4n: Structure of Tubulin Tyrosine Ligase in Complex with TB116

The structure of Structure of Tubulin Tyrosine Ligase in Complex with TB116, PDB code: 6y4n was solved by J.Gavrilyuk, B.Nocek, S.Rigol, K.C.Nicolaou, V.Stoll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	78.93 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.284, 154.969, 183.433, 90, 90, 90
R / Rfree (%)	18.3 / 22

The structure of Structure of Tubulin Tyrosine Ligase in Complex with TB116 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Structure of Tubulin Tyrosine Ligase in Complex with TB116 (pdb code 6y4n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Structure of Tubulin Tyrosine Ligase in Complex with TB116, PDB code: 6y4n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Structure of Tubulin Tyrosine Ligase in Complex with TB116


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Tubulin Tyrosine Ligase in Complex with TB116 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:45.1 occ:1.00 O1G A:GTP1001 2.0 44.8 1.0 O1B A:GTP1001 2.1 45.7 1.0 O A:HOH1116 2.2 46.1 1.0 O A:HOH1110 2.2 44.6 1.0 O A:HOH1166 2.2 45.2 1.0 O A:HOH1120 2.2 45.6 1.0 PG A:GTP1001 3.0 44.5 1.0 PB A:GTP1001 3.2 45.3 1.0 O3B A:GTP1001 3.4 45.0 1.0 O2G A:GTP1001 3.5 44.1 1.0 OE1 A:GLU71 3.6 84.9 1.0 O3A A:GTP1001 3.7 46.5 1.0 NZ B:LYS252 3.9 52.5 1.0 OD1 A:ASP69 4.0 62.2 1.0 OD2 A:ASP69 4.3 65.8 1.0 CB A:GLN11 4.3 43.1 1.0 O3G A:GTP1001 4.3 44.1 1.0 N A:GLN11 4.4 41.6 1.0 OD2 A:ASP98 4.4 61.4 1.0 CB A:ASP98 4.5 53.5 1.0 O2B A:GTP1001 4.5 45.0 1.0 CG A:ASP69 4.6 63.1 1.0 O1A A:GTP1001 4.6 47.8 1.0 CG A:ASP98 4.7 58.8 1.0 CD A:GLU71 4.7 82.4 1.0 PA A:GTP1001 4.7 47.2 1.0 CB A:GLU71 4.8 68.8 1.0 OG1 A:THR145 4.9 46.2 1.0 CE B:LYS252 5.0 50.3 1.0 CA A:GLN11 5.0 42.0 1.0

Magnesium binding site 2 out of 5 in the Structure of Tubulin Tyrosine Ligase in Complex with TB116


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Tubulin Tyrosine Ligase in Complex with TB116 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:58.1 occ:1.00 O C:HOH1263 2.8 57.5 1.0 O B:HOH1182 2.9 46.8 1.0 O1B B:GDP1001 3.0 40.4 1.0 O B:HOH1118 3.3 64.8 1.0 OE2 B:GLU69 3.5 83.0 1.0 CB B:GLN11 3.7 42.0 1.0 O B:HOH1111 3.8 36.5 1.0 OE1 B:GLN11 3.8 56.7 1.0 PB B:GDP1001 4.0 39.9 1.0 O1A B:GDP1001 4.0 39.6 1.0 O3A B:GDP1001 4.1 39.7 1.0 O3B B:GDP1001 4.4 39.6 1.0 O B:HOH1106 4.4 35.8 1.0 CD B:GLN11 4.5 54.0 1.0 N B:GLN11 4.5 40.0 1.0 CG B:GLN11 4.6 47.3 1.0 PA B:GDP1001 4.7 39.3 1.0 CA B:GLN11 4.7 40.2 1.0 CD B:GLU69 4.8 78.6 1.0

Magnesium binding site 3 out of 5 in the Structure of Tubulin Tyrosine Ligase in Complex with TB116


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Tubulin Tyrosine Ligase in Complex with TB116 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:42.9 occ:1.00 O1G C:GTP1001 2.0 43.6 1.0 O1B C:GTP1001 2.1 46.0 1.0 O C:HOH1121 2.2 43.5 1.0 O C:HOH1119 2.2 42.9 1.0 O C:HOH1187 2.2 43.2 1.0 O C:HOH1130 2.2 41.9 1.0 PG C:GTP1001 3.0 43.2 1.0 PB C:GTP1001 3.2 45.1 1.0 O3B C:GTP1001 3.3 44.2 1.0 O2G C:GTP1001 3.5 43.1 1.0 O3A C:GTP1001 3.7 45.1 1.0 NZ D:LYS252 3.7 49.8 1.0 OE1 C:GLU71 3.7 66.9 1.0 OD1 C:ASP69 4.0 46.6 1.0 OD2 C:ASP69 4.3 46.4 1.0 CB C:GLN11 4.3 40.8 1.0 O3G C:GTP1001 4.4 42.1 1.0 N C:GLN11 4.4 38.7 1.0 OD2 C:ASP98 4.4 57.1 1.0 CB C:ASP98 4.5 50.9 1.0 O2B C:GTP1001 4.5 44.6 1.0 CG C:ASP69 4.6 46.4 1.0 O1A C:GTP1001 4.6 45.0 1.0 CG C:ASP98 4.7 54.4 1.0 CD C:GLU71 4.7 65.7 1.0 PA C:GTP1001 4.8 44.8 1.0 CE D:LYS252 4.9 48.2 1.0 OG1 C:THR145 4.9 43.0 1.0 CA C:GLN11 5.0 39.0 1.0

Magnesium binding site 4 out of 5 in the Structure of Tubulin Tyrosine Ligase in Complex with TB116


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Tubulin Tyrosine Ligase in Complex with TB116 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:64.7 occ:1.00 O D:HOH1105 2.2 64.3 1.0 O D:HOH1118 2.2 64.6 1.0 O D:HOH1114 2.2 65.0 1.0 O D:HOH1158 2.2 65.1 1.0 O1B D:GTP1001 2.3 73.4 1.0 O1G D:GTP1001 2.4 74.8 1.0 O2G D:GTP1001 2.9 75.3 1.0 PG D:GTP1001 3.0 75.0 1.0 PB D:GTP1001 3.3 73.2 1.0 O3B D:GTP1001 3.4 74.0 1.0 O3A D:GTP1001 3.9 72.2 1.0 CB D:GLN11 4.3 70.0 1.0 N D:GLN11 4.3 67.1 1.0 OE1 D:GLU69 4.4 88.5 1.0 OD1 D:ASP67 4.4 77.8 1.0 O1A D:GTP1001 4.4 71.8 1.0 O3G D:GTP1001 4.4 75.3 1.0 CB D:GLU69 4.5 80.8 1.0 OD2 D:ASP67 4.6 78.5 1.0 O2B D:GTP1001 4.6 73.4 1.0 PA D:GTP1001 4.8 71.5 1.0 O D:HOH1162 4.8 66.5 1.0 CG D:GLU69 4.9 84.0 1.0 CA D:GLN11 4.9 67.6 1.0 CG D:ASP67 5.0 77.4 1.0

Magnesium binding site 5 out of 5 in the Structure of Tubulin Tyrosine Ligase in Complex with TB116


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Tubulin Tyrosine Ligase in Complex with TB116 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1002 b:68.6 occ:1.00 O1G F:ACP1001 2.0 105.1 1.0 OE2 F:GLU331 2.2 82.5 1.0 O1B F:ACP1001 2.5 102.6 1.0 ND2 F:ASN333 2.9 79.9 1.0 CD F:GLU331 3.2 79.5 1.0 PG F:ACP1001 3.3 105.1 1.0 OE1 F:GLU331 3.6 81.0 1.0 PB F:ACP1001 3.6 102.7 1.0 NZ F:LYS74 3.8 82.0 1.0 C3B F:ACP1001 3.9 104.0 1.0 O2B F:ACP1001 4.2 102.8 1.0 CG F:ASN333 4.2 77.9 1.0 O2G F:ACP1001 4.2 105.4 1.0 O3G F:ACP1001 4.5 104.9 1.0 CG F:GLU331 4.5 71.1 1.0 CE F:LYS74 4.8 79.8 1.0 O F:HOH1101 4.9 57.7 1.0 OD1 F:ASN333 5.0 79.9 1.0 O3A F:ACP1001 5.0 101.1 1.0 CB F:ASN333 5.0 69.9 1.0

J.Gavrilyuk, B.Nocek, S.Rigol, K.C.Nicolaou, V.Stoll. Structure of Tubulin Tyrosine Ligase in Complex with TB116 To Be Published.