Magnesium in PDB 6y4m: Structure of Tubulin Tyrosine Ligase in Complex with TB111

The structure of Structure of Tubulin Tyrosine Ligase in Complex with TB111, PDB code: 6y4m 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)	29.90 / 3.34
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	103.961, 152.59, 185.989, 90, 90, 90
R / Rfree (%)	20.7 / 23.4

The structure of Structure of Tubulin Tyrosine Ligase in Complex with TB111 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 TB111 (pdb code 6y4m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Tubulin Tyrosine Ligase in Complex with TB111, PDB code: 6y4m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Tubulin Tyrosine Ligase in Complex with TB111


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 TB111 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:47.4 occ:1.00 O1B A:GTP1001 1.9 55.0 1.0 O1G A:GTP1001 2.0 57.0 1.0 O A:HOH1105 2.2 46.2 1.0 O A:HOH1101 2.2 48.9 1.0 O A:HOH1103 2.2 49.2 1.0 O A:HOH1102 2.2 48.3 1.0 PB A:GTP1001 3.1 54.1 1.0 PG A:GTP1001 3.1 56.3 1.0 O3B A:GTP1001 3.3 54.6 1.0 O2G A:GTP1001 3.6 57.5 1.0 O3A A:GTP1001 3.8 54.6 1.0 OD1 A:ASP69 3.9 68.9 1.0 OE1 A:GLU71 3.9 77.3 1.0 NZ B:LYS252 4.0 66.3 1.0 OD2 A:ASP69 4.3 69.7 1.0 O2B A:GTP1001 4.4 55.2 1.0 CB A:GLN11 4.4 61.7 1.0 O3G A:GTP1001 4.4 54.9 1.0 OD2 A:ASP98 4.4 71.6 1.0 CB A:ASP98 4.4 70.6 1.0 N A:GLN11 4.4 62.3 1.0 CG A:ASP69 4.5 69.9 1.0 O1A A:GTP1001 4.6 54.4 1.0 CG A:ASP98 4.8 71.5 1.0 PA A:GTP1001 4.8 54.2 1.0 CB A:GLU71 4.8 79.7 1.0 CD A:GLU71 4.8 79.2 1.0 OG1 A:THR145 4.9 63.4 1.0 OE1 A:GLN11 5.0 63.8 1.0

Magnesium binding site 2 out of 4 in the Structure of Tubulin Tyrosine Ligase in Complex with TB111


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 TB111 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:34.5 occ:1.00 O B:HOH1109 2.6 33.1 1.0 O C:HOH1106 2.8 43.3 1.0 OE1 B:GLN11 3.4 61.6 1.0 O1B B:GDP1001 3.6 55.7 1.0 O1A B:GDP1001 3.6 53.8 1.0 CB B:GLN11 4.0 58.0 1.0 CD B:GLN11 4.2 60.3 1.0 O3A B:GDP1001 4.3 52.9 1.0 PB B:GDP1001 4.4 54.6 1.0 O3B B:GDP1001 4.4 55.1 1.0 OE2 B:GLU69 4.4 68.7 1.0 PA B:GDP1001 4.6 51.7 1.0 CG B:GLN11 4.7 59.4 1.0 ND2 B:ASN99 5.0 50.1 1.0 NE2 B:GLN11 5.0 60.8 1.0

Magnesium binding site 3 out of 4 in the Structure of Tubulin Tyrosine Ligase in Complex with TB111


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 TB111 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:51.7 occ:1.00 O1G C:GTP1001 2.0 54.1 1.0 O C:HOH1105 2.2 51.9 1.0 O C:HOH1103 2.2 54.2 1.0 O C:HOH1101 2.2 52.9 1.0 O C:HOH1102 2.2 52.2 1.0 O1B C:GTP1001 2.2 56.9 1.0 PG C:GTP1001 3.1 54.2 1.0 PB C:GTP1001 3.3 56.0 1.0 O3B C:GTP1001 3.4 54.7 1.0 O2G C:GTP1001 3.6 54.8 1.0 OE1 C:GLU71 3.7 67.1 1.0 OD1 C:ASP69 3.8 54.9 1.0 O3A C:GTP1001 3.9 56.3 1.0 NZ D:LYS252 4.1 69.8 1.0 OD2 C:ASP69 4.2 56.7 1.0 CB C:GLN11 4.3 60.8 1.0 N C:GLN11 4.4 59.6 1.0 O3G C:GTP1001 4.4 54.0 1.0 CG C:ASP69 4.5 56.4 1.0 OD2 C:ASP98 4.5 62.5 1.0 CB C:ASP98 4.5 61.2 1.0 O1A C:GTP1001 4.6 56.9 1.0 O2B C:GTP1001 4.6 55.2 1.0 CD C:GLU71 4.7 68.1 1.0 CB C:GLU71 4.7 66.8 1.0 PA C:GTP1001 4.8 56.0 1.0 CG C:ASP98 4.9 61.9 1.0 OE1 C:GLN11 4.9 64.0 1.0 CA C:GLN11 4.9 59.3 1.0 OG1 C:THR145 4.9 61.5 1.0

Magnesium binding site 4 out of 4 in the Structure of Tubulin Tyrosine Ligase in Complex with TB111


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 TB111 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:96.0 occ:1.00 O D:HOH1101 2.2 95.8 1.0 O D:HOH1103 2.2 101.0 1.0 O D:HOH1104 2.2 97.0 1.0 O D:HOH1105 2.2 97.7 1.0 O1B D:GTP1001 2.6 102.9 1.0 O1G D:GTP1001 2.8 105.1 1.0 O2G D:GTP1001 3.5 104.8 1.0 PG D:GTP1001 3.6 103.8 1.0 PB D:GTP1001 3.7 101.7 1.0 CB D:GLN11 3.7 100.4 1.0 O3B D:GTP1001 3.9 101.7 1.0 N D:GLN11 3.9 96.3 1.0 O3A D:GTP1001 4.1 103.2 1.0 OD2 D:ASP67 4.2 104.7 1.0 OD1 D:ASP67 4.3 104.1 1.0 OE1 D:GLN11 4.4 106.7 1.0 CA D:GLN11 4.4 98.0 1.0 OE1 D:GLU69 4.4 118.7 1.0 CB D:GLU69 4.5 114.5 1.0 O1A D:GTP1001 4.7 105.6 1.0 CG D:ASP67 4.7 103.8 1.0 C D:GLY10 4.9 93.7 1.0 PA D:GTP1001 4.9 102.8 1.0 CG D:GLN11 4.9 101.8 1.0 CG D:GLU69 4.9 118.2 1.0 CD D:GLN11 5.0 104.4 1.0 O3G D:GTP1001 5.0 104.2 1.0

J.Gavrilyuk, B.Nocek, S.Rigol, K.C.Nicolaou, V.Stoll. Structure of Tubulin Tyrosine Ligase in Complex with TB111 To Be Published.