Magnesium in PDB 3tii: Tubulin Tyrosine Ligase

The structure of Tubulin Tyrosine Ligase, PDB code: 3tii was solved by A.Roll-Mecak, A.Szyk, A.Deaconescu, G.Piszczek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.38 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.416, 74.663, 117.328, 90.00, 90.11, 90.00
R / Rfree (%)	25.4 / 28.5

The binding sites of Magnesium atom in the Tubulin Tyrosine Ligase (pdb code 3tii). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Tubulin Tyrosine Ligase, PDB code: 3tii:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Tubulin Tyrosine Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin Tyrosine Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg381 b:32.0 occ:1.00 OH A:TYR14 2.7 45.0 1.0 N A:LEU314 2.8 26.5 1.0 O A:ASN63 2.9 32.5 1.0 CZ A:TYR14 3.5 53.3 1.0 CB A:LEU314 3.5 41.5 1.0 CE2 A:TYR14 3.5 44.4 1.0 CG A:GLN313 3.6 35.4 1.0 CA A:GLN313 3.6 21.5 1.0 CA A:LEU314 3.7 36.3 1.0 C A:GLN313 3.7 29.7 1.0 O A:LEU314 4.0 32.8 1.0 C A:ASN63 4.0 38.0 1.0 CB A:GLN313 4.2 20.0 1.0 CB A:ASN63 4.3 31.9 1.0 C A:LEU314 4.3 38.2 1.0 CE1 A:TYR64 4.6 37.4 1.0 CZ A:TYR64 4.6 45.1 1.0 CE1 A:PHE312 4.6 30.2 1.0 O A:GLY334 4.6 39.0 1.0 ND2 A:ASN63 4.6 25.4 1.0 CG A:ASN63 4.7 39.7 1.0 CA A:ASN63 4.7 35.6 1.0 CE1 A:TYR14 4.7 58.3 1.0 O A:PHE312 4.7 33.7 1.0 CD A:GLN313 4.8 29.8 1.0 N A:GLN313 4.8 36.1 1.0 CD1 A:TYR64 4.8 27.7 1.0 CE2 A:TYR64 4.8 40.9 1.0 CD2 A:TYR14 4.8 50.9 1.0 O A:GLN313 4.9 27.6 1.0 CD1 A:PHE312 4.9 27.2 1.0 CG A:LEU314 4.9 40.3 1.0 OH A:TYR64 4.9 59.5 1.0

Magnesium binding site 2 out of 7 in the Tubulin Tyrosine Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin Tyrosine Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg382 b:39.2 occ:1.00 N A:ARG66 2.6 44.4 1.0 O A:HOH394 2.7 39.2 1.0 OH A:TYR309 2.7 48.1 1.0 CB A:ARG66 3.1 46.8 1.0 CA A:ARG66 3.4 38.0 1.0 C A:TYR65 3.5 44.9 1.0 OG A:SER311 3.6 47.6 1.0 CZ A:TYR309 3.6 41.5 1.0 CE1 A:TYR309 3.6 45.0 1.0 CA A:TYR65 3.6 31.7 1.0 O A:TYR64 3.9 23.8 1.0 CG2 A:THR304 3.9 51.0 1.0 CB A:SER311 4.0 34.2 1.0 CE1 A:PHE49 4.2 49.7 1.0 O A:ARG66 4.2 35.2 1.0 CD1 A:PHE49 4.3 44.6 1.0 C A:ARG66 4.3 37.2 1.0 CD1 A:TYR65 4.4 26.8 1.0 CD2 A:LEU307 4.6 54.1 1.0 CG A:ARG66 4.6 52.7 1.0 CB A:TYR65 4.6 32.4 1.0 N A:TYR65 4.7 33.3 1.0 O A:TYR65 4.7 38.8 1.0 C A:TYR64 4.7 33.8 1.0 O A:ILE302 4.8 43.6 1.0 CG A:TYR65 4.8 30.4 1.0 CE2 A:TYR309 4.9 50.8 1.0 CZ A:PHE49 4.9 46.0 1.0 CD1 A:TYR309 4.9 42.5 1.0

Magnesium binding site 3 out of 7 in the Tubulin Tyrosine Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin Tyrosine Ligase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg383 b:49.3 occ:1.00 O2B A:ANP700 1.9 0.5 1.0 O3G A:ANP700 2.1 0.2 1.0 O2A A:ANP700 2.2 99.5 1.0 PB A:ANP700 2.7 0.1 1.0 OE1 A:GLU331 3.0 97.5 1.0 O3A A:ANP700 3.1 0.1 1.0 N3B A:ANP700 3.1 0.4 1.0 PG A:ANP700 3.1 0.2 1.0 PA A:ANP700 3.2 99.6 1.0 CD A:GLU331 3.9 89.8 1.0 NH2 A:ARG222 4.0 0.5 1.0 O2G A:ANP700 4.1 0.4 1.0 O1A A:ANP700 4.1 98.1 1.0 O1B A:ANP700 4.1 0.6 1.0 OE2 A:GLU331 4.1 89.7 1.0 O1G A:ANP700 4.2 0.7 1.0 O5' A:ANP700 4.5 96.9 1.0 C5' A:ANP700 4.7 89.8 1.0 NH1 A:ARG222 4.9 98.7 1.0 CZ A:ARG222 4.9 0.1 1.0

Magnesium binding site 4 out of 7 in the Tubulin Tyrosine Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin Tyrosine Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg381 b:35.1 occ:1.00 OH B:TYR14 2.7 33.6 1.0 O B:ASN63 2.7 28.2 1.0 N B:LEU314 3.0 30.2 1.0 CZ B:TYR14 3.4 35.9 1.0 CE2 B:TYR14 3.5 22.2 1.0 CG B:GLN313 3.5 32.0 1.0 CA B:GLN313 3.6 27.6 1.0 CB B:LEU314 3.8 22.6 1.0 C B:GLN313 3.8 32.3 1.0 C B:ASN63 3.8 32.7 1.0 CA B:LEU314 3.9 27.9 1.0 CB B:ASN63 4.1 33.2 1.0 CB B:GLN313 4.1 24.9 1.0 O B:LEU314 4.1 24.3 1.0 ND2 B:ASN63 4.2 20.4 1.0 CG B:ASN63 4.3 34.0 1.0 CZ B:TYR64 4.4 37.3 1.0 CE1 B:TYR64 4.5 34.8 1.0 CA B:ASN63 4.5 28.6 1.0 C B:LEU314 4.5 31.2 1.0 CE1 B:PHE312 4.5 22.3 1.0 CE1 B:TYR14 4.6 23.4 1.0 O B:PHE312 4.6 26.3 1.0 CE2 B:TYR64 4.6 24.6 1.0 CD1 B:TYR64 4.6 17.9 1.0 O B:GLY334 4.7 49.0 1.0 CD B:GLN313 4.7 25.3 1.0 CD2 B:TYR14 4.7 19.5 1.0 N B:GLN313 4.7 32.2 1.0 CD2 B:TYR64 4.8 37.3 1.0 OH B:TYR64 4.8 46.6 1.0 CG B:TYR64 4.8 36.4 1.0 CD1 B:PHE312 4.9 20.7 1.0 N B:TYR64 4.9 30.0 1.0

Magnesium binding site 5 out of 7 in the Tubulin Tyrosine Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin Tyrosine Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg382 b:36.6 occ:1.00 N B:ARG66 2.6 41.5 1.0 OH B:TYR309 2.8 40.4 1.0 OG B:SER311 3.1 37.7 1.0 CB B:ARG66 3.3 28.8 1.0 C B:TYR65 3.5 38.1 1.0 CA B:TYR65 3.5 23.2 1.0 CE1 B:TYR309 3.5 29.9 1.0 CA B:ARG66 3.5 34.5 1.0 CZ B:TYR309 3.6 34.6 1.0 O B:TYR64 3.7 20.9 1.0 CB B:SER311 3.8 32.8 1.0 CE1 B:PHE49 3.9 35.8 1.0 CG2 B:THR304 4.0 43.6 1.0 CD1 B:PHE49 4.1 32.4 1.0 O B:ARG66 4.4 50.5 1.0 CD1 B:LEU307 4.4 43.5 1.0 CB B:TYR65 4.5 27.2 1.0 C B:ARG66 4.5 45.4 1.0 N B:TYR65 4.5 24.7 1.0 CD1 B:TYR65 4.5 26.5 1.0 C B:TYR64 4.5 32.9 1.0 O B:TYR65 4.7 37.5 1.0 CZ B:PHE49 4.7 29.9 1.0 CG B:TYR65 4.8 27.3 1.0 O B:ILE302 4.8 47.5 1.0 CD1 B:TYR309 4.8 29.8 1.0 CG B:ARG66 4.8 44.9 1.0 CE2 B:TYR309 5.0 34.4 1.0

Magnesium binding site 6 out of 7 in the Tubulin Tyrosine Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tubulin Tyrosine Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg383 b:68.9 occ:1.00 O2B B:ANP710 2.2 0.8 1.0 OE1 B:GLU331 2.3 87.8 1.0 O2G B:ANP710 2.7 0.7 1.0 O2A B:ANP710 2.8 0.2 1.0 PB B:ANP710 3.0 0.7 1.0 N3B B:ANP710 3.0 0.5 1.0 CD B:GLU331 3.2 68.7 1.0 O3A B:ANP710 3.4 1.0 1.0 PG B:ANP710 3.4 0.8 1.0 OE2 B:GLU331 3.5 64.6 1.0 NZ B:LYS74 3.5 78.9 1.0 PA B:ANP710 3.6 0.3 1.0 O1A B:ANP710 4.0 98.5 1.0 O1B B:ANP710 4.4 0.8 1.0 O1G B:ANP710 4.4 0.6 1.0 O3G B:ANP710 4.5 0.4 1.0 CG B:GLU331 4.5 53.2 1.0 CE B:LYS74 4.5 78.9 1.0

Magnesium binding site 7 out of 7 in the Tubulin Tyrosine Ligase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tubulin Tyrosine Ligase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg384 b:39.0 occ:1.00 OD2 B:ASP8 2.5 51.1 1.0 OH B:TYR64 2.6 46.6 1.0 O B:HOH388 2.7 33.3 1.0 CG B:ASP8 3.3 46.7 1.0 O B:GLY42 3.5 45.0 1.0 CZ B:TYR64 3.6 37.3 1.0 CB B:ASP8 3.7 48.2 1.0 CE2 B:TYR64 3.7 24.6 1.0 CB B:SER11 3.8 30.2 1.0 OG B:SER11 3.9 27.2 1.0 CG B:ARG44 4.1 67.2 1.0 CD2 B:TYR14 4.3 19.5 1.0 OD1 B:ASP8 4.3 49.6 1.0 NH1 B:ARG44 4.5 74.6 1.0 N B:ARG44 4.5 55.1 1.0 ND2 B:ASN63 4.6 20.4 1.0 CA B:ARG44 4.7 63.0 1.0 C B:GLY42 4.8 38.9 1.0 CZ B:ARG44 4.8 77.9 1.0 CE2 B:TYR14 4.8 22.2 1.0 C B:GLU43 4.8 53.0 1.0 CB B:ALA335 4.9 34.5 1.0 CE1 B:TYR64 4.9 34.8 1.0

A.Szyk, A.M.Deaconescu, G.Piszczek, A.Roll-Mecak. Tubulin Tyrosine Ligase Structure Reveals Adaptation of An Ancient Fold to Bind and Modify Tubulin. Nat.Struct.Mol.Biol. V. 18 1250 2011.
ISSN: ISSN 1545-9993
PubMed: 22020298
DOI: 10.1038/NSMB.2148