Magnesium in PDB 3tin: Tubulin Tyrosine Ligase

The structure of Tubulin Tyrosine Ligase, PDB code: 3tin 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)	29.24 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.970, 75.720, 44.230, 90.00, 90.83, 90.00
R / Rfree (%)	23.2 / 31.3

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

Magnesium binding site 1 out of 3 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:Mg602 b:46.5 occ:1.00 O A:ASN63 2.4 46.5 1.0 OH A:TYR14 2.8 45.9 1.0 N A:LEU314 3.4 36.3 1.0 CZ A:TYR14 3.5 37.1 1.0 CE2 A:TYR14 3.5 30.7 1.0 C A:ASN63 3.6 41.1 1.0 CA A:GLN313 3.6 30.8 1.0 CB A:ASN63 3.7 31.0 1.0 ND2 A:ASN63 3.8 41.0 1.0 C A:GLN313 3.9 39.6 1.0 CG A:GLN313 4.0 24.0 1.0 CG A:ASN63 4.1 39.0 1.0 CB A:GLN313 4.2 19.4 1.0 CA A:ASN63 4.2 41.7 1.0 CB A:LEU314 4.2 35.2 1.0 CE1 A:TYR64 4.3 47.5 1.0 CZ A:TYR64 4.3 47.0 1.0 CA A:LEU314 4.4 27.9 1.0 CE1 A:PHE312 4.5 27.0 1.0 O A:LEU314 4.5 31.7 1.0 CD1 A:TYR64 4.5 43.4 1.0 CE2 A:TYR64 4.5 42.2 1.0 O A:PHE312 4.5 30.9 1.0 O A:GLY334 4.5 43.7 1.0 CE1 A:TYR14 4.6 23.6 1.0 N A:GLN313 4.6 25.7 1.0 N A:TYR64 4.7 43.1 1.0 CD2 A:TYR14 4.7 24.9 1.0 OH A:TYR64 4.7 48.5 1.0 CG A:TYR64 4.7 42.1 1.0 CD2 A:TYR64 4.7 42.6 1.0 CD1 A:PHE312 4.7 33.1 1.0 CD A:GLN313 4.9 27.5 1.0 C A:LEU314 4.9 27.0 1.0 CA A:TYR64 5.0 40.1 1.0 C A:PHE312 5.0 28.6 1.0

Magnesium binding site 2 out of 3 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:Mg603 b:44.2 occ:1.00 N A:ARG66 2.8 42.0 1.0 OH A:TYR309 2.8 37.8 1.0 OG A:SER311 3.1 38.5 1.0 CE1 A:TYR309 3.4 31.8 1.0 CG2 A:THR304 3.4 59.2 1.0 CA A:TYR65 3.5 36.6 1.0 CB A:SER311 3.5 28.2 1.0 CZ A:TYR309 3.5 25.2 1.0 O A:TYR64 3.5 46.7 1.0 C A:TYR65 3.6 35.2 1.0 CB A:ARG66 3.7 56.5 1.0 CA A:ARG66 3.8 51.8 1.0 CE1 A:PHE49 3.9 29.8 1.0 CD1 A:PHE49 4.3 39.0 1.0 CD1 A:TYR65 4.3 34.1 1.0 C A:TYR64 4.4 38.5 1.0 N A:TYR65 4.4 42.7 1.0 CB A:TYR65 4.5 32.2 1.0 CZ A:PHE49 4.5 27.4 1.0 CG1 A:VAL62 4.7 33.9 1.0 CG A:TYR65 4.7 40.4 1.0 CD1 A:TYR309 4.7 40.6 1.0 O A:ARG66 4.7 45.9 1.0 O A:TYR65 4.8 32.0 1.0 C A:ARG66 4.8 51.2 1.0 CE2 A:TYR309 4.9 23.7 1.0 CB A:THR304 4.9 59.8 1.0 CD1 A:LEU307 4.9 42.8 1.0 O A:ILE302 5.0 62.7 1.0

Magnesium binding site 3 out of 3 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:Mg604 b:56.0 occ:1.00 ND2 A:ASN209 3.6 59.3 1.0 O A:SER357 4.1 53.9 1.0 CG2 A:VAL358 4.4 31.0 1.0 CA A:VAL358 4.5 43.8 1.0 CE1 A:HIS310 4.8 40.6 1.0 CG A:ASN209 4.8 55.8 1.0 NE2 A:HIS310 4.8 52.8 1.0 C A:SER357 4.9 56.8 1.0 CB A:VAL358 4.9 42.0 1.0 NE2 A:GLN210 5.0 88.4 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