Magnesium in PDB 2x6u: Crystal Structure of Human TBX5 in the Dna-Free Form

The structure of Crystal Structure of Human TBX5 in the Dna-Free Form, PDB code: 2x6u was solved by C.U.Stirnimann, C.W.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.662 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	36.710, 69.850, 80.500, 90.00, 90.00, 90.00
R / Rfree (%)	21.05 / 26.43

The binding sites of Magnesium atom in the Crystal Structure of Human TBX5 in the Dna-Free Form (pdb code 2x6u). 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 Human TBX5 in the Dna-Free Form, PDB code: 2x6u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of Human TBX5 in the Dna-Free Form


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 Human TBX5 in the Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1232 b:22.0 occ:1.00 N A:LYS78 3.4 22.9 1.0 OD1 A:ASN162 3.5 29.2 1.0 ND2 A:ASN162 3.9 16.7 1.0 CB A:LYS78 3.9 25.9 1.0 CG A:ASN162 4.1 25.8 1.0 CA A:THR77 4.2 27.1 1.0 CA A:LYS78 4.2 25.2 1.0 C A:THR77 4.2 26.0 1.0 O A:HOH2017 4.2 36.3 1.0 CB A:THR77 4.7 23.3 1.0 O A:HOH2020 4.9 31.9 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of Human TBX5 in the Dna-Free Form


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 Human TBX5 in the Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1233 b:20.2 occ:1.00 O A:HOH2059 3.0 30.0 1.0 CD2 A:HIS112 3.1 20.7 1.0 O A:GLY125 3.7 20.3 1.0 NE2 A:HIS112 3.7 28.9 1.0 CA A:LYS126 3.8 23.4 1.0 C A:GLY125 3.9 25.6 1.0 N A:LYS126 3.9 20.2 1.0 O A:ASP111 4.2 22.9 1.0 CB A:LYS126 4.2 23.2 1.0 CG A:HIS112 4.3 24.4 1.0 CG1 A:VAL123 4.7 23.4 1.0 CA A:GLY125 4.7 25.4 1.0 CG A:LYS126 4.9 33.1 1.0 CA A:HIS112 4.9 15.4 1.0 CB A:HIS112 5.0 21.3 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of Human TBX5 in the Dna-Free Form


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 Human TBX5 in the Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1234 b:32.4 occ:1.00 N A:ARG82 3.2 24.2 1.0 CD A:ARG81 3.5 29.3 0.5 CD A:ARG81 3.6 29.8 0.5 CG A:ARG82 3.6 25.0 1.0 CB A:ARG82 3.8 25.0 1.0 CA A:ARG81 3.9 24.2 0.5 CA A:ARG81 3.9 24.2 0.5 C A:ARG81 4.0 24.8 1.0 CA A:ARG82 4.1 23.9 1.0 CD A:ARG82 4.3 33.2 1.0 CG A:ARG81 4.3 30.3 0.5 O A:GLY80 4.4 28.9 1.0 NE A:ARG81 4.4 35.7 0.5 CG A:ARG81 4.5 30.2 0.5 CE A:LYS159 4.5 35.1 1.0 CB A:ARG81 4.6 26.5 0.5 CB A:ARG81 4.6 26.5 0.5 NE A:ARG81 4.7 36.5 0.5 NH1 A:ARG81 4.8 36.5 0.5 NE A:ARG82 4.9 45.0 1.0 O A:HOH2024 4.9 38.6 1.0 N A:ARG81 4.9 23.9 1.0 O A:HOH2025 5.0 34.0 1.0 O A:ARG82 5.0 22.9 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of Human TBX5 in the Dna-Free Form


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 Human TBX5 in the Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1235 b:42.6 occ:0.70 MG A:MG1235 0.0 42.6 0.7 MG A:MG1235 2.6 28.6 0.3 CD1 A:TRP121 4.0 22.1 1.0 CD1 A:ILE212 4.1 26.3 1.0 CA A:GLY71 4.1 26.5 1.0 NZ A:LYS178 4.1 39.8 1.0 CG A:TRP121 4.4 22.7 1.0 CG1 A:ILE212 4.4 22.8 1.0 CE A:LYS178 4.5 33.0 1.0 NE1 A:TRP121 4.5 21.9 1.0 CB A:TRP121 4.7 21.9 1.0 C A:GLY71 4.7 27.3 1.0 O A:HOH2136 4.8 27.7 1.0 CD A:LYS178 5.0 24.0 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of Human TBX5 in the Dna-Free Form


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 Human TBX5 in the Dna-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1235 b:28.6 occ:0.30 MG A:MG1235 0.0 28.6 0.3 MG A:MG1235 2.6 42.6 0.7 NZ A:LYS178 3.9 39.8 1.0 CB A:TRP121 3.9 21.9 1.0 CE2 A:TYR114 4.1 22.6 1.0 CD1 A:ILE212 4.4 26.3 1.0 CG A:TRP121 4.4 22.7 1.0 CZ A:TYR114 4.6 22.3 1.0 CD2 A:TYR114 4.6 19.0 1.0 CE A:LYS178 4.6 33.0 1.0 CD A:LYS178 4.6 24.0 1.0 OH A:TYR114 4.7 27.3 1.0 CD1 A:TRP121 4.7 22.1 1.0 O A:HOH2073 4.9 46.6 1.0

C.U.Stirnimann, D.Ptchelkine, C.Grimm, C.W.Muller. Structural Basis of TBX5-Dna Recognition: the T- Box Domain in Its Dna-Bound and -Unbound Form. J.Mol.Biol. V. 400 71 2010.
ISSN: ISSN 0022-2836
PubMed: 20450920
DOI: 10.1016/J.JMB.2010.04.052