Magnesium in PDB 5bqd: Crystal Structure of TBX5 (1-239) Dimer

The structure of Crystal Structure of TBX5 (1-239) Dimer, PDB code: 5bqd was solved by L.Pradhan, S.Gopal, A.Patel, H.Kasahara, H.J.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.03 / 2.58
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.455, 81.455, 341.022, 90.00, 90.00, 120.00
R / Rfree (%)	24.6 / 28.9

The binding sites of Magnesium atom in the Crystal Structure of TBX5 (1-239) Dimer (pdb code 5bqd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of TBX5 (1-239) Dimer, PDB code: 5bqd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of TBX5 (1-239) Dimer


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 TBX5 (1-239) Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:67.3 occ:1.00 NH2 B:ARG81 3.0 58.0 1.0 CD1 B:ILE75 3.4 56.8 1.0 NH1 B:ARG81 3.5 55.1 1.0 CZ B:ARG81 3.7 57.2 1.0 CG2 B:ILE75 4.0 54.7 1.0 CG1 B:ILE75 4.5 59.5 1.0 CB B:ILE75 4.7 57.1 1.0 O B:THR215 4.8 65.6 1.0 CB B:SER216 4.9 58.7 1.0 CA B:SER216 5.0 60.9 1.0 NE B:ARG81 5.0 59.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of TBX5 (1-239) Dimer


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 TBX5 (1-239) Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:66.2 occ:1.00 CD B:ARG81 3.7 56.6 1.0 NH1 B:ARG82 3.8 85.9 1.0 N B:ARG82 4.0 60.5 1.0 CG B:ARG82 4.2 67.6 1.0 CB B:ARG82 4.5 61.1 1.0 NE B:ARG81 4.5 59.9 1.0 CA B:ARG81 4.6 59.4 1.0 CD B:ARG82 4.8 71.0 1.0 C B:ARG81 4.9 59.8 1.0 CB B:ARG81 4.9 56.0 1.0 CG B:ARG81 4.9 60.3 1.0 CA B:ARG82 4.9 58.9 1.0 CZ B:ARG82 5.0 87.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of TBX5 (1-239) Dimer


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 TBX5 (1-239) Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:51.3 occ:1.00 OG1 B:THR77 3.6 62.0 1.0 NE B:ARG81 3.6 59.9 1.0 CG2 B:THR77 3.9 61.4 1.0 CB B:THR77 4.0 62.5 1.0 NH2 B:ARG81 4.1 58.0 1.0 CZ B:ARG81 4.3 57.2 1.0 CB B:ALA79 4.5 43.4 1.0 CD B:ARG81 4.5 56.6 1.0

L.Pradhan, S.Gopal, S.Li, S.Ashur, S.Suryanarayanan, H.Kasahara, H.J.Nam. Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5. Biochemistry V. 55 1702 2016.
ISSN: ISSN 0006-2960
PubMed: 26926761
DOI: 10.1021/ACS.BIOCHEM.6B00171