Magnesium in PDB 2xd4: Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase

All present enzymatic activity of Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase:
6.3.4.13;

The structure of Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase, PDB code: 2xd4 was solved by J.A.Bertrand, S.Chen, H.Zalkin, J.L.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.22 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.990, 84.410, 85.720, 90.00, 90.00, 90.00
R / Rfree (%)	24.3 / 28.7

The binding sites of Magnesium atom in the Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase (pdb code 2xd4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase, PDB code: 2xd4:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg451 b:40.3 occ:1.00 O A:HOH2070 2.1 21.9 1.0 OE1 A:GLU283 2.1 34.6 1.0 OD1 A:ASN285 2.2 26.2 1.0 O3B A:ADP461 2.5 47.3 1.0 OE2 A:GLU283 2.7 36.3 1.0 CD A:GLU283 2.7 35.4 1.0 CG A:ASN285 3.2 28.8 1.0 ND2 A:ASN285 3.7 29.5 1.0 PB A:ADP461 3.8 48.7 1.0 OE2 A:GLU100 4.0 28.1 1.0 O2B A:ADP461 4.1 47.5 1.0 NZ A:LYS103 4.1 27.6 1.0 NH2 A:ARG287 4.1 27.4 1.0 CG A:GLU283 4.2 30.8 1.0 O A:PHE284 4.4 25.1 1.0 O3A A:ADP461 4.4 42.6 1.0 MG A:MG453 4.5 44.8 1.0 CD A:GLU100 4.5 25.3 1.0 CG A:GLU100 4.5 23.8 1.0 CB A:ASN285 4.5 26.9 1.0 O1B A:ADP461 4.8 50.7 1.0 CB A:GLU283 4.9 31.3 1.0 CA A:ASN285 4.9 25.2 1.0

Magnesium binding site 2 out of 3 in the Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg452 b:29.4 occ:1.00 NE2 A:GLN306 3.9 23.4 1.0 CD A:GLN306 4.3 23.9 1.0 OD2 A:ASP310 4.6 27.5 1.0 OE1 A:GLN306 4.7 23.5 1.0 OD1 A:ASP310 4.7 24.8 1.0

Magnesium binding site 3 out of 3 in the Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg453 b:44.8 occ:1.00 OE2 A:GLU283 2.5 36.3 1.0 O2B A:ADP461 2.5 47.5 1.0 O2A A:ADP461 2.8 36.9 1.0 CE A:LYS214 3.2 71.5 1.0 NZ A:LYS214 3.5 70.9 1.0 CD A:GLU283 3.7 35.4 1.0 PB A:ADP461 3.7 48.7 1.0 O3' A:ADP461 3.8 34.3 1.0 PA A:ADP461 3.9 38.9 1.0 O A:HOH2053 4.0 27.1 1.0 O3A A:ADP461 4.1 42.6 1.0 O3B A:ADP461 4.1 47.3 1.0 C5' A:ADP461 4.4 38.0 1.0 CG A:GLU283 4.4 30.8 1.0 MG A:MG451 4.5 40.3 1.0 OE1 A:GLU283 4.6 34.6 1.0 C3' A:ADP461 4.6 34.9 1.0 O5' A:ADP461 4.6 38.5 1.0 CD A:LYS214 4.6 71.2 1.0 OH A:TYR269 4.6 32.4 1.0 ND2 A:ASN285 4.7 29.5 1.0 O1B A:ADP461 4.9 50.7 1.0 C4' A:ADP461 5.0 35.0 1.0

J.A.Bertrand, S.Chen, H.Zalkin, J.L.Smith. Nucleotide-Bound Structures of Bacillus Subtilis Glycinamide Ribonucleotide Synthetase To Be Published.