Magnesium in PDB 1b6s: Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase

All present enzymatic activity of Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase:
4.1.1.21;

The structure of Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase, PDB code: 1b6s was solved by J.B.Thoden, T.J.Kappock, J.Stubbe, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	60.600, 92.100, 102.600, 66.10, 82.70, 81.80
R / Rfree (%)	18.5 / n/a

The binding sites of Magnesium atom in the Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase (pdb code 1b6s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase, PDB code: 1b6s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1101 b:39.1 occ:1.00 O3' A:ADP1100 2.8 26.7 1.0 OE1 A:GLU226 3.0 41.9 1.0 O3A A:ADP1100 3.0 89.8 1.0 C5' A:ADP1100 3.2 29.5 1.0 NE2 A:HIS184 3.2 23.0 1.0 O3B A:ADP1100 3.4 63.9 1.0 CD A:GLU226 3.5 26.9 1.0 OE2 A:GLU226 3.5 54.5 1.0 OE1 A:GLU238 3.6 31.3 1.0 CE1 A:HIS184 3.7 32.1 1.0 PA A:ADP1100 3.8 38.2 1.0 C3' A:ADP1100 3.8 0.0 1.0 O5' A:ADP1100 3.8 90.0 1.0 CD2 A:HIS184 3.9 61.1 1.0 C4' A:ADP1100 3.9 55.8 1.0 PB A:ADP1100 4.0 0.0 1.0 O2A A:ADP1100 4.0 46.8 1.0 ND2 A:ASN237 4.1 35.5 1.0 O A:HOH2155 4.4 30.6 1.0 ND1 A:HIS184 4.5 25.5 1.0 CG A:HIS184 4.6 41.9 1.0 CG A:GLU226 4.8 67.7 1.0 O1B A:ADP1100 4.8 0.0 1.0 O A:HOH2156 4.8 23.9 1.0 CD A:GLU238 4.9 0.0 1.0 OE1 A:GLU161 4.9 45.4 1.0 O A:HOH2069 5.0 23.9 1.0

Magnesium binding site 2 out of 4 in the Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1201 b:38.8 occ:1.00 OE1 B:GLU238 2.4 18.9 1.0 O3A B:ADP1200 2.6 48.2 1.0 OE2 B:GLU226 2.6 79.8 1.0 OE1 B:GLU226 2.8 49.8 1.0 O3B B:ADP1200 2.9 82.4 1.0 CD B:GLU226 3.0 9.6 1.0 PB B:ADP1200 3.2 81.6 1.0 CD B:GLU238 3.6 57.8 1.0 O2B B:ADP1200 3.7 47.3 1.0 PA B:ADP1200 3.7 77.1 1.0 O2A B:ADP1200 3.7 52.3 1.0 C5' B:ADP1200 4.3 25.1 1.0 OE2 B:GLU238 4.3 54.1 1.0 ND2 B:ASN237 4.3 31.3 1.0 NE2 B:HIS184 4.5 36.0 1.0 CG B:GLU226 4.5 8.8 1.0 O5' B:ADP1200 4.5 0.0 1.0 CG B:GLU238 4.6 12.7 1.0 O1B B:ADP1200 4.6 36.0 1.0 O3' B:ADP1200 4.7 40.4 1.0 CB B:GLU238 4.7 4.0 1.0 O1A B:ADP1200 4.9 32.2 1.0

Magnesium binding site 3 out of 4 in the Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1301 b:33.8 occ:1.00 OE1 C:GLU238 2.3 29.3 1.0 OE1 C:GLU226 2.4 25.5 1.0 O3A C:ADP1300 2.6 0.0 1.0 O3B C:ADP1300 2.7 54.0 1.0 OE2 C:GLU226 3.1 56.0 1.0 PB C:ADP1300 3.1 0.0 1.0 CD C:GLU226 3.1 27.0 1.0 O C:HOH2345 3.4 25.3 1.0 CD C:GLU238 3.4 51.9 1.0 O2B C:ADP1300 3.5 74.8 1.0 O2A C:ADP1300 3.7 91.3 1.0 PA C:ADP1300 3.7 30.9 1.0 OE2 C:GLU238 3.8 31.5 1.0 C5' C:ADP1300 4.4 29.1 1.0 NE2 C:HIS184 4.4 14.8 1.0 O1B C:ADP1300 4.5 84.6 1.0 CG C:GLU226 4.5 37.8 1.0 O5' C:ADP1300 4.6 45.7 1.0 CG C:GLU238 4.6 24.3 1.0 CB C:GLU238 4.8 63.4 1.0 O3' C:ADP1300 4.8 19.6 1.0 ND2 C:ASN237 4.8 47.6 1.0 O1A C:ADP1300 4.8 64.7 1.0 O C:HOH2323 4.9 58.7 1.0 NE2 C:HIS244 5.0 41.0 1.0

Magnesium binding site 4 out of 4 in the Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1401 b:22.5 occ:1.00 OE1 D:GLU238 2.3 25.0 1.0 OE1 D:GLU226 2.3 27.0 1.0 O3A D:ADP1400 2.4 63.5 1.0 O3B D:ADP1400 3.0 67.1 1.0 O2A D:ADP1400 3.2 36.0 1.0 CD D:GLU226 3.3 12.5 1.0 PB D:ADP1400 3.3 82.6 1.0 PA D:ADP1400 3.4 46.6 1.0 CD D:GLU238 3.5 53.8 1.0 OE2 D:GLU226 3.5 0.0 1.0 O2B D:ADP1400 3.9 36.0 1.0 ND2 D:ASN237 4.0 23.3 1.0 OE2 D:GLU238 4.1 53.0 1.0 C5' D:ADP1400 4.3 37.7 1.0 O5' D:ADP1400 4.3 60.8 1.0 CB D:GLU238 4.4 13.5 1.0 O1A D:ADP1400 4.5 40.3 1.0 CG D:GLU226 4.6 1.0 1.0 CG D:GLU238 4.6 34.8 1.0 O3' D:ADP1400 4.6 49.5 1.0 O1B D:ADP1400 4.6 62.6 1.0 NE2 D:HIS184 4.8 83.5 1.0

J.B.Thoden, T.J.Kappock, J.Stubbe, H.M.Holden. Three-Dimensional Structure of N5-Carboxyaminoimidazole Ribonucleotide Synthetase: A Member of the Atp Grasp Protein Superfamily. Biochemistry V. 38 15480 1999.
ISSN: ISSN 0006-2960
PubMed: 10569930
DOI: 10.1021/BI991618S