Magnesium in PDB 3r5h: Crystal Structure of Adp-Air Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase

All present enzymatic activity of Crystal Structure of Adp-Air Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase:
4.1.1.21;

The structure of Crystal Structure of Adp-Air Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase, PDB code: 3r5h was solved by L.W.Fung, M.L.Tuntland, B.D.Santarsiero, M.E.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.76 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.442, 82.785, 168.233, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Adp-Air Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase (pdb code 3r5h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Adp-Air Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase, PDB code: 3r5h:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Adp-Air Complex of Purk: 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 Crystal Structure of Adp-Air Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:39.8 occ:1.00 O1A A:ADP400 2.1 38.8 1.0 OE1 A:GLU268 2.2 33.2 1.0 O A:HOH387 2.2 45.0 1.0 O A:HOH656 2.7 42.3 1.0 O3B A:ADP400 2.7 42.2 1.0 O A:HOH579 2.7 35.0 1.0 O2B A:ADP400 3.0 41.5 1.0 O A:HOH466 3.0 49.8 1.0 PB A:ADP400 3.2 39.2 1.0 CD A:GLU268 3.3 31.4 1.0 PA A:ADP400 3.4 36.7 1.0 O3A A:ADP400 3.7 39.2 1.0 OE1 A:GLU255 3.9 25.8 1.0 ND2 A:ASN267 3.9 24.2 1.0 O A:HOH464 4.0 49.6 1.0 OE2 A:GLU268 4.1 31.4 1.0 OE2 A:GLU255 4.2 27.1 1.0 CG A:GLU268 4.2 23.5 1.0 CD A:GLU255 4.3 25.3 1.0 O2A A:ADP400 4.4 37.4 1.0 O5' A:ADP400 4.4 35.3 1.0 C5' A:ADP400 4.5 34.2 1.0 O3' A:ADP400 4.6 34.5 1.0 O1B A:ADP400 4.7 42.0 1.0 NE2 A:HIS213 4.9 21.7 1.0 OD1 A:ASN216 4.9 35.8 1.0 C3' A:ADP400 4.9 34.0 1.0 O A:HOH504 5.0 28.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Adp-Air Complex of Purk: 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 Crystal Structure of Adp-Air Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:34.6 occ:1.00 OE1 B:GLU268 2.2 30.3 1.0 O1A B:ADP400 2.4 34.8 1.0 O B:HOH571 2.5 36.4 1.0 OE1 B:GLU255 2.6 30.9 1.0 O B:HOH611 2.9 41.6 1.0 O1B B:ADP400 3.1 42.0 1.0 O B:HOH473 3.1 61.7 1.0 O2B B:ADP400 3.2 42.8 1.0 CD B:GLU255 3.4 30.0 1.0 CD B:GLU268 3.4 31.1 1.0 PB B:ADP400 3.6 41.0 1.0 OE2 B:GLU255 3.7 34.0 1.0 PA B:ADP400 3.8 33.8 1.0 O B:HOH639 3.9 44.5 1.0 O3A B:ADP400 4.2 39.5 1.0 OE2 B:GLU268 4.2 33.1 1.0 ND2 B:ASN267 4.2 28.0 1.0 CB B:GLU268 4.4 25.7 1.0 CG B:GLU268 4.4 27.8 1.0 CG B:GLU255 4.6 25.5 1.0 O B:HOH559 4.6 34.9 1.0 O2A B:ADP400 4.7 34.5 1.0 O5' B:ADP400 4.8 35.1 1.0 O3' B:ADP400 5.0 38.2 1.0

M.L.Tuntland, B.D.Santarsiero, M.E.Johnson, L.W.Fung. Elucidation of the Bicarbonate Binding Site and Insights Into the Carboxylation Mechanism of (N(5))-Carboxyaminoimidazole Ribonucleotide Synthase (Purk) From Bacillus Anthracis Acta Crystallogr.,Sect.D V. 70 3057 2014.
ISSN: ISSN 0907-4449
PubMed: 25372694
DOI: 10.1107/S1399004714021166