Magnesium in PDB 3v4s: Crystal Structure of Adp-Atp Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase

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

The structure of Crystal Structure of Adp-Atp Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase, PDB code: 3v4s 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)	19.96 / 2.02
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.744, 82.870, 167.928, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.5

The binding sites of Magnesium atom in the Crystal Structure of Adp-Atp Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase (pdb code 3v4s). 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 Adp-Atp Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase, PDB code: 3v4s:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Adp-Atp 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-Atp Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:46.2 occ:1.00 OE1 A:GLU268 2.0 39.4 1.0 O1A A:ADP401 2.1 39.7 1.0 O3B A:ADP401 2.1 47.9 1.0 O A:HOH710 2.2 45.6 1.0 O A:HOH730 2.7 50.6 1.0 CD A:GLU268 3.2 35.4 1.0 PB A:ADP401 3.4 45.6 1.0 PA A:ADP401 3.5 37.9 1.0 O2B A:ADP401 3.8 45.3 1.0 OE1 A:GLU255 3.8 23.8 1.0 O3A A:ADP401 3.8 42.0 1.0 OE2 A:GLU255 3.9 24.0 1.0 OE2 A:GLU268 3.9 36.3 1.0 O A:HOH636 4.0 38.1 1.0 ND2 A:ASN267 4.0 27.1 1.0 CD A:GLU255 4.2 22.9 1.0 CG A:GLU268 4.2 29.7 1.0 O2A A:ADP401 4.5 37.4 1.0 O5' A:ADP401 4.5 37.0 1.0 C5' A:ADP401 4.6 36.9 1.0 OD1 A:ASN216 4.6 59.0 1.0 O1B A:ADP401 4.6 48.0 1.0 O A:HOH536 4.9 25.7 1.0 NE2 A:HIS213 5.0 25.3 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Adp-Atp 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-Atp Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:32.4 occ:1.00 O B:HOH618 2.0 39.7 1.0 O1A B:ATP401 2.1 32.7 1.0 OE1 B:GLU268 2.2 28.4 1.0 O1G B:ATP401 2.2 30.8 0.7 OE1 B:GLU255 2.3 39.4 1.0 OE2 B:GLU255 2.6 32.9 1.0 CD B:GLU255 2.8 34.2 1.0 O3B B:ATP401 3.0 34.2 1.0 PG B:ATP401 3.2 28.5 0.7 CD B:GLU268 3.4 30.3 1.0 PA B:ATP401 3.5 33.0 1.0 O B:HOH658 3.9 46.0 1.0 ND2 B:ASN267 3.9 27.5 1.0 PB B:ATP401 4.0 34.6 1.0 CG B:GLU268 4.0 27.1 1.0 O2B B:ATP401 4.0 35.6 1.0 O3G B:ATP401 4.0 28.4 0.7 O B:HOH539 4.0 29.4 1.0 O B:HOH558 4.1 34.3 1.0 O3A B:ATP401 4.1 34.0 1.0 OE2 B:GLU268 4.3 29.1 1.0 CG B:GLU255 4.3 32.9 1.0 O5' B:ATP401 4.3 31.8 1.0 C5' B:ATP401 4.4 32.8 1.0 O3' B:ATP401 4.4 32.6 1.0 O2G B:ATP401 4.5 28.5 0.7 O2A B:ATP401 4.6 32.2 1.0 NE2 B:HIS213 4.8 30.5 1.0 C3' B:ATP401 4.9 34.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Adp-Atp 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 3 of Crystal Structure of Adp-Atp Complex of Purk: N5-Carboxyaminoimidazole Ribonucleotide Synthetase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:35.4 occ:1.00 O B:HOH607 2.1 38.7 1.0 O B:HOH579 2.2 35.5 1.0 O B:THR104 2.4 35.9 1.0 O B:LEU269 2.4 24.0 1.0 OE1 B:GLU110 2.5 31.4 1.0 CD B:GLU110 3.3 33.5 1.0 C B:THR104 3.4 34.0 1.0 C B:LEU269 3.6 25.7 1.0 OE2 B:GLU110 3.6 37.1 1.0 N B:LEU269 3.9 25.8 1.0 CB B:THR104 3.9 33.0 1.0 CA B:THR104 4.0 33.6 1.0 O B:HOH616 4.1 39.0 1.0 O B:HOH596 4.2 36.6 1.0 OE2 B:GLU268 4.2 29.1 1.0 OE2 B:GLU78 4.2 66.6 1.0 CA B:LEU269 4.3 25.6 1.0 CB B:GLU268 4.4 27.2 1.0 CG B:GLU110 4.6 32.6 1.0 N B:GLN105 4.6 32.5 1.0 N B:ALA270 4.6 25.6 1.0 OG1 B:THR104 4.7 34.1 1.0 CB B:LEU269 4.7 26.6 1.0 OE1 B:GLU78 4.8 60.4 1.0 CD B:GLU268 4.8 30.3 1.0 O B:HOH551 4.8 32.4 1.0 C B:GLU268 4.9 26.9 1.0 CA B:ALA270 4.9 25.0 1.0 CG B:GLU268 4.9 27.1 1.0 CD B:GLU78 4.9 63.9 1.0 CG2 B:THR104 5.0 31.9 1.0 CA B:GLN105 5.0 33.6 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