Magnesium in PDB 3eth: Crystal Structure of E. Coli Purk in Complex with Mgatp

All present enzymatic activity of Crystal Structure of E. Coli Purk in Complex with Mgatp:
4.1.1.21;

The structure of Crystal Structure of E. Coli Purk in Complex with Mgatp, PDB code: 3eth was solved by H.M.Holden, J.B.Thoden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.101, 57.109, 59.215, 77.46, 82.39, 77.26
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Purk in Complex with Mgatp (pdb code 3eth). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Purk in Complex with Mgatp, PDB code: 3eth:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of E. Coli Purk in Complex with Mgatp


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 E. Coli Purk in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:17.4 occ:1.00 OE1 A:GLU238 2.0 18.4 1.0 O1G A:ATP400 2.0 22.1 1.0 O2A A:ATP400 2.0 14.0 1.0 O A:HOH738 2.1 25.0 1.0 OE1 A:GLU226 2.1 19.8 1.0 OE2 A:GLU226 2.3 17.3 1.0 CD A:GLU226 2.5 18.1 1.0 CD A:GLU238 3.0 21.0 1.0 PG A:ATP400 3.2 23.0 1.0 O3B A:ATP400 3.3 21.5 1.0 PA A:ATP400 3.5 18.9 1.0 CG A:GLU238 3.5 16.3 1.0 O A:HOH737 3.6 21.7 1.0 MG A:MG402 3.7 16.9 1.0 ND2 A:ASN237 3.8 18.6 1.0 O2G A:ATP400 3.9 17.4 1.0 O A:HOH740 3.9 27.9 1.0 O2B A:ATP400 3.9 22.1 1.0 O A:HOH739 4.0 23.4 1.0 OE2 A:GLU238 4.0 15.8 1.0 CG A:GLU226 4.0 18.9 1.0 O3A A:ATP400 4.1 23.4 1.0 PB A:ATP400 4.1 19.7 1.0 O5' A:ATP400 4.4 13.8 1.0 O3G A:ATP400 4.5 17.6 1.0 O1A A:ATP400 4.5 21.2 1.0 O A:HOH445 4.5 26.5 1.0 C5' A:ATP400 4.5 16.8 1.0 O3' A:ATP400 4.5 19.2 1.0 O A:HOH736 4.6 16.6 1.0 CB A:GLU226 4.7 15.2 1.0 CB A:GLU238 4.9 12.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of E. Coli Purk in Complex with Mgatp


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 E. Coli Purk in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:16.9 occ:1.00 O2G A:ATP400 1.9 17.4 1.0 O2B A:ATP400 1.9 22.1 1.0 OE1 A:GLU238 2.1 18.4 1.0 O A:HOH734 2.1 15.6 1.0 O A:HOH736 2.1 16.6 1.0 OE2 A:GLU238 2.2 15.8 1.0 CD A:GLU238 2.5 21.0 1.0 PG A:ATP400 2.9 23.0 1.0 PB A:ATP400 3.1 19.7 1.0 O3B A:ATP400 3.4 21.5 1.0 O1G A:ATP400 3.4 22.1 1.0 O A:HOH737 3.6 21.7 1.0 MG A:MG401 3.7 17.4 1.0 O A:HOH735 3.9 32.2 1.0 O2A A:ATP400 3.9 14.0 1.0 NH2 A:ARG80 4.0 26.6 1.0 CG A:GLU238 4.0 16.3 1.0 O3A A:ATP400 4.1 23.4 1.0 O A:GLY125 4.1 19.0 1.0 O A:HOH522 4.2 22.6 1.0 O3G A:ATP400 4.2 17.6 1.0 O1B A:ATP400 4.2 19.3 1.0 O A:HOH417 4.3 34.4 1.0 O A:HOH418 4.4 21.2 1.0 NH1 A:ARG80 4.5 14.5 1.0 O A:HOH645 4.6 58.2 1.0 PA A:ATP400 4.6 18.9 1.0 CZ A:ARG80 4.7 38.1 1.0 CA A:TYR126 4.8 14.2 1.0 CB A:GLU238 4.9 12.9 1.0 C A:GLY125 4.9 25.3 1.0 OE2 A:GLU226 5.0 17.3 1.0 O1A A:ATP400 5.0 21.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of E. Coli Purk in Complex with Mgatp


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 E. Coli Purk in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:17.6 occ:1.00 O2A B:ATP400 1.9 19.4 1.0 O1G B:ATP400 2.0 22.0 1.0 O B:HOH651 2.0 21.4 1.0 OE2 B:GLU238 2.1 15.0 1.0 OE2 B:GLU226 2.1 26.2 1.0 OE1 B:GLU226 2.5 26.9 1.0 CD B:GLU226 2.6 25.6 1.0 CD B:GLU238 3.1 18.9 1.0 PG B:ATP400 3.2 24.0 1.0 O3B B:ATP400 3.3 21.5 1.0 PA B:ATP400 3.4 18.8 1.0 O B:HOH658 3.6 28.1 1.0 CG B:GLU238 3.7 20.6 1.0 MG B:MG402 3.8 19.2 1.0 ND2 B:ASN237 3.8 19.3 1.0 O2B B:ATP400 3.9 31.5 1.0 O3A B:ATP400 3.9 21.1 1.0 O2G B:ATP400 3.9 29.1 1.0 PB B:ATP400 3.9 21.5 1.0 O B:HOH527 4.1 21.1 1.0 C5' B:ATP400 4.1 17.7 1.0 OE1 B:GLU238 4.1 16.3 1.0 CG B:GLU226 4.2 14.7 1.0 O B:HOH649 4.2 30.1 1.0 O5' B:ATP400 4.3 15.1 1.0 O B:HOH545 4.3 29.0 1.0 O1A B:ATP400 4.4 18.3 1.0 O3' B:ATP400 4.4 16.8 1.0 O3G B:ATP400 4.5 24.1 1.0 O B:HOH653 4.6 19.7 1.0 CB B:GLU226 4.8 15.7 1.0 C3' B:ATP400 5.0 16.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of E. Coli Purk in Complex with Mgatp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E. Coli Purk in Complex with Mgatp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:19.2 occ:1.00 O2B B:ATP400 1.9 31.5 1.0 O B:HOH652 2.0 17.9 1.0 O2G B:ATP400 2.0 29.1 1.0 O B:HOH653 2.0 19.7 1.0 OE1 B:GLU238 2.2 16.3 1.0 OE2 B:GLU238 2.3 15.0 1.0 CD B:GLU238 2.6 18.9 1.0 PB B:ATP400 3.1 21.5 1.0 PG B:ATP400 3.1 24.0 1.0 O3B B:ATP400 3.5 21.5 1.0 O1G B:ATP400 3.6 22.0 1.0 NH2 B:ARG80 3.7 31.5 1.0 O B:HOH658 3.8 28.1 1.0 MG B:MG401 3.8 17.6 1.0 O B:HOH655 3.9 27.2 1.0 CG B:GLU238 4.1 20.6 1.0 O2A B:ATP400 4.1 19.4 1.0 O B:GLY125 4.2 21.9 1.0 O1B B:ATP400 4.2 19.9 1.0 O3A B:ATP400 4.2 21.1 1.0 O B:HOH654 4.2 34.7 1.0 O B:HOH657 4.3 25.6 1.0 O3G B:ATP400 4.4 24.1 1.0 NH1 B:ARG80 4.4 19.5 1.0 CZ B:ARG80 4.5 24.3 1.0 PA B:ATP400 4.6 18.8 1.0 CA B:TYR126 4.9 18.3 1.0 CB B:GLU238 4.9 17.8 1.0 O1A B:ATP400 4.9 18.3 1.0 C B:GLY125 5.0 26.6 1.0

J.B.Thoden, H.M.Holden, S.M.Firestine. Structural Analysis of the Active Site Geometry of N(5)-Carboxyaminoimidazole Ribonucleotide Synthetase From Escherichia Coli. Biochemistry V. 47 13346 2008.
ISSN: ISSN 0006-2960
PubMed: 19053251
DOI: 10.1021/BI801734Z