Magnesium in PDB 5a60: Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions

All present enzymatic activity of Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions:
3.6.1.25;

The structure of Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions, PDB code: 5a60 was solved by J.Martinez, V.Truffault, M.Hothorn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.88 / 1.82
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	89.924, 89.924, 125.577, 90.00, 90.00, 120.00
R / Rfree (%)	15.1 / 18.9

The binding sites of Magnesium atom in the Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions (pdb code 5a60). 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 Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions, PDB code: 5a60:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions


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 Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:38.7 occ:1.00 O1G A:3PO1000 1.9 49.0 1.0 O5' A:3PO1000 1.9 45.9 1.0 O1B A:3PO1000 2.1 46.9 1.0 OE2 A:GLU6 2.2 49.7 1.0 OE1 A:GLU160 2.3 48.4 1.0 OE2 A:GLU160 2.3 49.1 1.0 CD A:GLU160 2.6 48.0 1.0 PB A:3PO1000 3.0 46.9 1.0 PA A:3PO1000 3.1 49.8 1.0 O3A A:3PO1000 3.1 47.9 1.0 PG A:3PO1000 3.1 49.2 1.0 CD A:GLU6 3.2 54.6 1.0 O3B A:3PO1000 3.4 44.5 1.0 OE1 A:GLU6 3.5 53.6 1.0 MG A:MG501 3.6 54.6 1.0 O A:HOH3009 3.8 49.7 1.0 O2G A:3PO1000 3.9 45.0 1.0 O1A A:3PO1000 3.9 47.0 1.0 O A:HOH3008 3.9 55.1 1.0 CG A:GLU160 4.1 47.0 1.0 NZ A:LYS8 4.2 46.5 1.0 O2A A:3PO1000 4.2 44.3 1.0 NH2 A:ARG81 4.2 54.1 1.0 NH2 A:ARG126 4.3 45.7 1.0 O3G A:3PO1000 4.3 47.5 1.0 O2B A:3PO1000 4.4 44.8 1.0 NZ A:LYS69 4.5 61.3 1.0 NZ A:LYS191 4.5 44.0 1.0 CG A:GLU6 4.6 50.8 1.0 OE2 A:GLU4 4.8 61.4 1.0 CB A:GLU160 4.9 43.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions


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 Full-Length E. Coli Ygif in Complex with Tripolyphosphate and Two Magnesium Ions within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:54.6 occ:1.00 OE1 A:GLU6 2.1 53.6 1.0 OE2 A:GLU4 2.2 61.4 1.0 OE1 A:GLU162 2.3 64.9 1.0 O A:HOH3003 2.3 63.0 1.0 O5' A:3PO1000 2.3 45.9 1.0 O A:HOH3008 2.4 55.1 1.0 CD A:GLU6 3.1 54.6 1.0 PA A:3PO1000 3.2 49.8 1.0 CD A:GLU4 3.2 61.4 1.0 CD A:GLU162 3.4 61.2 1.0 O2A A:3PO1000 3.5 44.3 1.0 OE2 A:GLU6 3.5 49.7 1.0 MG A:MG500 3.6 38.7 1.0 O A:HOH3004 3.6 57.4 1.0 O1A A:3PO1000 3.8 47.0 1.0 OE1 A:GLU160 3.9 48.4 1.0 OE1 A:GLU4 3.9 56.6 1.0 OE2 A:GLU162 4.0 67.0 1.0 CG A:GLU4 4.2 63.5 1.0 O A:HOH3005 4.3 65.7 1.0 CG A:GLU162 4.4 55.1 1.0 CB A:GLU162 4.4 49.2 1.0 CG A:GLU6 4.4 50.8 1.0 O3A A:3PO1000 4.6 47.9 1.0 NZ A:LYS69 4.6 61.3 1.0 CB A:GLU6 4.8 48.0 1.0 O A:HOH3083 4.8 59.6 1.0 O1G A:3PO1000 4.9 49.0 1.0 O1B A:3PO1000 5.0 46.9 1.0 CD A:GLU160 5.0 48.0 1.0

J.Martinez, V.Truffault, M.Hothorn. Structural Determinants For Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. J.Biol.Chem. V. 290 23348 2015.
ISSN: ISSN 0021-9258
PubMed: 26221030
DOI: 10.1074/JBC.M115.674473