Magnesium in PDB 7sf0: Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate

The structure of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate, PDB code: 7sf0 was solved by J.K.Peters, R.W.Tibble, M.Warminski, J.Jemielity, J.D.Gross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.00 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.74, 139.99, 76.02, 90, 90, 90
R / Rfree (%)	20.1 / 24.7

The structure of Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate (pdb code 7sf0). 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 Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate, PDB code: 7sf0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate


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 Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:55.1 occ:1.00 O3B A:8NK301 2.0 77.1 1.0 O1A A:8NK301 2.5 68.2 1.0 NE2 A:GLN57 2.9 40.3 1.0 PB A:8NK301 3.3 81.7 1.0 NH2 A:ARG50 3.6 27.3 1.0 PA A:8NK301 3.7 74.4 1.0 CD A:GLN57 3.7 36.0 1.0 OE1 A:GLN57 3.7 34.5 1.0 O3A A:8NK301 3.8 66.4 1.0 O1B A:8NK301 3.9 57.7 1.0 CM7 A:8NK301 3.9 32.1 1.0 O2B A:8NK301 4.4 82.1 1.0 O2A A:8NK301 4.5 73.1 1.0 C8 A:8NK301 4.7 36.4 1.0 N7 A:8NK301 4.8 35.3 1.0 CZ A:ARG50 4.9 28.8 1.0 O5' A:8NK301 4.9 58.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate


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 Vaccinia Virus Decapping Enzyme D9 in Complex with Trinucleotide Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:40.5 occ:1.00 O A:HOH473 2.0 38.0 1.0 O A:HOH414 2.1 44.6 1.0 O A:HOH444 2.2 40.7 1.0 OE2 A:GLU183 2.2 42.4 1.0 OE1 A:GLU126 2.2 40.9 1.0 OE2 A:GLU130 2.2 44.5 1.0 CD A:GLU183 3.0 52.2 1.0 OE1 A:GLU183 3.1 61.9 1.0 CD A:GLU130 3.2 42.7 1.0 CD A:GLU126 3.4 38.6 1.0 O A:HOH540 3.5 47.8 1.0 CG A:GLU130 3.5 36.3 1.0 O A:GLY110 3.7 39.2 1.0 O A:HOH420 3.7 44.1 1.0 O A:HOH432 3.7 49.8 1.0 OE2 A:GLU126 3.9 37.4 1.0 CA A:GLY111 4.4 32.7 1.0 O A:HOH452 4.4 51.0 1.0 OE1 A:GLU130 4.4 41.7 1.0 C A:GLY110 4.4 31.0 1.0 CG A:GLU183 4.5 40.1 1.0 OE1 A:GLU129 4.5 40.9 1.0 CG A:GLU126 4.6 31.2 1.0 O A:HOH526 4.7 42.7 1.0 CB A:GLU126 4.7 29.2 1.0 N A:GLY111 4.8 27.0 1.0 CB A:GLU183 5.0 31.7 1.0 O A:GLU126 5.0 31.1 1.0

J.K.Peters, R.W.Tibble, M.Warminski, J.Jemielity, J.D.Gross. Structure of the Poxvirus Decapping Enzyme D9 Reveals Its Mechanism of Cap Recognition and Catalysis. Structure V. 30 721 2022.
ISSN: ISSN 0969-2126
PubMed: 35290794
DOI: 10.1016/J.STR.2022.02.012