Magnesium in PDB 7x9o: Crystal Structure of Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+

All present enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+:
3.6.1.55;

The structure of Crystal Structure of Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+, PDB code: 7x9o was solved by T.Nakamura, Y.Yamagata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.66 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.449, 56.014, 59.126, 90, 90, 90
R / Rfree (%)	16.7 / 18.9

The binding sites of Magnesium atom in the Crystal Structure of Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+ (pdb code 7x9o). 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 Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+, PDB code: 7x9o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+


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 Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:11.2 occ:0.90 O A:HOH343 2.0 15.8 1.0 O A:GLY37 2.0 9.4 1.0 O A:HOH356 2.1 10.8 1.0 OE2 A:GLU57 2.1 14.2 1.0 OP2 A:8OG201 2.1 13.3 1.0 O A:HOH386 2.2 14.8 1.0 CD A:GLU57 3.1 11.7 1.0 MG A:MG204 3.1 17.8 0.5 C A:GLY37 3.3 9.6 1.0 P A:8OG201 3.3 13.1 1.0 OE1 A:GLU57 3.5 11.2 1.0 OP1 A:8OG201 3.6 15.1 1.0 O A:HOH348 3.8 23.5 1.0 N2 A:8OG201 3.9 8.8 1.0 CA A:GLY38 4.0 9.4 1.0 N A:GLY38 4.1 8.9 1.0 OE1 A:GLU53 4.1 15.0 1.0 N A:GLY37 4.1 7.1 1.0 O A:HOH320 4.2 17.7 1.0 OP3 A:8OG201 4.2 13.8 1.0 CA A:GLY37 4.3 7.4 1.0 CG A:GLU57 4.4 10.0 1.0 NH1 A:ARG23 4.4 11.5 1.0 O A:HOH313 4.5 22.1 1.0 O5' A:8OG201 4.5 13.3 1.0 OE1 A:GLU34 4.6 10.6 1.0 C5' A:8OG201 4.9 10.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+


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 Mutt-8-Oxo-Dgmp Complex with MG2+ Ions: Reaction Using MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:17.8 occ:0.50 O A:HOH343 2.1 15.8 1.0 O A:HOH311 2.2 23.8 1.0 O A:HOH348 2.3 23.5 1.0 OE2 A:GLU57 2.3 14.2 1.0 OE1 A:GLU53 2.4 15.0 1.0 MG A:MG203 3.1 11.2 0.9 CD A:GLU57 3.2 11.7 1.0 CG A:GLU57 3.4 10.0 1.0 CD A:GLU53 3.5 12.6 1.0 O A:HOH357 3.5 20.3 1.0 O A:GLY37 3.7 9.4 1.0 OE2 A:GLU53 3.8 15.8 1.0 O A:HOH386 3.9 14.8 1.0 OE1 A:GLU56 4.2 21.1 1.0 OE2 A:GLU98 4.2 19.5 1.0 O A:HOH355 4.3 26.8 1.0 OE1 A:GLU57 4.4 11.2 1.0 C A:GLY37 4.5 9.6 1.0 OE1 A:GLU98 4.5 18.6 1.0 CA A:GLY38 4.6 9.4 1.0 OP1 A:8OG201 4.7 15.1 1.0 O A:HOH303 4.8 18.7 1.0 OP2 A:8OG201 4.8 13.3 1.0 CD A:GLU98 4.8 15.3 1.0 CG A:GLU53 4.8 10.4 1.0 O A:HOH356 4.8 10.8 1.0 CB A:GLU57 4.9 8.6 1.0 N A:GLY38 4.9 8.9 1.0

T.Nakamura, Y.Yamagata. Visualization of Mutagenic Nucleotide Processing By Escherichia Coli Mutt, A Nudix Hydrolase. Proc.Natl.Acad.Sci.Usa V. 119 18119 2022.
ISSN: ESSN 1091-6490
PubMed: 35594391
DOI: 10.1073/PNAS.2203118119