Magnesium in PDB 7x9n: Crystal Structure of Mutt-8-Oxo-Dgtp Complex with Three MG2+ Ions: Reaction Using MG2+

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

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex with Three MG2+ Ions: Reaction Using MG2+, PDB code: 7x9n 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)	31.63 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.348, 55.931, 59.079, 90, 90, 90
R / Rfree (%)	16 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex with Three MG2+ Ions: Reaction Using MG2+ (pdb code 7x9n). 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 Mutt-8-Oxo-Dgtp Complex with Three MG2+ Ions: Reaction Using MG2+, PDB code: 7x9n:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex with Three 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-Dgtp Complex with Three MG2+ Ions: Reaction Using MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:11.5 occ:1.00 O1A A:8DG202 2.0 12.9 0.7 O2B A:8DG202 2.0 12.9 0.7 OE2 A:GLU57 2.1 12.1 1.0 O A:GLY37 2.1 10.2 1.0 O A:HOH344 2.1 12.0 1.0 O A:HOH314 2.2 14.7 0.3 O A:HOH328 2.2 11.6 1.0 OP2 A:8OG203 2.2 13.0 0.3 CD A:GLU57 3.1 12.7 1.0 MG A:MG206 3.2 22.5 0.7 PA A:8DG202 3.2 12.9 0.7 C A:GLY37 3.3 9.9 1.0 PB A:8DG202 3.3 19.0 0.7 P A:8OG203 3.3 12.8 0.3 OE1 A:GLU57 3.4 10.8 1.0 OP1 A:8OG203 3.5 16.0 0.3 O3A A:8DG202 3.6 16.2 0.7 O1G A:8DG202 3.9 34.5 0.7 N2 A:8OG203 3.9 9.1 0.3 N2 A:8DG202 3.9 9.1 0.7 O A:HOH307 4.0 28.1 1.0 CA A:GLY38 4.0 9.7 1.0 OE1 A:GLU53 4.1 17.1 1.0 N A:GLY38 4.1 8.3 1.0 O2A A:8DG202 4.1 13.5 0.7 O A:HOH329 4.2 15.5 1.0 OP3 A:8OG203 4.2 13.5 0.3 N A:GLY37 4.2 8.6 1.0 O3B A:8DG202 4.3 24.7 0.7 CA A:GLY37 4.4 7.6 1.0 NH1 A:ARG23 4.4 10.9 1.0 CG A:GLU57 4.4 9.1 1.0 O1B A:8DG202 4.4 18.1 0.7 O5' A:8DG202 4.4 12.1 0.7 O A:HOH311 4.5 31.1 1.0 O5' A:8OG203 4.5 12.2 0.3 OE1 A:GLU34 4.6 11.7 1.0 PG A:8DG202 4.8 48.3 0.7 C5' A:8OG203 4.9 10.9 0.3 C5' A:8DG202 4.9 10.7 0.7 O A:HOH422 5.0 14.2 0.3

Magnesium binding site 2 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex with Three 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-Dgtp Complex with Three MG2+ Ions: Reaction Using MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:19.1 occ:0.70 O1B A:8DG202 2.1 18.1 0.7 O A:HOH302 2.2 23.0 1.0 O A:HOH400 2.3 38.2 1.0 O A:HOH322 2.3 29.2 1.0 OE2 A:GLU53 2.4 19.8 1.0 O A:HOH422 2.8 14.2 0.3 PB A:8DG202 3.2 19.0 0.7 CD A:GLU53 3.4 16.5 1.0 MG A:MG206 3.5 22.5 0.7 O3G A:8DG202 3.6 35.8 0.7 OE1 A:GLU53 3.6 17.1 1.0 O A:HOH314 3.6 14.7 0.3 O3B A:8DG202 3.7 24.7 0.7 O2B A:8DG202 3.8 12.9 0.7 NH1 A:ARG52 4.1 15.0 1.0 N A:LYS39 4.2 10.4 0.4 N A:LYS39 4.2 10.4 0.6 OE1 A:GLU56 4.4 25.8 1.0 O A:HOH325 4.4 28.0 1.0 PG A:8DG202 4.4 48.3 0.7 OE2 A:GLU41 4.4 29.9 0.5 OE2 A:GLU41 4.5 22.4 0.5 OP1 A:8OG203 4.5 16.0 0.3 O3A A:8DG202 4.5 16.2 0.7 O A:LYS39 4.6 12.5 0.4 O A:LYS39 4.6 12.5 0.6 CA A:GLY38 4.7 9.7 1.0 NH2 A:ARG52 4.7 11.8 1.0 CG A:GLU53 4.8 12.1 1.0 C A:GLY38 4.8 10.0 1.0 CZ A:ARG52 4.9 14.8 1.0 CB A:LYS39 4.9 14.2 0.4 O A:HOH307 4.9 28.1 1.0 CB A:LYS39 4.9 14.2 0.6

Magnesium binding site 3 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex with Three 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 3 of Crystal Structure of Mutt-8-Oxo-Dgtp Complex with Three MG2+ Ions: Reaction Using MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:22.5 occ:0.70 O A:HOH314 2.0 14.7 0.3 O A:HOH325 2.0 28.0 1.0 O2B A:8DG202 2.1 12.9 0.7 O A:HOH307 2.2 28.1 1.0 OE1 A:GLU53 2.3 17.1 1.0 OE2 A:GLU57 2.4 12.1 1.0 PB A:8DG202 3.2 19.0 0.7 MG A:MG204 3.2 11.5 1.0 CD A:GLU57 3.3 12.7 1.0 CD A:GLU53 3.3 16.5 1.0 CG A:GLU57 3.5 9.1 1.0 MG A:MG205 3.5 19.1 0.7 O3G A:8DG202 3.6 35.8 0.7 O1B A:8DG202 3.6 18.1 0.7 OE2 A:GLU53 3.7 19.8 1.0 O1G A:8DG202 3.7 34.5 0.7 O A:GLY37 3.8 10.2 1.0 PG A:8DG202 4.0 48.3 0.7 O A:HOH328 4.0 11.6 1.0 O3B A:8DG202 4.0 24.7 0.7 OE1 A:GLU56 4.1 25.8 1.0 O A:HOH322 4.1 29.2 1.0 OE2 A:GLU98 4.3 22.0 1.0 OE1 A:GLU57 4.4 10.8 1.0 O A:HOH422 4.5 14.2 0.3 OP1 A:8OG203 4.5 16.0 0.3 OE1 A:GLU98 4.6 16.6 1.0 C A:GLY37 4.6 9.9 1.0 CA A:GLY38 4.6 9.7 1.0 O3A A:8DG202 4.6 16.2 0.7 CG A:GLU53 4.7 12.1 1.0 O1A A:8DG202 4.8 12.9 0.7 CD A:GLU98 4.9 17.9 1.0 OP2 A:8OG203 4.9 13.0 0.3 CB A:GLU53 4.9 13.7 1.0 O A:HOH344 5.0 12.0 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