Sodium in PDB 7ww5: Crystal Structure of Mutt-8-Oxo-Dgtp Complex

All present enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgtp Complex:
3.6.1.55;

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex, PDB code: 7ww5 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)	29.71 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.87, 55.89, 59.41, 90, 90, 90
R / Rfree (%)	18.6 / 20.7

The binding sites of Sodium atom in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex (pdb code 7ww5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex, PDB code: 7ww5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mutt-8-Oxo-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:25.6 occ:1.00 O A:GLY37 2.3 14.1 1.0 O1A A:8DG201 2.4 17.6 0.6 O A:HOH392 2.4 30.6 1.0 O2B A:8DG201 2.4 24.9 0.4 O2B A:8DG201 2.4 25.4 0.6 OE2 A:GLU57 2.4 22.9 1.0 O A:HOH346 2.5 24.4 1.0 CD A:GLU57 3.4 21.1 1.0 PA A:8DG201 3.5 18.9 0.6 C A:GLY37 3.5 14.8 1.0 O A:HOH322 3.5 25.8 1.0 PB A:8DG201 3.6 23.4 0.6 O2A A:8DG201 3.6 23.4 0.4 PB A:8DG201 3.7 23.4 0.4 O3A A:8DG201 3.8 21.9 0.6 OE1 A:GLU57 3.8 22.0 1.0 O A:HOH301 3.8 35.1 1.0 O3A A:8DG201 4.0 22.7 0.4 N2 A:8DG201 4.0 14.0 1.0 CA A:GLY38 4.0 13.4 1.0 O A:HOH305 4.1 33.7 1.0 O2A A:8DG201 4.2 21.9 0.6 N A:GLY38 4.2 12.8 1.0 O A:HOH376 4.3 32.7 1.0 NH1 A:ARG23 4.3 17.7 1.0 O1B A:8DG201 4.4 22.7 0.6 OE1 A:GLU53 4.4 15.1 1.0 N A:GLY37 4.5 11.7 1.0 PA A:8DG201 4.5 20.7 0.4 CA A:GLY37 4.6 9.9 1.0 OE1 A:GLU34 4.7 17.2 1.0 CG A:GLU57 4.7 13.3 1.0 O1B A:8DG201 4.7 23.0 0.4 O3B A:8DG201 4.8 28.6 0.4 O5' A:8DG201 4.8 18.7 0.6 O3B A:8DG201 4.8 28.5 0.6

Sodium binding site 2 out of 2 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Mutt-8-Oxo-Dgtp Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:26.6 occ:1.00 O1B A:8DG201 2.3 22.7 0.6 O1B A:8DG201 2.4 23.0 0.4 O2G A:8DG201 2.4 40.4 0.6 O A:HOH335 2.4 23.9 1.0 O A:HOH342 2.5 20.7 1.0 O2G A:8DG201 2.6 40.5 0.4 OE2 A:GLU53 2.7 16.4 1.0 O A:HOH322 2.8 25.8 1.0 PB A:8DG201 3.4 23.4 0.6 PB A:8DG201 3.4 23.4 0.4 CD A:GLU53 3.6 14.1 1.0 O2B A:8DG201 3.7 24.9 0.4 OE1 A:GLU53 3.8 15.1 1.0 PG A:8DG201 3.8 41.5 0.6 O2B A:8DG201 3.8 25.4 0.6 PG A:8DG201 4.0 41.2 0.4 O3B A:8DG201 4.0 28.5 0.6 N A:LYS39 4.0 13.7 1.0 O3B A:8DG201 4.2 28.6 0.4 NH1 A:ARG52 4.2 15.4 1.0 O A:HOH318 4.4 20.5 1.0 O A:LYS39 4.5 14.8 1.0 O A:HOH320 4.5 39.8 1.0 OE1 A:GLU56 4.5 22.3 1.0 OE2 A:GLU41 4.5 31.6 1.0 CA A:GLY38 4.6 13.4 1.0 CB A:LYS39 4.7 18.4 1.0 O1G A:8DG201 4.7 41.1 0.6 C A:GLY38 4.7 13.4 1.0 O3A A:8DG201 4.7 21.9 0.6 O3A A:8DG201 4.8 22.7 0.4 O3G A:8DG201 4.8 42.7 0.6 NH2 A:ARG52 4.8 15.8 1.0 CA A:LYS39 4.8 14.8 1.0 O3G A:8DG201 4.9 41.9 0.4 O1G A:8DG201 5.0 40.2 0.4 CZ A:ARG52 5.0 12.9 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