Sodium in PDB 7ww6: Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 20 Min in 5 Mm MN2+

All present enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 20 Min in 5 Mm MN2+:
3.6.1.55;

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 20 Min in 5 Mm MN2+, PDB code: 7ww6 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 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.04, 55.9, 59.24, 90, 90, 90
R / Rfree (%)	15 / 18.5

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 20 Min in 5 Mm MN2+ also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 20 Min in 5 Mm MN2+ (pdb code 7ww6). 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: Reaction For 20 Min in 5 Mm MN2+, PDB code: 7ww6:
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: Reaction For 20 Min in 5 Mm MN2+


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: Reaction For 20 Min in 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:29.2 occ:0.40 MN A:MN202 0.0 11.6 0.6 O A:GLY37 2.2 10.1 1.0 O2B A:8DG201 2.2 15.0 1.0 OE2 A:GLU57 2.2 13.4 1.0 O1A A:8DG201 2.2 14.2 1.0 O A:HOH413 2.2 17.0 1.0 O A:HOH342 2.3 12.5 1.0 CD A:GLU57 3.2 12.2 1.0 PA A:8DG201 3.3 13.0 1.0 C A:GLY37 3.4 8.6 1.0 PB A:8DG201 3.5 14.1 1.0 OE1 A:GLU57 3.5 12.0 1.0 O3A A:8DG201 3.7 12.7 1.0 O A:HOH307 3.8 18.9 1.0 N2 A:8DG201 3.9 10.2 1.0 O A:HOH320 3.9 22.0 1.0 CA A:GLY38 4.0 10.1 1.0 O2A A:8DG201 4.0 13.9 1.0 N A:GLY38 4.2 9.2 1.0 NH1 A:ARG23 4.2 11.8 1.0 O A:HOH334 4.3 19.4 1.0 N A:GLY37 4.3 9.1 1.0 O A:HOH335 4.4 28.6 1.0 OE1 A:GLU53 4.4 12.7 1.0 O3B A:8DG201 4.5 22.4 1.0 CA A:GLY37 4.5 8.6 1.0 O1B A:8DG201 4.5 13.5 1.0 CG A:GLU57 4.5 10.2 1.0 O2G A:8DG201 4.6 52.0 0.5 OE1 A:GLU34 4.6 11.7 1.0 O5' A:8DG201 4.7 13.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 20 Min in 5 Mm MN2+


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: Reaction For 20 Min in 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:14.1 occ:1.00 O1B A:8DG201 2.3 13.5 1.0 O A:HOH357 2.4 16.3 1.0 O A:HOH328 2.4 15.6 1.0 O2G A:8DG201 2.5 44.5 0.5 OE2 A:GLU53 2.5 12.1 1.0 O A:HOH307 2.8 18.9 1.0 PB A:8DG201 3.4 14.1 1.0 CD A:GLU53 3.5 11.5 1.0 OE1 A:GLU53 3.7 12.7 1.0 O2B A:8DG201 3.8 15.0 1.0 O A:HOH365 3.8 41.2 1.0 O2G A:8DG201 3.8 52.0 0.5 PG A:8DG201 3.9 38.8 0.5 N A:LYS39 4.0 10.7 1.0 O1G A:8DG201 4.0 53.3 0.5 O3B A:8DG201 4.1 22.4 1.0 NH1 A:ARG52 4.1 12.3 1.0 PG A:8DG201 4.3 51.5 0.5 O A:HOH311 4.4 18.2 1.0 OE1 A:GLU56 4.5 18.6 1.0 O A:LYS39 4.5 11.9 1.0 OE2 A:GLU41 4.5 28.3 1.0 CA A:GLY38 4.6 10.1 1.0 NH2 A:ARG52 4.7 11.3 1.0 CB A:LYS39 4.7 14.3 1.0 O3A A:8DG201 4.7 12.7 1.0 C A:GLY38 4.7 10.9 1.0 O1G A:8DG201 4.8 42.1 0.5 CA A:LYS39 4.9 11.5 1.0 CG A:GLU53 4.9 11.3 1.0 CZ A:ARG52 4.9 10.5 1.0 O3G A:8DG201 4.9 39.8 0.5

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