Manganese in PDB 7ww8: Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+

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

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+, PDB code: 7ww8 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)	40.69 / 1.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.264, 56.051, 59.155, 90, 90, 90
R / Rfree (%)	15.6 / 18.1

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

Sodium

(Na)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+ (pdb code 7ww8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+, PDB code: 7ww8:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:10.5 occ:1.00 O A:GLY37 2.1 8.1 1.0 O2B A:8DG202 2.1 12.6 1.0 O1A A:8DG202 2.2 10.2 1.0 OE2 A:GLU57 2.2 9.9 1.0 O A:HOH328 2.2 9.4 1.0 O A:HOH402 2.2 10.5 1.0 CD A:GLU57 3.2 9.9 1.0 MN A:MN206 3.3 14.8 0.6 PA A:8DG202 3.3 10.1 1.0 C A:GLY37 3.4 7.2 1.0 PB A:8DG202 3.4 15.2 1.0 OE1 A:GLU57 3.5 9.2 1.0 O3A A:8DG202 3.6 9.8 1.0 O A:HOH304 3.7 17.1 0.4 N2 A:8DG202 3.9 6.4 1.0 O A:HOH301 3.9 14.8 1.0 CA A:GLY38 3.9 7.2 1.0 O2A A:8DG202 4.1 11.8 1.0 N A:GLY38 4.1 5.8 1.0 O A:HOH335 4.2 17.2 1.0 NH1 A:ARG23 4.2 9.4 1.0 OE1 A:GLU53 4.3 12.5 1.0 N A:GLY37 4.3 6.2 1.0 O1G A:8DG202 4.3 61.0 1.0 O3B A:8DG202 4.4 18.0 1.0 CA A:GLY37 4.4 6.1 1.0 O1B A:8DG202 4.5 12.4 1.0 CG A:GLU57 4.5 6.6 1.0 OE1 A:GLU34 4.5 11.5 1.0 O5' A:8DG202 4.6 10.7 1.0 O A:HOH313 4.6 30.6 1.0 O A:HOH304 4.8 16.2 0.6 C5' A:8DG202 5.0 7.8 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:14.5 occ:0.60 NA A:NA205 0.1 13.7 0.4 O A:HOH304 2.3 16.2 0.6 O A:HOH302 2.3 20.2 0.6 O A:HOH303 2.3 13.3 1.0 O A:HOH338 2.3 14.0 1.0 O1B A:8DG202 2.4 12.4 1.0 OE2 A:GLU53 2.4 11.6 1.0 O A:HOH304 2.8 17.1 0.4 PB A:8DG202 3.4 15.2 1.0 CD A:GLU53 3.4 9.8 1.0 O3G A:8DG202 3.6 50.3 1.0 MN A:MN206 3.6 14.8 0.6 OE1 A:GLU53 3.6 12.5 1.0 O2B A:8DG202 3.8 12.6 1.0 O3B A:8DG202 4.0 18.0 1.0 N A:LYS39 4.1 6.7 1.0 NH1 A:ARG52 4.1 11.3 1.0 PG A:8DG202 4.3 60.5 1.0 OE1 A:GLU56 4.4 15.4 1.0 O A:HOH314 4.4 20.4 1.0 OE2 A:GLU41 4.4 24.7 0.6 OE2 A:GLU41 4.5 23.3 0.4 O A:LYS39 4.5 9.7 1.0 O3A A:8DG202 4.6 9.8 1.0 CA A:GLY38 4.7 7.2 1.0 NH2 A:ARG52 4.7 8.5 1.0 O1G A:8DG202 4.7 61.0 1.0 CG A:GLU53 4.8 8.4 1.0 CB A:LYS39 4.8 11.8 1.0 C A:GLY38 4.8 7.0 1.0 CZ A:ARG52 4.9 9.2 1.0 CA A:LYS39 4.9 8.4 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 5 Hr in 5 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn206 b:14.8 occ:0.60 O A:HOH304 0.8 17.1 0.4 OE2 A:GLU57 2.3 9.9 1.0 O2B A:8DG202 2.3 12.6 1.0 O A:HOH304 2.3 16.2 0.6 O A:HOH314 2.3 20.4 1.0 O A:HOH301 2.3 14.8 1.0 OE1 A:GLU53 2.4 12.5 1.0 CD A:GLU57 3.2 9.9 1.0 MN A:MN203 3.3 10.5 1.0 CG A:GLU57 3.4 6.6 1.0 PB A:8DG202 3.4 15.2 1.0 CD A:GLU53 3.5 9.8 1.0 O1G A:8DG202 3.5 61.0 1.0 MN A:MN204 3.6 14.5 0.6 NA A:NA205 3.6 13.7 0.4 OE2 A:GLU53 3.8 11.6 1.0 O A:GLY37 3.8 8.1 1.0 O1B A:8DG202 3.9 12.4 1.0 O A:HOH402 4.1 10.5 1.0 OE1 A:GLU56 4.2 15.4 1.0 O3B A:8DG202 4.3 18.0 1.0 PG A:8DG202 4.3 60.5 1.0 OE1 A:GLU57 4.3 9.2 1.0 OE2 A:GLU98 4.4 16.4 1.0 O A:HOH338 4.4 14.0 1.0 OE1 A:GLU98 4.4 16.0 1.0 O3G A:8DG202 4.5 50.3 1.0 C A:GLY37 4.6 7.2 1.0 CA A:GLY38 4.6 7.2 1.0 O3A A:8DG202 4.8 9.8 1.0 CG A:GLU53 4.8 8.4 1.0 CD A:GLU98 4.8 14.5 1.0 CB A:GLU57 4.9 5.6 1.0 O1A A:8DG202 5.0 10.2 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