Manganese in PDB 7ww9: Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1.5 Hr in 20 Mm MN2+

All present enzymatic activity of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1.5 Hr in 20 Mm MN2+:
3.6.1.55;

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1.5 Hr in 20 Mm MN2+, PDB code: 7ww9 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)	31.94 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.962, 55.906, 59.12, 90, 90, 90
R / Rfree (%)	16.1 / 17.8

The structure of Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1.5 Hr in 20 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 1.5 Hr in 20 Mm MN2+ (pdb code 7ww9). 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 1.5 Hr in 20 Mm MN2+, PDB code: 7ww9:
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 1.5 Hr in 20 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 1.5 Hr in 20 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn204 b:12.3 occ:1.00 O A:HOH398 2.1 13.3 0.8 O1A A:8DG201 2.1 11.8 0.2 O2B A:8DG201 2.1 13.7 0.2 OE2 A:GLU57 2.2 9.0 1.0 OP2 A:8OG202 2.2 12.2 0.8 O A:GLY37 2.2 6.9 1.0 O A:HOH341 2.2 10.7 1.0 O A:HOH405 2.3 12.1 1.0 CD A:GLU57 3.2 12.0 1.0 NA A:NA207 3.3 22.9 0.8 MN A:MN206 3.3 23.9 0.2 PA A:8DG201 3.3 11.8 0.2 C A:GLY37 3.4 8.7 1.0 P A:8OG202 3.4 12.2 0.8 PB A:8DG201 3.5 13.7 0.2 OE1 A:GLU57 3.5 7.0 1.0 OP1 A:8OG202 3.7 16.2 0.8 O3A A:8DG201 3.8 15.6 0.2 N2 A:8OG202 3.8 4.7 0.8 N2 A:8DG201 3.9 4.8 0.2 O A:HOH359 3.9 25.1 1.0 CA A:GLY38 4.1 9.2 1.0 O2A A:8DG201 4.2 12.3 0.2 N A:GLY38 4.2 5.1 1.0 OP3 A:8OG202 4.2 12.4 0.8 O A:HOH318 4.3 13.0 1.0 N A:GLY37 4.3 6.0 1.0 OE1 A:GLU53 4.3 12.8 1.0 O A:HOH306 4.3 20.8 1.0 NH1 A:ARG23 4.4 8.7 1.0 CA A:GLY37 4.5 5.5 1.0 O1B A:8DG201 4.5 13.4 0.2 O3B A:8DG201 4.5 17.6 0.2 CG A:GLU57 4.5 4.9 1.0 O5' A:8DG201 4.6 11.3 0.2 OE1 A:GLU34 4.6 8.3 1.0 O5' A:8OG202 4.6 11.4 0.8 C5' A:8OG202 4.9 11.0 0.8 C5' A:8DG201 4.9 10.3 0.2 O A:HOH353 5.0 17.6 0.8

Manganese binding site 2 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1.5 Hr in 20 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 1.5 Hr in 20 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn205 b:17.1 occ:0.20 O A:HOH350 0.2 17.9 0.8 O1B A:8DG201 2.2 13.4 0.2 O A:HOH374 2.3 25.1 1.0 O2G A:8DG201 2.4 19.6 0.2 O A:HOH326 2.5 16.4 1.0 OE2 A:GLU53 2.7 14.6 1.0 O A:HOH353 2.9 17.6 0.8 PB A:8DG201 3.3 13.7 0.2 PG A:8DG201 3.4 18.1 0.2 NA A:NA207 3.4 22.9 0.8 CD A:GLU53 3.6 12.1 1.0 MN A:MN206 3.6 23.9 0.2 O3G A:8DG201 3.6 20.1 0.2 OE1 A:GLU53 3.7 12.8 1.0 O A:HOH398 3.8 13.3 0.8 O3B A:8DG201 3.8 17.6 0.2 O2B A:8DG201 3.8 13.7 0.2 NH1 A:ARG52 4.1 13.2 1.0 N A:LYS39 4.2 5.8 1.0 O A:HOH308 4.3 25.7 1.0 OE2 A:GLU41 4.5 26.4 0.6 OE1 A:GLU56 4.5 17.5 1.0 O3A A:8DG201 4.6 15.6 0.2 CA A:GLY38 4.7 9.2 1.0 O A:LYS39 4.7 7.9 1.0 OP1 A:8OG202 4.7 16.2 0.8 OE2 A:GLU41 4.7 24.8 0.4 O A:HOH437 4.8 26.8 0.8 O1G A:8DG201 4.8 24.4 0.2 NH2 A:ARG52 4.9 9.1 1.0 C A:GLY38 4.9 8.5 1.0 CB A:LYS39 4.9 10.7 1.0 CZ A:ARG52 5.0 11.6 1.0 CG A:GLU53 5.0 6.6 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Mutt-8-Oxo-Dgtp Complex: Reaction For 1.5 Hr in 20 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 1.5 Hr in 20 Mm MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn206 b:23.9 occ:0.20 NA A:NA207 0.2 22.9 0.8 O A:HOH398 2.3 13.3 0.8 O A:HOH308 2.3 25.7 1.0 OE2 A:GLU57 2.4 9.0 1.0 O2B A:8DG201 2.4 13.7 0.2 OE1 A:GLU53 2.6 12.8 1.0 O A:HOH359 2.6 25.1 1.0 O3G A:8DG201 3.2 20.1 0.2 CD A:GLU57 3.3 12.0 1.0 MN A:MN204 3.3 12.3 1.0 CG A:GLU57 3.4 4.9 1.0 PB A:8DG201 3.5 13.7 0.2 O A:HOH350 3.5 17.9 0.8 CD A:GLU53 3.6 12.1 1.0 MN A:MN205 3.6 17.1 0.2 O1B A:8DG201 3.8 13.4 0.2 OE2 A:GLU53 3.9 14.6 1.0 O A:GLY37 3.9 6.9 1.0 O3B A:8DG201 4.1 17.6 0.2 PG A:8DG201 4.2 18.1 0.2 OE2 A:GLU98 4.2 15.2 1.0 O A:HOH405 4.2 12.1 1.0 O A:HOH374 4.2 25.1 1.0 OE1 A:GLU56 4.2 17.5 1.0 OE1 A:GLU57 4.4 7.0 1.0 OE1 A:GLU98 4.5 15.2 1.0 O2G A:8DG201 4.5 19.6 0.2 C A:GLY37 4.7 8.7 1.0 O A:HOH353 4.8 17.6 0.8 CD A:GLU98 4.8 15.8 1.0 CA A:GLY38 4.8 9.2 1.0 OP1 A:8OG202 4.8 16.2 0.8 O3A A:8DG201 4.9 15.6 0.2 CG A:GLU53 4.9 6.6 1.0 O1A A:8DG201 4.9 11.8 0.2 OP2 A:8OG202 4.9 12.2 0.8 CB A:GLU57 5.0 7.0 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